From a7bbf2ded6320bf032917e0215a039be92bd8601 Mon Sep 17 00:00:00 2001 From: Lukas Heumos Date: Thu, 3 Oct 2024 09:59:15 +0200 Subject: [PATCH] =?UTF-8?q?=F0=9F=8E=A8=20Simplify=20use=20case=20by=20mov?= =?UTF-8?q?ing=20to=20nf-core/scrnaseq=20(#42)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * :art: Simplify use case Signed-off-by: zethson * :art: Fix use case Signed-off-by: zethson * :art: Fix use case Signed-off-by: zethson * :art: Fix use case Signed-off-by: zethson * :art: Debug Signed-off-by: zethson * :art: Properly install lamindb Signed-off-by: zethson * :art: Properly install lamindb Signed-off-by: zethson * :art: Proper script again Signed-off-by: zethson * :art: Refactoring Signed-off-by: zethson * :art: Refactoring Signed-off-by: zethson * :art: Split into two parts Signed-off-by: zethson * :art: Improve wording Signed-off-by: zethson * :art: Not str Signed-off-by: zethson * :art: Try linage Signed-off-by: zethson * :art: Try linage Signed-off-by: zethson * :art: Try lineage Signed-off-by: zethson * :art: Try lineage Signed-off-by: zethson * :art: Show cell again Signed-off-by: zethson * :art: Remove tests lineage Signed-off-by: zethson * :art: Display code Signed-off-by: zethson * :sparkles: Move to nf-core/scrnaseq Signed-off-by: zethson * :art: Add jupyter ot lamindb deps Signed-off-by: zethson * :art: Add jupyter ot lamindb deps Signed-off-by: zethson * :art: Debug Signed-off-by: zethson * :art: Debug Signed-off-by: zethson * :art: Tree Signed-off-by: zethson * :art: Fix output dir Signed-off-by: zethson * Polish Signed-off-by: zethson * :art: Polish Signed-off-by: zethson * :art: Polish Signed-off-by: zethson * :art: Functionize Signed-off-by: zethson * :art: Polishing and fix script display Signed-off-by: zethson * :art: Less scary script Signed-off-by: zethson * :art: Ruff Signed-off-by: zethson * :art: Polish Signed-off-by: zethson * :art: Polish Signed-off-by: zethson * :art: Polish Signed-off-by: zethson * :art: Polish Signed-off-by: zethson * :art: Polish Signed-off-by: zethson * :art: Hide-cell Signed-off-by: zethson * 💄 Polish notebook * 💚 Add a comment to the script * 🎨 Remove ln.track() from registration script * 💚 Fix by no longer relying on global run context * :art: Fix script Signed-off-by: zethson * :art: Add screenshot Signed-off-by: zethson * :art: Improve workflow Signed-off-by: zethson --------- Signed-off-by: zethson Co-authored-by: Alex Wolf --- .github/workflows/build.yml | 18 +- .gitignore | 11 +- docs/index.md | 2 +- docs/mcmicro.ipynb | 257 - docs/mcmicro.py | 74 - docs/mcmicro_exemplar.py | 67 - docs/nf_core_scrnaseq.ipynb | 287 + docs/register_nf_run.py | 32 - docs/register_scrnaseq_run.py | 71 + nextflow_bulk_rna.ipynb | 20344 -------------------------------- noxfile.py | 4 +- pyproject.toml | 2 +- 12 files changed, 376 insertions(+), 20793 deletions(-) delete mode 100644 docs/mcmicro.ipynb delete mode 100644 docs/mcmicro.py delete mode 100644 docs/mcmicro_exemplar.py create mode 100644 docs/nf_core_scrnaseq.ipynb delete mode 100644 docs/register_nf_run.py create mode 100644 docs/register_scrnaseq_run.py delete mode 100644 nextflow_bulk_rna.ipynb diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 465247a..2585b88 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -10,32 +10,32 @@ on: jobs: build: - runs-on: ubuntu-22.04 + runs-on: ubuntu-latest env: GITHUB_EVENT_NAME: ${{ github.event_name }} NXF_ANSI_LOG: false strategy: fail-fast: false - timeout-minutes: 50 + timeout-minutes: 30 steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: fetch-depth: 0 - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: repository: laminlabs/lndocs ssh-key: ${{ secrets.READ_LNDOCS }} path: lndocs ref: main - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v5 with: - python-version: "3.10" - cache: "pip" - cache-dependency-path: ".github/workflows/build.yml" - - uses: nf-core/setup-nextflow@v1 + python-version: "3.11" + + - uses: nf-core/setup-nextflow@v2 with: version: "latest-stable" + - uses: actions/cache@v3 with: path: ~/.cache/pre-commit diff --git a/.gitignore b/.gitignore index 28a9e18..fb14261 100644 --- a/.gitignore +++ b/.gitignore @@ -112,12 +112,9 @@ _docs_tmp* # Nextflow .nextflow* work -fetchngs-results -nextflow_rna_seq -rna-seq-results multiqc_report.html -differentialabundance-results test-datasets -nextflow-mcmicro -exemplar-001 -exemplar-001-mcmicro-execution_report.html +test-nextflow +scrnaseq_input +scrnaseq_output +test.ipynb diff --git a/docs/index.md b/docs/index.md index 3c88919..4037b23 100644 --- a/docs/index.md +++ b/docs/index.md @@ -7,6 +7,6 @@ :maxdepth: 1 :hidden: -mcmicro +nf_core_scrnaseq changelog ``` diff --git a/docs/mcmicro.ipynb b/docs/mcmicro.ipynb deleted file mode 100644 index 108037e..0000000 --- a/docs/mcmicro.ipynb +++ /dev/null @@ -1,257 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "id": "a1c40541-e05e-48a3-8b50-33baf3d6d0d4", - "metadata": {}, - "source": [ - "# Nextflow" - ] - }, - { - "cell_type": "markdown", - "id": "cd12ac1a-73e6-44e2-a854-6fa5e52cfd41", - "metadata": {}, - "source": [ - "[Nextflow](https://www.nextflow.io/) is a workflow management system used for executing scientific workflows across platforms scalably, portably, and reproducibly.\n", - "\n", - "Here, we'll run a demo of the microscopy pipeline [mcmicro](https://github.com/labsyspharm/mcmicro) to correct uneven illumination. [Reference](https://mcmicro.org/)" - ] - }, - { - "cell_type": "markdown", - "id": "8e7d3a5e", - "metadata": {}, - "source": [ - "```{note}\n", - "\n", - "Typically, you run the Nextflow workflow from the command line or Seqera Platform and then register input and output data with a script.\n", - "The Seqera Platform allows for [post-run scripts](https://docs.seqera.io/platform/23.4.0/launch/advanced#pre-and-post-run-scripts) that can automate this process.\n", - "```" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "756e24d7-b2a0-4a10-bf6c-f532e0cc323b", - "metadata": { - "tags": [ - "hide-output" - ] - }, - "outputs": [], - "source": [ - "!lamin init --storage . --name nextflow-mcmicro" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "3358a50f", - "metadata": {}, - "outputs": [], - "source": [ - "import lamindb as ln" - ] - }, - { - "cell_type": "markdown", - "id": "27c76922", - "metadata": {}, - "source": [ - "## Run mcmicro/exemplar pipeline" - ] - }, - { - "cell_type": "markdown", - "id": "2d7fa65b", - "metadata": {}, - "source": [ - "Register the `exemplar-001` data as input of the mcmicro pipeline by running the script below:" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "6cd3e0a0", - "metadata": { - "tags": [ - "hide-input", - "hide-output" - ] - }, - "outputs": [], - "source": [ - "from IPython.display import display, Code\n", - "\n", - "with open('mcmicro_exemplar.py', 'r') as file:\n", - " display(Code(file.read(), language='python'))" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "cc5c9e59", - "metadata": { - "tags": [ - "hide-output" - ] - }, - "outputs": [], - "source": [ - "!python mcmicro_exemplar.py exemplar-001" - ] - }, - { - "cell_type": "markdown", - "id": "ecb68cf2-1188-4f8b-a2ab-01c60d5779b8", - "metadata": {}, - "source": [ - "## Run mcmicro pipeline\n", - "\n", - "Run mcmicro pipeline and track input/output data with the script below:" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "2d0a0e06", - "metadata": { - "tags": [ - "hide-input" - ] - }, - "outputs": [], - "source": [ - "with open('mcmicro.py', 'r') as file:\n", - " display(Code(file.read(), language='python'))" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "285ee7b8", - "metadata": { - "tags": [ - "hide-output" - ] - }, - "outputs": [], - "source": [ - "!python mcmicro.py exemplar-001" - ] - }, - { - "cell_type": "markdown", - "id": "9f607150", - "metadata": {}, - "source": [ - "## Data lineage" - ] - }, - { - "cell_type": "markdown", - "id": "54595d81", - "metadata": {}, - "source": [ - "View data lineage:" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "dda2b400", - "metadata": {}, - "outputs": [], - "source": [ - "output = ln.Artifact.filter(key__icontains=\"exemplar-001.ome.tif\").one()" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "ba83bfee-5cb8-4520-9a32-0deccd47ff34", - "metadata": {}, - "outputs": [], - "source": [ - "output.view_lineage()" - ] - }, - { - "cell_type": "markdown", - "id": "038286a7", - "metadata": {}, - "source": [ - "## View transforms and runs in LaminHub\n", - "\n", - "[![hub](https://img.shields.io/badge/View%20in%20LaminHub-mediumseagreen)](https://lamin.ai/laminlabs/lamindata/transform/vMwsczN6lGZWRm8w/foyuuRRmEt7KYiaU8hPD)\n", - "\n", - "" - ] - }, - { - "cell_type": "markdown", - "id": "ee3db779", - "metadata": {}, - "source": [ - "## View the database content" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "e45c2584", - "metadata": {}, - "outputs": [], - "source": [ - "ln.view()" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "5f3f95a8", - "metadata": { - "tags": [ - "hide-cell" - ] - }, - "outputs": [], - "source": [ - "# clean up the test instance:\n", - "!lamin delete --force nextflow-mcmicro" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.1.-1" - }, - "nbproject": { - "id": "8124Vtle6ZrO", - "parent": null, - "pypackage": null, - "time_init": "2023-07-24T13:06:04.795992+00:00", - "user_handle": null, - "user_id": null, - "user_name": null, - "version": "0" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/docs/mcmicro.py b/docs/mcmicro.py deleted file mode 100644 index 63d3649..0000000 --- a/docs/mcmicro.py +++ /dev/null @@ -1,74 +0,0 @@ -# mcmicro.py - -"""This script runs the MCMICRO pipeline and tracks input/output data in LaminDB. - -Usage: python mcmicro.py exemplar-001 -""" - -import subprocess -import argparse -import lamindb as ln -import yaml - -# get args from command line -parser = argparse.ArgumentParser() -parser.add_argument("input", type=str, help="Input folder name.") -args = parser.parse_args() - -transform = ln.Transform( - name="MCMICRO", - version="1.0.0", - type="pipeline", - reference="https://github.com/labsyspharm/mcmicro", -) -ln.context.track(transform=transform) -run = ln.context.run - -# get the input data from LaminDB -mcmicro_input = ln.Artifact.filter(description=args.input).one() -input_dir = mcmicro_input.cache() - -# execute the nextflow pipeline to download example data -report = f"{args.input}-mcmicro-execution_report.html" -subprocess.run( - [ - "nextflow", - "run", - "https://github.com/labsyspharm/mcmicro", - "--in", - input_dir, - "--start-at", - "illumination", - "--stop-at", - "registration", - "-with-report", - report, - ] -) - -# get the nextflow execution id from the log (first row) -nextflow_id = subprocess.getoutput( - "nextflow log | tail -n 1 | awk -F '\t' '{print $6}'" -) -# optionally, tag the transform -ulabel = ln.ULabel(name="nextflow").save() -run.transform.ulabels.add(ulabel) -# track the execution report, set visibility to "hidden" to avoid cluttering the artifacts -report_artifact = ln.Artifact( - report, description=f"nextflow report of {nextflow_id}", visibility=0, run=False -).save() -run.report = report_artifact -run.reference = nextflow_id -run.reference_type = "nextflow_id" -run.save() -# optionally, track the pipeline parameters -with open(f"{input_dir}/qc/params.yml") as params_file: - qc_params = yaml.safe_load(params_file) -ln.Param(name="qc_params", dtype="dict").save() -run.params.add_values({"qc_params": qc_params}) - -# register the output artifact -output = ln.Artifact.from_dir(f"{input_dir}/registration") -ln.save(output) - -ln.finish() diff --git a/docs/mcmicro_exemplar.py b/docs/mcmicro_exemplar.py deleted file mode 100644 index 4ffa238..0000000 --- a/docs/mcmicro_exemplar.py +++ /dev/null @@ -1,67 +0,0 @@ -# mcmicro_exemplar.py - -"""This script downloads the MCMICRO exemplar data and registers it in LaminDB. - -Usage: python mcmicro_exemplar.py exemplar-001 -""" - -import lamindb as ln -import subprocess -import argparse - - -# get args from command line -parser = argparse.ArgumentParser() -parser.add_argument("name", type=str, help="Name of the example data.") -args = parser.parse_args() -if args.name not in ["exemplar-001", "exemplar-002"]: - raise ValueError("Invalid name. Use 'exemplar-001' or 'exemplar-002'.") - -# execute the nextflow pipeline to download example data -report = f"{args.name}_mcmicro-exemplar_execution_report.html" -subprocess.run( - [ - "nextflow", - "run", - "labsyspharm/mcmicro/exemplar.nf", - "--name", - args.name, - "-with-report", - report, - ] -) - -# get the nextflow execution id from the log (last row, latest run is at the bottom) -nextflow_id = subprocess.getoutput( - "nextflow log | tail -n 1 | awk -F '\t' '{print $6}'" -) - -# track the pipeline transform -transform = ln.Transform( - name="MCMICRO exemplar", - version="1.0.0", - type="pipeline", - reference="https://github.com/labsyspharm/mcmicro", -) -ln.context.track(transform=transform) -run = ln.context.run -# optionally, tag the transform -ulabel = ln.ULabel(name="nextflow").save() -run.transform.ulabels.add(ulabel) -# track the execution report, set visibility to "hidden" to avoid cluttering the artifacts -report_artifact = ln.Artifact( - report, description=f"nextflow report of {nextflow_id}", visibility=0, run=False -).save() -run.report = report_artifact -run.reference = nextflow_id -run.reference_type = "nextflow_id" -run.save() -# optionally, track the pipeline parameters -ln.Param(name="name", dtype="str").save() -run.params.add_values({"name": args.name}) - -# register the downloaded folder -exemplar_dir = ln.Artifact(args.name, description=args.name) -exemplar_dir.save() - -ln.finish() diff --git a/docs/nf_core_scrnaseq.ipynb b/docs/nf_core_scrnaseq.ipynb new file mode 100644 index 0000000..21d3505 --- /dev/null +++ b/docs/nf_core_scrnaseq.ipynb @@ -0,0 +1,287 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "a1c40541-e05e-48a3-8b50-33baf3d6d0d4", + "metadata": {}, + "source": [ + "# Nextflow" + ] + }, + { + "cell_type": "markdown", + "id": "cd12ac1a-73e6-44e2-a854-6fa5e52cfd41", + "metadata": {}, + "source": [ + "[Nextflow](https://www.nextflow.io/) is the most widely used workflow manager in bioinformatics.\n", + "\n", + "This guide shows how to register a Nextflow run with inputs & outputs for the example of the [nf-core/scrnaseq](https://nf-co.re/scrnaseq/latest) pipeline by running a Python script.\n", + "\n", + "The approach could be automated by deploying the script via\n", + "\n", + "1. a serverless environment trigger (e.g., AWS Lambda)\n", + "2. a [post-run script](https://docs.seqera.io/platform/23.4.0/launch/advanced#pre-and-post-run-scripts) on the Seqera Platform" + ] + }, + { + "cell_type": "markdown", + "id": "f003e7d4", + "metadata": {}, + "source": [ + ":::{dropdown} What steps are executed by the nf-core/scrnaseq pipeline?\n", + "\n", + "![](https://github.com/nf-core/scrnaseq/blob/master/docs/images/scrnaseq_pipeline_v1.0_metro_clean.png?raw=true)\n", + "\n", + ":::" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "756e24d7-b2a0-4a10-bf6c-f532e0cc323b", + "metadata": { + "tags": [ + "hide-output" + ] + }, + "outputs": [], + "source": [ + "!lamin init --storage ./test-nextflow --name test-nextflow" + ] + }, + { + "cell_type": "markdown", + "id": "ecb68cf2-1188-4f8b-a2ab-01c60d5779b8", + "metadata": {}, + "source": [ + "## Run the pipeline\n", + "\n", + "Let's download the input data from an S3 bucket." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "258cdd13", + "metadata": {}, + "outputs": [], + "source": [ + "import lamindb as ln\n", + "\n", + "input_path = ln.UPath(\"s3://lamindb-test/scrnaseq_input\")\n", + "input_path.download_to(\"scrnaseq_input\")" + ] + }, + { + "cell_type": "markdown", + "id": "5a3671cb", + "metadata": {}, + "source": [ + "And run the `nf-core/scrnaseq` pipeline." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2e98958f", + "metadata": { + "tags": [ + "hide-output" + ] + }, + "outputs": [], + "source": [ + "# the test profile uses all downloaded input files as an input\n", + "!nextflow run nf-core/scrnaseq -r 2.7.1 -profile docker,test -resume --outdir scrnaseq_output" + ] + }, + { + "cell_type": "markdown", + "id": "d1a77f5a", + "metadata": {}, + "source": [ + ":::{dropdown} What is the full run command for the test profile?\n", + "\n", + "```\n", + "nextflow run nf-core/scrnaseq -r 2.7.1 \\\n", + " -profile docker \\\n", + " -resume \\\n", + " --outdir scrnaseq_output \\\n", + " --input 'scrnaseq_input/samplesheet-2-0.csv' \\\n", + " --skip_emptydrops \\\n", + " --fasta 'https://github.com/nf-core/test-datasets/raw/scrnaseq/reference/GRCm38.p6.genome.chr19.fa' \\\n", + " --gtf 'https://github.com/nf-core/test-datasets/raw/scrnaseq/reference/gencode.vM19.annotation.chr19.gtf' \\\n", + " --aligner 'star' \\\n", + " --protocol '10XV2' \\\n", + " --max_cpus 2 \\\n", + " --max_memory '6.GB' \\\n", + " --max_time '6.h'\n", + "```\n", + ":::" + ] + }, + { + "cell_type": "markdown", + "id": "4b1c950f", + "metadata": {}, + "source": [ + "## Run the registration script" + ] + }, + { + "cell_type": "markdown", + "id": "45ec5b04", + "metadata": {}, + "source": [ + "After the pipeline has completed, a Python script registers inputs & outputs in LaminDB." + ] + }, + { + "cell_type": "markdown", + "id": "2d0a0e06", + "metadata": {}, + "source": [ + "```{eval-rst}\n", + ".. literalinclude:: register_scrnaseq_run.py\n", + " :language: python\n", + " :caption: nf-core/scrnaseq run registration\n", + "```" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "285ee7b8", + "metadata": { + "tags": [ + "hide-output" + ] + }, + "outputs": [], + "source": [ + "!python register_scrnaseq_run.py --input scrnaseq_input --output scrnaseq_output" + ] + }, + { + "cell_type": "markdown", + "id": "9f607150", + "metadata": {}, + "source": [ + "## Data lineage" + ] + }, + { + "cell_type": "markdown", + "id": "806408d0", + "metadata": {}, + "source": [ + "The output data could now be accessed (in a different notebook/script) for analysis with full lineage." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "bc17c815", + "metadata": { + "tags": [ + "hide-output" + ] + }, + "outputs": [], + "source": [ + "matrix_af = ln.Artifact.get(description__icontains=\"filtered count matrix\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "482d78b9", + "metadata": {}, + "outputs": [], + "source": [ + "matrix_af.view_lineage()" + ] + }, + { + "cell_type": "markdown", + "id": "038286a7", + "metadata": {}, + "source": [ + "## View transforms & runs on the hub\n", + "\n", + "[![hub](https://img.shields.io/badge/View%20on%20LaminHub-mediumseagreen)](https://lamin.ai/laminlabs/lamindata/transform/cpMwOcY2YJ5G0000/214dWyrIPWHX7pg24EDR)\n", + "\n", + "" + ] + }, + { + "cell_type": "markdown", + "id": "ee3db779", + "metadata": {}, + "source": [ + "## View the database content" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e45c2584", + "metadata": { + "tags": [ + "hide-output" + ] + }, + "outputs": [], + "source": [ + "ln.view()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5f3f95a8", + "metadata": { + "tags": [ + "hide-cell" + ] + }, + "outputs": [], + "source": [ + "# clean up the test instance:\n", + "!rm -rf test-nextflow\n", + "!lamin delete --force test-nextflow" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.7" + }, + "nbproject": { + "id": "8124Vtle6ZrO", + "parent": null, + "pypackage": null, + "time_init": "2023-07-24T13:06:04.795992+00:00", + "user_handle": null, + "user_id": null, + "user_name": null, + "version": "0" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/docs/register_nf_run.py b/docs/register_nf_run.py deleted file mode 100644 index 2df212a..0000000 --- a/docs/register_nf_run.py +++ /dev/null @@ -1,32 +0,0 @@ -import argparse -from subprocess import getoutput - -import lamindb as ln - -parser = argparse.ArgumentParser() -parser.add_argument("-p", "--pipeline-name", required=True) -parser.add_argument("-v", "--pipeline-version", required=True) -parser.add_argument("-r", "--pipeline-reference", required=True) -args = parser.parse_args() - -transform = ln.Transform( - name=args.pipeline_name, - version=args.pipeline_version, - type="pipeline", - reference=args.pipeline_reference, -) -ln.context.track(transform=transform) -run = ln.context.run - -mcmicro_input = ln.Artifact.filter(key__startswith="exemplar-001") -input_paths = [input_fastq.cache() for input_fastq in mcmicro_input] - -output = ln.Artifact( - "exemplar-001/registration/exemplar-001.ome.tif", description="mcmicro" -) -output.save() - -nextflow_id = getoutput(f"nextflow log | awk '/{run.id}/{{print $8}}'") -run.reference = nextflow_id -run.reference_type = "nextflow_id" -run.save() diff --git a/docs/register_scrnaseq_run.py b/docs/register_scrnaseq_run.py new file mode 100644 index 0000000..1e92830 --- /dev/null +++ b/docs/register_scrnaseq_run.py @@ -0,0 +1,71 @@ +import argparse +import lamindb as ln +import json +import re +from pathlib import Path + + +def parse_arguments() -> argparse.Namespace: + parser = argparse.ArgumentParser() + parser.add_argument("--input", type=str, required=True) + parser.add_argument("--output", type=str, required=True) + return parser.parse_args() + + +def register_pipeline_io(input_dir: str, output_dir: str, run: ln.Run) -> None: + """Register input and output artifacts for an `nf-core/scrnaseq` run.""" + input_artifacts = ln.Artifact.from_dir(input_dir, run=False) + ln.save(input_artifacts) + run.input_artifacts.set(input_artifacts) + ln.Artifact(f"{output_dir}/multiqc", description="multiqc report", run=run).save() + ln.Artifact( + f"{output_dir}/star/mtx_conversions/combined_filtered_matrix.h5ad", + description="filtered count matrix", + run=run, + ).save() + + +def register_pipeline_metadata(output_dir: str, run: ln.Run) -> None: + """Register nf-core run metadata stored in the 'pipeline_info' folder.""" + ulabel = ln.ULabel(name="nextflow").save() + run.transform.ulabels.add(ulabel) + + # nextflow run id + content = next(Path(f"{output_dir}/pipeline_info").glob("execution_report_*.html")).read_text() + match = re.search(r"run id \[([^\]]+)\]", content) + nextflow_id = match.group(1) if match else "" + run.reference = nextflow_id + run.reference_type = "nextflow_id" + + # execution report and software versions + for file_pattern, description, run_attr in [ + ("execution_report*", "execution report", "report"), + ("nf_core_pipeline_software*", "software versions", "environment"), + ]: + artifact = ln.Artifact( + next(Path(f"{output_dir}/pipeline_info").glob(file_pattern)), + description=f"nextflow run {description} of {nextflow_id}", + visibility=0, + run=False, + ).save() + setattr(run, run_attr, artifact) + + # nextflow run parameters + params_path = next(Path(f"{output_dir}/pipeline_info").glob("params*")) + with params_path.open() as params_file: + params = json.load(params_file) + ln.Param(name="params", dtype="dict").save() + run.params.add_values({"params": params}) + run.save() + + +args = parse_arguments() +scrnaseq_transform = ln.Transform( + name="scrna-seq", + version="2.7.1", + type="pipeline", + reference="https://github.com/nf-core/scrnaseq", +).save() +run = ln.Run(transform=scrnaseq_transform).save() +register_pipeline_io(args.input, args.output, run) +register_pipeline_metadata(args.output, run) diff --git a/nextflow_bulk_rna.ipynb b/nextflow_bulk_rna.ipynb deleted file mode 100644 index 440486d..0000000 --- a/nextflow_bulk_rna.ipynb +++ /dev/null @@ -1,20344 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "id": "a1c40541-e05e-48a3-8b50-33baf3d6d0d4", - "metadata": {}, - "source": [ - "# Nextflow nf-core/rnaseq" - ] - }, - { - "cell_type": "markdown", - "id": "cd12ac1a-73e6-44e2-a854-6fa5e52cfd41", - "metadata": {}, - "source": [ - "[Nextflow](https://www.nextflow.io/) is a workflow management system used for executing scientific workflows across platforms scalably, portably, and reproducibly.\n", - "\n", - "Here, we'll run `nf-core/rnaseq` to process `.fastq` files from bulk RNA sequencing using STAR, RSEM, HISAT2, Salmon with gene/isoform counts and extensive quality control ([reference](https://nf-co.re/rnaseq/3.12.0)).\n", - "\n", - "![](https://raw.githubusercontent.com/nf-core/rnaseq/3.12.0//docs/images/nf-core-rnaseq_metro_map_grey.png)\n" - ] - }, - { - "cell_type": "markdown", - "id": "8e7d3a5e", - "metadata": {}, - "source": [ - "```{note}\n", - "\n", - "This notebook serves as a demo for Python scripting that you could run before and after Nextflow runs.\n", - "\n", - "Typically, you'd run the workflows from the command line or Nextflow Tower.\n", - "```" - ] - }, - { - "cell_type": "markdown", - "id": "fe9ab200", - "metadata": {}, - "source": [ - "## Setup" - ] - }, - { - "cell_type": "markdown", - "id": "b7c8e52d", - "metadata": {}, - "source": [ - "Let's create a test instance:" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "id": "756e24d7-b2a0-4a10-bf6c-f532e0cc323b", - "metadata": { - "tags": [ - "hide-output" - ] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "✅ saved: User(uid='I5DPZdiE', handle='zethson', updated_at=2023-12-06 11:09:01 UTC)\n", - "✅ saved: Storage(uid='pfjurGAu', root='/home/zeth/PycharmProjects/nextflow-lamin-usecases/docs', type='local', updated_at=2023-12-06 11:09:01 UTC, created_by_id=1)\n", - "💡 loaded instance: zethson/nextflow-bulkrna\n", - "💡 did not register local instance on hub\n", - "\u001b[0m" - ] - } - ], - "source": [ - "!lamin init --storage . --name nextflow-bulkrna" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "id": "3358a50f", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "💡 lamindb instance: zethson/nextflow-bulkrna\n" - ] - } - ], - "source": [ - "import lamindb as ln\n", - "from subprocess import getoutput" - ] - }, - { - "cell_type": "markdown", - "id": "cff2c742", - "metadata": {}, - "source": [ - "## Download test data" - ] - }, - { - "cell_type": "markdown", - "id": "4f32ae96", - "metadata": {}, - "source": [ - "Download test data using git:" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "id": "3f03dc98-c23d-439e-838d-147134470cf7", - "metadata": { - "tags": [ - "hide-output" - ] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "fatal: destination path 'test-datasets' already exists and is not an empty directory.\n" - ] - } - ], - "source": [ - "!git clone https://github.com/nf-core/test-datasets --single-branch --branch rnaseq3 --depth 1" - ] - }, - { - "cell_type": "markdown", - "id": "26d980c5", - "metadata": {}, - "source": [ - "(Optional) Register input files:" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "id": "e80ed3ad-3588-4b47-9720-66fbe7492ffd", - "metadata": { - "tags": [ - "hide-output" - ] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "❗ no run & transform get linked, consider passing a `run` or calling ln.track()\n", - "❗ no run & transform get linked, consider passing a `run` or calling ln.track()\n", - "❗ file has more than one suffix (path.suffixes), inferring: '.fastq.gz'\n", - "❗ no run & transform get linked, consider passing a `run` or calling ln.track()\n", - "❗ file has more than one suffix (path.suffixes), inferring: '.fastq.gz'\n", - "❗ no run & transform get linked, consider passing a `run` or calling ln.track()\n", - "❗ file has more than one suffix (path.suffixes), inferring: '.fastq.gz'\n", - "❗ no run & transform get linked, consider passing a `run` or calling ln.track()\n", - "❗ file has more than one suffix (path.suffixes), inferring: '.fastq.gz'\n", - "❗ no run & transform get linked, consider passing a `run` or calling ln.track()\n", - "❗ file has more than one suffix (path.suffixes), inferring: '.fastq.gz'\n", - "❗ no run & transform get linked, consider passing a `run` or calling ln.track()\n", - "❗ file has more than one suffix (path.suffixes), inferring: '.fastq.gz'\n", - "❗ no run & transform get linked, consider passing a `run` or calling ln.track()\n", - "❗ file has more than one suffix (path.suffixes), inferring: '.fastq.gz'\n", - "❗ no run & transform get linked, consider passing a `run` or calling ln.track()\n", - "❗ file has more than one suffix (path.suffixes), inferring: '.fastq.gz'\n", - "❗ no run & transform get linked, consider passing a `run` or calling ln.track()\n", - "❗ file has more than one suffix (path.suffixes), inferring: '.fastq.gz'\n", - "❗ no run & transform get linked, consider passing a `run` or calling ln.track()\n", - "❗ file has more than one suffix (path.suffixes), inferring: '.fastq.gz'\n", - "❗ no run & transform get linked, consider passing a `run` or calling ln.track()\n", - "❗ file has more than one suffix (path.suffixes), inferring: '.fastq.gz'\n" - ] - } - ], - "source": [ - "# register files\n", - "sample_sheet = ln.Artifact(\"test-datasets/samplesheet/v3.10/samplesheet_test.csv\")\n", - "sample_sheet.save()\n", - "input_fastqs = ln.Artifact.from_dir(\"test-datasets/testdata/GSE110004/\")\n", - "ln.save(input_fastqs)" - ] - }, - { - "cell_type": "markdown", - "id": "ecb68cf2-1188-4f8b-a2ab-01c60d5779b8", - "metadata": {}, - "source": [ - "## Track the Nextflow run" - ] - }, - { - "cell_type": "markdown", - "id": "3e1224fd", - "metadata": {}, - "source": [ - "Track the Nextflow workflow & run:" - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "id": "05a03bf4-81e5-45b4-a126-002def01f81a", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "💡 saved: Transform(uid='A3xe64gBMC18zK', name='nf-core rnaseq', version='3.11.2', type='pipeline', reference='https://github.com/laminlabs/nextflow-lamin-usecases', updated_at=2023-12-06 11:09:03 UTC, created_by_id=1)\n", - "💡 saved: Run(uid='Bcs8m6VxzFM42qhCD4VF', run_at=2023-12-06 11:09:03 UTC, transform_id=1, created_by_id=1)\n" - ] - } - ], - "source": [ - "transform = ln.Transform(\n", - " name=\"nf-core rnaseq\",\n", - " version=\"3.11.2\",\n", - " type=\"pipeline\",\n", - " reference=\"https://github.com/laminlabs/nextflow-lamin-usecases\",\n", - ")\n", - "ln.track(transform)\n", - "# let's grab the run of the global run context\n", - "run = ln.dev.run_context.run" - ] - }, - { - "cell_type": "markdown", - "id": "670533a7", - "metadata": {}, - "source": [ - "If we now stage input files, they'll be tracked as inputs for the global run:" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "id": "27294132", - "metadata": { - "tags": [ - "hide-output" - ] - }, - "outputs": [], - "source": [ - "input_sample_sheet_path = sample_sheet.cache()\n", - "input_paths = [input_fastq.cache() for input_fastq in input_fastqs]" - ] - }, - { - "cell_type": "markdown", - "id": "17f9905e-0a34-4335-b0c4-eb9b598c8eaf", - "metadata": {}, - "source": [ - "Run the nextflow pipeline:" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "id": "2219c55e", - "metadata": { - "tags": [ - "hide-output" - ] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "N E X T F L O W ~ version 23.04.2\n", - "Launching `https://github.com/nf-core/rnaseq` [lamin_Bcs8m6VxzFM42qhCD4VF] DSL2 - revision: 5671b65af9 [3.11.2]\n", - "\n", - "\n", - "------------------------------------------------------\n", - " ,--./,-.\n", - " ___ __ __ __ ___ /,-._.--~'\n", - " |\\ | |__ __ / ` / \\ |__) |__ } {\n", - " | \\| | \\__, \\__/ | \\ |___ \\`-._,-`-,\n", - " `._,._,'\n", - " nf-core/rnaseq v3.11.2-g5671b65\n", - "------------------------------------------------------\n", - "Core Nextflow options\n", - " revision : 3.11.2\n", - " runName : lamin_Bcs8m6VxzFM42qhCD4VF\n", - " containerEngine : docker\n", - " launchDir : /home/zeth/PycharmProjects/nextflow-lamin-usecases/docs\n", - " workDir : /home/zeth/PycharmProjects/nextflow-lamin-usecases/docs/work\n", - " projectDir : /home/zeth/.nextflow/assets/nf-core/rnaseq\n", - " userName : zeth\n", - " profile : test,docker\n", - " configFiles : /home/zeth/.nextflow/assets/nf-core/rnaseq/nextflow.config\n", - "\n", - "Input/output options\n", - " input : https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/samplesheet/v3.10/samplesheet_test.csv\n", - " outdir : rna-seq-results\n", - "\n", - "UMI options\n", - " umitools_bc_pattern : NNNN\n", - "\n", - "Read filtering options\n", - " bbsplit_fasta_list : https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/bbsplit_fasta_list.txt\n", - " skip_bbsplit : false\n", - "\n", - "Reference genome options\n", - " fasta : https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genome.fasta\n", - " gtf : https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genes.gtf.gz\n", - " gff : https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/genes.gff.gz\n", - " transcript_fasta : https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/transcriptome.fasta\n", - " additional_fasta : https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/gfp.fa.gz\n", - " hisat2_index : https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/hisat2.tar.gz\n", - " rsem_index : https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/rsem.tar.gz\n", - " salmon_index : https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3/reference/salmon.tar.gz\n", - "\n", - "Alignment options\n", - " pseudo_aligner : salmon\n", - "\n", - "Institutional config options\n", - " config_profile_name : Test profile\n", - " config_profile_description: Minimal test dataset to check pipeline function\n", - "\n", - "Max job request options\n", - " max_cpus : 2\n", - " max_memory : 6.GB\n", - " max_time : 6.h\n", - "\n", - "!! Only displaying parameters that differ from the pipeline defaults !!\n", - "------------------------------------------------------\n", - "If you use nf-core/rnaseq for your analysis please cite:\n", - "\n", - "* The pipeline\n", - " https://doi.org/10.5281/zenodo.1400710\n", - "\n", - "* The nf-core framework\n", - " https://doi.org/10.1038/s41587-020-0439-x\n", - "\n", - "* Software dependencies\n", - " https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md\n", - "------------------------------------------------------\n", - "WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - " Both '--gtf' and '--gff' parameters have been provided.\n", - " Using GTF file as priority.\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - " '--transcript_fasta' parameter has been provided.\n", - " Make sure transcript names in this file match those in the GFF/GTF file.\n", - "\n", - " Please see:\n", - " https://github.com/nf-core/rnaseq/issues/753\n", - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:INPUT_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - 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"[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:STRING... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:SUBREA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:INPUT_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BBMAP_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:STRING... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:SUBREA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUALIM... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:INPUT_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BBMAP_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:STRING... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:SUBREA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUALIM... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... -\n", - "\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:INPUT_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BBMAP_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:STRING... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:SUBREA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUALIM... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -\n", - "\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:INPUT_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BBMAP_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:STRING... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:SUBREA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUALIM... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -\n", - "\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... 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[100%] 1 of 1 ✔\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BBMAP_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:STRING... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:SUBREA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUALIM... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -\n", - "\n", - "executor > local (7)\n", - "[bf/cd0d9d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... 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[100%] 1 of 1 ✔\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BBMAP_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:STRING... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:SUBREA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUALIM... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -\n", - "\n", - "executor > local (8)\n", - "[bf/cd0d9d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... 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[100%] 1 of 1 ✔\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CAT_FASTQ -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BBMAP_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\u001b[K\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:STRING... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:SUBREA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUALIM... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:DUPRADAR -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:QUANTI... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -\n", - "\n", - "executor > local (8)\n", - "[bf/cd0d9d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[5c/bbd5f9] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[f3/460f93] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[0f/d33896] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [ 0%] 0 of 1\n", - "[77/49b796] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:PREPAR... -\n", - "[d6/908096] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [ 0%] 0 of 1\n", - "[30/e7d2c8] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[c5/6c2904] process > NFCORE_RNASEQ:RNASEQ:INPUT_... 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[ 80%] 4 of 5\n", - "[39/92f97c] process > NFCORE_RNASEQ:RNASEQ:QUALIM... [100%] 5 of 5 ✔\n", - "[93/ee7586] process > NFCORE_RNASEQ:RNASEQ:DUPRAD... [100%] 5 of 5 ✔\n", - "[8e/1cb5bc] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [ 80%] 4 of 5\n", - "[53/96e96e] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [ 80%] 4 of 5\n", - "[2f/762663] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [ 80%] 4 of 5\n", - "[37/cca121] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [ 80%] 4 of 5\n", - "[8f/e1d5b9] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [ 80%] 4 of 5\n", - "[f9/dd5080] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [ 80%] 4 of 5\n", - "[32/d48667] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [ 80%] 4 of 5\n", - "[bc/8d3eae] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[4d/d2edfb] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[7a/6718e8] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[0b/f4bcf2] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/35bff4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[b1/faaa94] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[12/163264] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[17/662343] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -\n", - "\n", - "executor > local (167)\n", - "[bf/cd0d9d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[5c/bbd5f9] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[f3/460f93] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[0f/d33896] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[77/49b796] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[8d/6b59d1] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[d6/908096] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[30/e7d2c8] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[c5/6c2904] process > NFCORE_RNASEQ:RNASEQ:INPUT_... [100%] 1 of 1 ✔\n", - "[77/317e3a] process > NFCORE_RNASEQ:RNASEQ:CAT_FA... [100%] 2 of 2 ✔\n", - "[43/d93bf3] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[6a/24ca0d] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[5e/cf9ba9] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[d5/6397d1] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[27/85c96b] process > NFCORE_RNASEQ:RNASEQ:BBMAP_... [100%] 5 of 5 ✔\n", - "[51/fa5357] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[71/ba06f7] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[ed/974851] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[33/60bf71] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[6a/4c51fc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... 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[100%] 5 of 5 ✔\n", - "[f5/40882a] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [ 80%] 4 of 5\n", - "[d1/3bf954] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... [100%] 5 of 5 ✔\n", - "[ee/396753] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[4b/716a5a] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[18/7476ba] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[95/82f4ff] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[39/92f97c] process > NFCORE_RNASEQ:RNASEQ:QUALIM... [100%] 5 of 5 ✔\n", - "[93/ee7586] process > NFCORE_RNASEQ:RNASEQ:DUPRAD... [100%] 5 of 5 ✔\n", - "[8e/1cb5bc] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [ 80%] 4 of 5\n", - "[53/96e96e] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [ 80%] 4 of 5\n", - "[2f/762663] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [ 80%] 4 of 5\n", - "[cd/4a48c2] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [ 80%] 4 of 5\n", - "[8f/e1d5b9] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... 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[ 80%] 4 of 5\n", - "[d1/3bf954] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... [100%] 5 of 5 ✔\n", - "[ee/396753] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[4b/716a5a] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[18/7476ba] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[95/82f4ff] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[39/92f97c] process > NFCORE_RNASEQ:RNASEQ:QUALIM... [100%] 5 of 5 ✔\n", - "[93/ee7586] process > NFCORE_RNASEQ:RNASEQ:DUPRAD... [100%] 5 of 5 ✔\n", - "[8e/1cb5bc] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [ 80%] 4 of 5\n", - "[a9/78a120] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [ 80%] 4 of 5\n", - "[2f/762663] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [ 80%] 4 of 5\n", - "[cd/4a48c2] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[5d/e95635] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [ 80%] 4 of 5\n", - "[f9/dd5080] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... 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[100%] 5 of 5 ✔\n", - "[f5/40882a] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [ 80%] 4 of 5\n", - "[d1/3bf954] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... [100%] 5 of 5 ✔\n", - "[ee/396753] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[4b/716a5a] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[18/7476ba] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[95/82f4ff] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[39/92f97c] process > NFCORE_RNASEQ:RNASEQ:QUALIM... [100%] 5 of 5 ✔\n", - "[93/ee7586] process > NFCORE_RNASEQ:RNASEQ:DUPRAD... [100%] 5 of 5 ✔\n", - "[8e/1cb5bc] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [ 80%] 4 of 5\n", - "[a9/78a120] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [ 80%] 4 of 5\n", - "[be/279ad8] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[cd/4a48c2] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[5d/e95635] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... 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[100%] 1 of 1 ✔\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -\n", - "\n", - "executor > local (178)\n", - "[bf/cd0d9d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[5c/bbd5f9] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[f3/460f93] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[0f/d33896] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[77/49b796] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[8d/6b59d1] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[d6/908096] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[30/e7d2c8] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[c5/6c2904] process > NFCORE_RNASEQ:RNASEQ:INPUT_... [100%] 1 of 1 ✔\n", - "[77/317e3a] process > NFCORE_RNASEQ:RNASEQ:CAT_FA... [100%] 2 of 2 ✔\n", - "[43/d93bf3] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... 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[100%] 1 of 1 ✔\n", - "[1c/2abfbb] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[ee/ba02e4] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[b9/0f85cb] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[9d/7ccd59] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [ 20%] 1 of 5\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [ 0%] 0 of 5\n", - "[99/2f5007] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [ 20%] 1 of 5\n", - "[41/801c12] process > NFCORE_RNASEQ:RNASEQ:STRING... [100%] 5 of 5 ✔\n", - "[b5/1066ee] process > NFCORE_RNASEQ:RNASEQ:SUBREA... [100%] 5 of 5 ✔\n", - "[f5/40882a] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [ 80%] 4 of 5\n", - "[d1/3bf954] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... [100%] 5 of 5 ✔\n", - "[ee/396753] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[4b/716a5a] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[18/7476ba] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... 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[100%] 1 of 1 ✔\n", - "[17/662343] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -\n", - "\n", - "executor > local (181)\n", - "[bf/cd0d9d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[5c/bbd5f9] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[f3/460f93] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[0f/d33896] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[77/49b796] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[8d/6b59d1] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[d6/908096] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[30/e7d2c8] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[c5/6c2904] process > NFCORE_RNASEQ:RNASEQ:INPUT_... [100%] 1 of 1 ✔\n", - "[77/317e3a] process > NFCORE_RNASEQ:RNASEQ:CAT_FA... [100%] 2 of 2 ✔\n", - "[43/d93bf3] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[6a/24ca0d] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[5e/cf9ba9] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[d5/6397d1] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[27/85c96b] process > NFCORE_RNASEQ:RNASEQ:BBMAP_... [100%] 5 of 5 ✔\n", - "[51/fa5357] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[71/ba06f7] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[ed/974851] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[33/60bf71] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[6a/4c51fc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[4a/d5e328] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[52/39a759] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[09/0eb606] process > NFCORE_RNASEQ:RNASEQ:QUANTI... 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[100%] 5 of 5 ✔\n", - "[f5/40882a] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [ 80%] 4 of 5\n", - "[d1/3bf954] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... [100%] 5 of 5 ✔\n", - "[ee/396753] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[4b/716a5a] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[18/7476ba] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[95/82f4ff] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[39/92f97c] process > NFCORE_RNASEQ:RNASEQ:QUALIM... [100%] 5 of 5 ✔\n", - "[93/ee7586] process > NFCORE_RNASEQ:RNASEQ:DUPRAD... [100%] 5 of 5 ✔\n", - "[bf/b249b6] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[a9/78a120] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[be/279ad8] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[cd/4a48c2] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[5d/e95635] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... 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[100%] 1 of 1 ✔\n", - "[9d/0ba5d1] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[1c/2abfbb] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[ee/ba02e4] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[b9/0f85cb] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[9d/7ccd59] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [ 20%] 1 of 5\n", - "[dd/ea35bf] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [ 40%] 2 of 5\n", - "[82/284fb3] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [ 40%] 2 of 5\n", - "[41/801c12] process > NFCORE_RNASEQ:RNASEQ:STRING... [100%] 5 of 5 ✔\n", - "[b5/1066ee] process > NFCORE_RNASEQ:RNASEQ:SUBREA... [100%] 5 of 5 ✔\n", - "[f5/40882a] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [ 80%] 4 of 5\n", - "[d1/3bf954] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... [100%] 5 of 5 ✔\n", - "[ee/396753] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[4b/716a5a] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[18/7476ba] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[95/82f4ff] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[39/92f97c] process > NFCORE_RNASEQ:RNASEQ:QUALIM... [100%] 5 of 5 ✔\n", - "[93/ee7586] process > NFCORE_RNASEQ:RNASEQ:DUPRAD... [100%] 5 of 5 ✔\n", - "[bf/b249b6] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[a9/78a120] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[be/279ad8] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[cd/4a48c2] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[5d/e95635] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[33/efe883] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[f7/a302cd] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[bc/8d3eae] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[4d/d2edfb] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[7a/6718e8] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[0b/f4bcf2] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/35bff4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[b1/faaa94] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[12/163264] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[17/662343] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -\n", - "\n", - "executor > local (183)\n", - "[bf/cd0d9d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[5c/bbd5f9] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[f3/460f93] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[0f/d33896] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[77/49b796] process > NFCORE_RNASEQ:RNASEQ:PREPAR... 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[100%] 5 of 5 ✔\n", - "[9d/7ccd59] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [ 20%] 1 of 5\n", - "[dd/ea35bf] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [ 40%] 2 of 5\n", - "[82/284fb3] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [ 40%] 2 of 5\n", - "[41/801c12] process > NFCORE_RNASEQ:RNASEQ:STRING... [100%] 5 of 5 ✔\n", - "[b5/1066ee] process > NFCORE_RNASEQ:RNASEQ:SUBREA... [100%] 5 of 5 ✔\n", - "[f5/40882a] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [ 80%] 4 of 5\n", - "[d1/3bf954] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... [100%] 5 of 5 ✔\n", - "[ee/396753] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[4b/716a5a] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[18/7476ba] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[95/82f4ff] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[39/92f97c] process > NFCORE_RNASEQ:RNASEQ:QUALIM... [100%] 5 of 5 ✔\n", - "[93/ee7586] process > NFCORE_RNASEQ:RNASEQ:DUPRAD... [100%] 5 of 5 ✔\n", - "[bf/b249b6] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[a9/78a120] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[be/279ad8] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[cd/4a48c2] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[5d/e95635] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[33/efe883] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[f7/a302cd] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[bc/8d3eae] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[4d/d2edfb] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[7a/6718e8] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[0b/f4bcf2] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/35bff4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[b1/faaa94] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[12/163264] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[17/662343] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -\n", - "\n", - "executor > local (184)\n", - "[bf/cd0d9d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[5c/bbd5f9] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[f3/460f93] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[0f/d33896] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[77/49b796] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[8d/6b59d1] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[d6/908096] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[30/e7d2c8] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[c5/6c2904] process > NFCORE_RNASEQ:RNASEQ:INPUT_... [100%] 1 of 1 ✔\n", - "[77/317e3a] process > NFCORE_RNASEQ:RNASEQ:CAT_FA... [100%] 2 of 2 ✔\n", - "[43/d93bf3] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[6a/24ca0d] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[5e/cf9ba9] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[d5/6397d1] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[27/85c96b] process > NFCORE_RNASEQ:RNASEQ:BBMAP_... [100%] 5 of 5 ✔\n", - "[51/fa5357] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[71/ba06f7] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[ed/974851] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[33/60bf71] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[6a/4c51fc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[4a/d5e328] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[52/39a759] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[09/0eb606] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[dc/460b62] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/3fc9d7] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[c4/7d5fd4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[57/195f6e] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[9d/0ba5d1] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[1c/2abfbb] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[ee/ba02e4] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[b9/0f85cb] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[9d/7ccd59] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [ 20%] 1 of 5\n", - "[dd/ea35bf] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [ 40%] 2 of 5\n", - "[d4/63c07c] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [ 60%] 3 of 5\n", - "[41/801c12] process > NFCORE_RNASEQ:RNASEQ:STRING... [100%] 5 of 5 ✔\n", - "[b5/1066ee] process > NFCORE_RNASEQ:RNASEQ:SUBREA... [100%] 5 of 5 ✔\n", - "[f5/40882a] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [ 80%] 4 of 5\n", - "[d1/3bf954] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... [100%] 5 of 5 ✔\n", - "[ee/396753] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[4b/716a5a] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[18/7476ba] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[95/82f4ff] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[39/92f97c] process > NFCORE_RNASEQ:RNASEQ:QUALIM... [100%] 5 of 5 ✔\n", - "[93/ee7586] process > NFCORE_RNASEQ:RNASEQ:DUPRAD... [100%] 5 of 5 ✔\n", - "[bf/b249b6] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[a9/78a120] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[be/279ad8] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[cd/4a48c2] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... 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[ 80%] 4 of 5\n", - "[d1/3bf954] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... [100%] 5 of 5 ✔\n", - "[ee/396753] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[4b/716a5a] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[18/7476ba] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[95/82f4ff] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[39/92f97c] process > NFCORE_RNASEQ:RNASEQ:QUALIM... [100%] 5 of 5 ✔\n", - "[93/ee7586] process > NFCORE_RNASEQ:RNASEQ:DUPRAD... [100%] 5 of 5 ✔\n", - "[bf/b249b6] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[a9/78a120] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[be/279ad8] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[cd/4a48c2] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[5d/e95635] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[33/efe883] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... 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[100%] 1 of 1 ✔\n", - "[1c/2abfbb] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[ee/ba02e4] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[b9/0f85cb] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[5f/cfa0af] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [ 20%] 1 of 5\n", - "[03/79bb12] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [ 60%] 3 of 5\n", - "[d4/63c07c] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [ 80%] 4 of 5\n", - "[41/801c12] process > NFCORE_RNASEQ:RNASEQ:STRING... [100%] 5 of 5 ✔\n", - "[b5/1066ee] process > NFCORE_RNASEQ:RNASEQ:SUBREA... [100%] 5 of 5 ✔\n", - "[f5/40882a] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [ 80%] 4 of 5\n", - "[d1/3bf954] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... [100%] 5 of 5 ✔\n", - "[ee/396753] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[4b/716a5a] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[18/7476ba] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[95/82f4ff] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[39/92f97c] process > NFCORE_RNASEQ:RNASEQ:QUALIM... [100%] 5 of 5 ✔\n", - "[93/ee7586] process > NFCORE_RNASEQ:RNASEQ:DUPRAD... [100%] 5 of 5 ✔\n", - "[bf/b249b6] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[a9/78a120] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[be/279ad8] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[cd/4a48c2] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[5d/e95635] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[33/efe883] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[f7/a302cd] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[bc/8d3eae] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[4d/d2edfb] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[7a/6718e8] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[0b/f4bcf2] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/35bff4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[b1/faaa94] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[12/163264] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[17/662343] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -\n", - "\n", - "executor > local (187)\n", - "[bf/cd0d9d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[5c/bbd5f9] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[f3/460f93] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[0f/d33896] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[77/49b796] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[8d/6b59d1] process > NFCORE_RNASEQ:RNASEQ:PREPAR... 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[100%] 5 of 5 ✔\n", - "[bf/b249b6] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[a9/78a120] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[be/279ad8] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[cd/4a48c2] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[5d/e95635] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[33/efe883] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[f7/a302cd] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[bc/8d3eae] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[4d/d2edfb] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[7a/6718e8] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[0b/f4bcf2] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/35bff4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[b1/faaa94] process > NFCORE_RNASEQ:RNASEQ:QUANTI... 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[100%] 1 of 1 ✔\n", - "[77/317e3a] process > NFCORE_RNASEQ:RNASEQ:CAT_FA... [100%] 2 of 2 ✔\n", - "[43/d93bf3] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[6a/24ca0d] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[5e/cf9ba9] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[d5/6397d1] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[27/85c96b] process > NFCORE_RNASEQ:RNASEQ:BBMAP_... [100%] 5 of 5 ✔\n", - "[51/fa5357] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[71/ba06f7] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[ed/974851] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[33/60bf71] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[6a/4c51fc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[4a/d5e328] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[52/39a759] process > NFCORE_RNASEQ:RNASEQ:QUANTI... 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[ 80%] 4 of 5\n", - "[d1/3bf954] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... [100%] 5 of 5 ✔\n", - "[ee/396753] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[4b/716a5a] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[18/7476ba] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[95/82f4ff] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[39/92f97c] process > NFCORE_RNASEQ:RNASEQ:QUALIM... [100%] 5 of 5 ✔\n", - "[93/ee7586] process > NFCORE_RNASEQ:RNASEQ:DUPRAD... [100%] 5 of 5 ✔\n", - "[bf/b249b6] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[a9/78a120] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[be/279ad8] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[cd/4a48c2] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[5d/e95635] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[33/efe883] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... 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[100%] 1 of 1 ✔\n", - "[1c/2abfbb] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[ee/ba02e4] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[b9/0f85cb] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[f7/32da83] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [ 40%] 2 of 5\n", - "[90/4d1486] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[a6/50142d] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[41/801c12] process > NFCORE_RNASEQ:RNASEQ:STRING... [100%] 5 of 5 ✔\n", - "[b5/1066ee] process > NFCORE_RNASEQ:RNASEQ:SUBREA... [100%] 5 of 5 ✔\n", - "[f5/40882a] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [ 80%] 4 of 5\n", - "[d1/3bf954] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... [100%] 5 of 5 ✔\n", - "[ee/396753] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[4b/716a5a] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[18/7476ba] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[95/82f4ff] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[39/92f97c] process > NFCORE_RNASEQ:RNASEQ:QUALIM... [100%] 5 of 5 ✔\n", - "[93/ee7586] process > NFCORE_RNASEQ:RNASEQ:DUPRAD... [100%] 5 of 5 ✔\n", - "[bf/b249b6] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[a9/78a120] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[be/279ad8] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[cd/4a48c2] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[5d/e95635] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[33/efe883] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[f7/a302cd] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[bc/8d3eae] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[4d/d2edfb] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[7a/6718e8] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[0b/f4bcf2] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/35bff4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[b1/faaa94] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[12/163264] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[17/662343] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -\n", - "\n", - "executor > local (191)\n", - "[bf/cd0d9d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[5c/bbd5f9] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[f3/460f93] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[0f/d33896] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[77/49b796] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[8d/6b59d1] process > NFCORE_RNASEQ:RNASEQ:PREPAR... 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[100%] 1 of 1 ✔\n", - "[17/662343] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -\n", - "\n", - "executor > local (191)\n", - "[bf/cd0d9d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[5c/bbd5f9] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[f3/460f93] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[0f/d33896] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[77/49b796] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[8d/6b59d1] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[d6/908096] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[30/e7d2c8] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[c5/6c2904] process > NFCORE_RNASEQ:RNASEQ:INPUT_... [100%] 1 of 1 ✔\n", - "[77/317e3a] process > NFCORE_RNASEQ:RNASEQ:CAT_FA... [100%] 2 of 2 ✔\n", - "[43/d93bf3] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[6a/24ca0d] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[5e/cf9ba9] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[d5/6397d1] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[27/85c96b] process > NFCORE_RNASEQ:RNASEQ:BBMAP_... [100%] 5 of 5 ✔\n", - "[51/fa5357] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[71/ba06f7] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[ed/974851] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[33/60bf71] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[6a/4c51fc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[4a/d5e328] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[52/39a759] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[09/0eb606] process > NFCORE_RNASEQ:RNASEQ:QUANTI... 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[100%] 5 of 5 ✔\n", - "[f5/40882a] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [ 80%] 4 of 5\n", - "[d1/3bf954] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... [100%] 5 of 5 ✔\n", - "[ee/396753] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[4b/716a5a] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[18/7476ba] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[95/82f4ff] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[39/92f97c] process > NFCORE_RNASEQ:RNASEQ:QUALIM... [100%] 5 of 5 ✔\n", - "[93/ee7586] process > NFCORE_RNASEQ:RNASEQ:DUPRAD... [100%] 5 of 5 ✔\n", - "[bf/b249b6] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[a9/78a120] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[be/279ad8] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[cd/4a48c2] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[5d/e95635] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... 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[100%] 5 of 5 ✔\n", - "[27/85c96b] process > NFCORE_RNASEQ:RNASEQ:BBMAP_... [100%] 5 of 5 ✔\n", - "[51/fa5357] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[71/ba06f7] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[ed/974851] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[33/60bf71] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[6a/4c51fc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[4a/d5e328] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[52/39a759] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[09/0eb606] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[dc/460b62] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/3fc9d7] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[c4/7d5fd4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[57/195f6e] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[9d/0ba5d1] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[1c/2abfbb] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[ee/ba02e4] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[b9/0f85cb] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[f7/32da83] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [ 80%] 4 of 5\n", - "[90/4d1486] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[a6/50142d] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[41/801c12] process > NFCORE_RNASEQ:RNASEQ:STRING... [100%] 5 of 5 ✔\n", - "[b5/1066ee] process > NFCORE_RNASEQ:RNASEQ:SUBREA... [100%] 5 of 5 ✔\n", - "[f5/40882a] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [ 80%] 4 of 5\n", - "[d1/3bf954] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... [100%] 5 of 5 ✔\n", - "[ee/396753] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[e5/1b69c6] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[18/7476ba] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[95/82f4ff] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[39/92f97c] process > NFCORE_RNASEQ:RNASEQ:QUALIM... [100%] 5 of 5 ✔\n", - "[93/ee7586] process > NFCORE_RNASEQ:RNASEQ:DUPRAD... [100%] 5 of 5 ✔\n", - "[bf/b249b6] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[a9/78a120] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[be/279ad8] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[cd/4a48c2] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[5d/e95635] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[33/efe883] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[f7/a302cd] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[bc/8d3eae] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[4d/d2edfb] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[7a/6718e8] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[0b/f4bcf2] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/35bff4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[b1/faaa94] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[12/163264] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[17/662343] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -\n", - "\n", - "executor > local (193)\n", - "[bf/cd0d9d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[5c/bbd5f9] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[f3/460f93] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[0f/d33896] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[77/49b796] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[8d/6b59d1] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[d6/908096] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[30/e7d2c8] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[c5/6c2904] process > NFCORE_RNASEQ:RNASEQ:INPUT_... [100%] 1 of 1 ✔\n", - "[77/317e3a] process > NFCORE_RNASEQ:RNASEQ:CAT_FA... [100%] 2 of 2 ✔\n", - "[43/d93bf3] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[6a/24ca0d] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[5e/cf9ba9] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[d5/6397d1] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[27/85c96b] process > NFCORE_RNASEQ:RNASEQ:BBMAP_... [100%] 5 of 5 ✔\n", - "[51/fa5357] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[71/ba06f7] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[ed/974851] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... 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[100%] 5 of 5 ✔\n", - "[bf/b249b6] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[a9/78a120] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[be/279ad8] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[cd/4a48c2] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[5d/e95635] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[33/efe883] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[f7/a302cd] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[bc/8d3eae] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[4d/d2edfb] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[7a/6718e8] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[0b/f4bcf2] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/35bff4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[b1/faaa94] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[12/163264] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[17/662343] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... -\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -\n", - "\n", - "executor > local (193)\n", - "[bf/cd0d9d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[5c/bbd5f9] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[f3/460f93] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[0f/d33896] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[77/49b796] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[8d/6b59d1] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[d6/908096] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[30/e7d2c8] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[c5/6c2904] process > NFCORE_RNASEQ:RNASEQ:INPUT_... [100%] 1 of 1 ✔\n", - "[77/317e3a] process > NFCORE_RNASEQ:RNASEQ:CAT_FA... [100%] 2 of 2 ✔\n", - "[43/d93bf3] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[6a/24ca0d] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[5e/cf9ba9] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[d5/6397d1] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[27/85c96b] process > NFCORE_RNASEQ:RNASEQ:BBMAP_... [100%] 5 of 5 ✔\n", - "[51/fa5357] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[71/ba06f7] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[ed/974851] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[33/60bf71] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[6a/4c51fc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[4a/d5e328] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[52/39a759] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[09/0eb606] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[dc/460b62] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/3fc9d7] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[c4/7d5fd4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[57/195f6e] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[9d/0ba5d1] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[1c/2abfbb] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[ee/ba02e4] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[b9/0f85cb] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[19/70962f] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[90/4d1486] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[a6/50142d] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[41/801c12] process > NFCORE_RNASEQ:RNASEQ:STRING... 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[100%] 2 of 2 ✔\n", - "[5e/cf9ba9] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[d5/6397d1] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[27/85c96b] process > NFCORE_RNASEQ:RNASEQ:BBMAP_... [100%] 5 of 5 ✔\n", - "[51/fa5357] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[71/ba06f7] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[ed/974851] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[33/60bf71] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[6a/4c51fc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[4a/d5e328] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[52/39a759] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[09/0eb606] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[dc/460b62] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/3fc9d7] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[c4/7d5fd4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[57/195f6e] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[9d/0ba5d1] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[1c/2abfbb] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[ee/ba02e4] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[b9/0f85cb] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[19/70962f] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[90/4d1486] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[a6/50142d] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[41/801c12] process > NFCORE_RNASEQ:RNASEQ:STRING... [100%] 5 of 5 ✔\n", - "[b5/1066ee] process > NFCORE_RNASEQ:RNASEQ:SUBREA... [100%] 5 of 5 ✔\n", - "[ba/3fe174] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [100%] 5 of 5 ✔\n", - "[d1/3bf954] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... [100%] 5 of 5 ✔\n", - "[ee/396753] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[e5/1b69c6] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[18/7476ba] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[72/0f1ad5] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[39/92f97c] process > NFCORE_RNASEQ:RNASEQ:QUALIM... [100%] 5 of 5 ✔\n", - "[93/ee7586] process > NFCORE_RNASEQ:RNASEQ:DUPRAD... [100%] 5 of 5 ✔\n", - "[bf/b249b6] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[a9/78a120] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[be/279ad8] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[cd/4a48c2] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[5d/e95635] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[33/efe883] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[f7/a302cd] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[bc/8d3eae] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[4d/d2edfb] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[7a/6718e8] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[0b/f4bcf2] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/35bff4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[b1/faaa94] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[12/163264] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[17/662343] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... [ 0%] 0 of 1\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -\n", - "\n", - "executor > local (195)\n", - "[bf/cd0d9d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[5c/bbd5f9] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[f3/460f93] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[0f/d33896] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[77/49b796] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[8d/6b59d1] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[d6/908096] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[30/e7d2c8] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[c5/6c2904] process > NFCORE_RNASEQ:RNASEQ:INPUT_... [100%] 1 of 1 ✔\n", - "[77/317e3a] process > NFCORE_RNASEQ:RNASEQ:CAT_FA... [100%] 2 of 2 ✔\n", - "[43/d93bf3] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[6a/24ca0d] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[5e/cf9ba9] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[d5/6397d1] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[27/85c96b] process > NFCORE_RNASEQ:RNASEQ:BBMAP_... [100%] 5 of 5 ✔\n", - "[51/fa5357] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[71/ba06f7] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[ed/974851] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[33/60bf71] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[6a/4c51fc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[4a/d5e328] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[52/39a759] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[09/0eb606] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[dc/460b62] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/3fc9d7] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[c4/7d5fd4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[57/195f6e] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[9d/0ba5d1] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[1c/2abfbb] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[ee/ba02e4] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[b9/0f85cb] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[19/70962f] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[90/4d1486] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[a6/50142d] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[41/801c12] process > NFCORE_RNASEQ:RNASEQ:STRING... [100%] 5 of 5 ✔\n", - "[b5/1066ee] process > NFCORE_RNASEQ:RNASEQ:SUBREA... [100%] 5 of 5 ✔\n", - "[ba/3fe174] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [100%] 5 of 5 ✔\n", - "[d1/3bf954] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... [100%] 5 of 5 ✔\n", - "[ee/396753] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[e5/1b69c6] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[18/7476ba] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[72/0f1ad5] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[39/92f97c] process > NFCORE_RNASEQ:RNASEQ:QUALIM... [100%] 5 of 5 ✔\n", - "[93/ee7586] process > NFCORE_RNASEQ:RNASEQ:DUPRAD... [100%] 5 of 5 ✔\n", - "[bf/b249b6] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[a9/78a120] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[be/279ad8] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[cd/4a48c2] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[5d/e95635] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[33/efe883] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[f7/a302cd] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[bc/8d3eae] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[4d/d2edfb] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[7a/6718e8] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[0b/f4bcf2] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/35bff4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[b1/faaa94] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[12/163264] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[17/662343] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[e3/e99594] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... [ 0%] 0 of 1\n", - "[- ] process > NFCORE_RNASEQ:RNASEQ:MULTIQC -\n", - "\n", - "executor > local (196)\n", - "[bf/cd0d9d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[5c/bbd5f9] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[f3/460f93] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[0f/d33896] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[77/49b796] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[8d/6b59d1] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[d6/908096] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[30/e7d2c8] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[c5/6c2904] process > NFCORE_RNASEQ:RNASEQ:INPUT_... [100%] 1 of 1 ✔\n", - "[77/317e3a] process > NFCORE_RNASEQ:RNASEQ:CAT_FA... [100%] 2 of 2 ✔\n", - "[43/d93bf3] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[6a/24ca0d] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[5e/cf9ba9] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[d5/6397d1] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[27/85c96b] process > NFCORE_RNASEQ:RNASEQ:BBMAP_... [100%] 5 of 5 ✔\n", - "[51/fa5357] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[71/ba06f7] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[ed/974851] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[33/60bf71] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[6a/4c51fc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[4a/d5e328] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[52/39a759] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[09/0eb606] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[dc/460b62] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/3fc9d7] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[c4/7d5fd4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[57/195f6e] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[9d/0ba5d1] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[1c/2abfbb] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[ee/ba02e4] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[b9/0f85cb] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[19/70962f] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[90/4d1486] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[a6/50142d] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[41/801c12] process > NFCORE_RNASEQ:RNASEQ:STRING... [100%] 5 of 5 ✔\n", - "[b5/1066ee] process > NFCORE_RNASEQ:RNASEQ:SUBREA... [100%] 5 of 5 ✔\n", - "[ba/3fe174] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [100%] 5 of 5 ✔\n", - "[d1/3bf954] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... [100%] 5 of 5 ✔\n", - "[ee/396753] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[e5/1b69c6] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[18/7476ba] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[72/0f1ad5] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[39/92f97c] process > NFCORE_RNASEQ:RNASEQ:QUALIM... [100%] 5 of 5 ✔\n", - "[93/ee7586] process > NFCORE_RNASEQ:RNASEQ:DUPRAD... [100%] 5 of 5 ✔\n", - "[bf/b249b6] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[a9/78a120] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[be/279ad8] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[cd/4a48c2] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[5d/e95635] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[33/efe883] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[f7/a302cd] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[bc/8d3eae] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[4d/d2edfb] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[7a/6718e8] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[0b/f4bcf2] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/35bff4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[b1/faaa94] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[12/163264] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[17/662343] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[e3/e99594] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... [100%] 1 of 1 ✔\n", - "[6b/d2ebb3] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [ 0%] 0 of 1\n", - "\n", - "executor > local (196)\n", - "[bf/cd0d9d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[5c/bbd5f9] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[f3/460f93] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[0f/d33896] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[77/49b796] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[8d/6b59d1] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[d6/908096] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[30/e7d2c8] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[c5/6c2904] process > NFCORE_RNASEQ:RNASEQ:INPUT_... [100%] 1 of 1 ✔\n", - "[77/317e3a] process > NFCORE_RNASEQ:RNASEQ:CAT_FA... [100%] 2 of 2 ✔\n", - "[43/d93bf3] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[6a/24ca0d] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[5e/cf9ba9] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[d5/6397d1] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[27/85c96b] process > NFCORE_RNASEQ:RNASEQ:BBMAP_... [100%] 5 of 5 ✔\n", - "[51/fa5357] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[71/ba06f7] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[ed/974851] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[33/60bf71] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[6a/4c51fc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[4a/d5e328] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[52/39a759] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[09/0eb606] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[dc/460b62] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/3fc9d7] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[c4/7d5fd4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[57/195f6e] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[9d/0ba5d1] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[1c/2abfbb] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[ee/ba02e4] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[b9/0f85cb] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[19/70962f] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[90/4d1486] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[a6/50142d] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[41/801c12] process > NFCORE_RNASEQ:RNASEQ:STRING... [100%] 5 of 5 ✔\n", - "[b5/1066ee] process > NFCORE_RNASEQ:RNASEQ:SUBREA... [100%] 5 of 5 ✔\n", - "[ba/3fe174] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [100%] 5 of 5 ✔\n", - "[d1/3bf954] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... [100%] 5 of 5 ✔\n", - "[ee/396753] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[e5/1b69c6] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[18/7476ba] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[72/0f1ad5] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [ 80%] 4 of 5\n", - "[39/92f97c] process > NFCORE_RNASEQ:RNASEQ:QUALIM... [100%] 5 of 5 ✔\n", - "[93/ee7586] process > NFCORE_RNASEQ:RNASEQ:DUPRAD... [100%] 5 of 5 ✔\n", - "[bf/b249b6] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[a9/78a120] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[be/279ad8] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[cd/4a48c2] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[5d/e95635] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[33/efe883] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[f7/a302cd] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[bc/8d3eae] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[4d/d2edfb] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[7a/6718e8] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[0b/f4bcf2] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/35bff4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[b1/faaa94] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[12/163264] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[17/662343] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[e3/e99594] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... [100%] 1 of 1 ✔\n", - "[6b/d2ebb3] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [ 0%] 0 of 1\n", - "\n", - "executor > local (196)\n", - "[bf/cd0d9d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[5c/bbd5f9] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[f3/460f93] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[0f/d33896] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[77/49b796] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[8d/6b59d1] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[d6/908096] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[30/e7d2c8] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[c5/6c2904] process > NFCORE_RNASEQ:RNASEQ:INPUT_... [100%] 1 of 1 ✔\n", - "[77/317e3a] process > NFCORE_RNASEQ:RNASEQ:CAT_FA... [100%] 2 of 2 ✔\n", - "[43/d93bf3] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[6a/24ca0d] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[5e/cf9ba9] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[d5/6397d1] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[27/85c96b] process > NFCORE_RNASEQ:RNASEQ:BBMAP_... [100%] 5 of 5 ✔\n", - "[51/fa5357] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[71/ba06f7] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[ed/974851] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[33/60bf71] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[6a/4c51fc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[4a/d5e328] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[52/39a759] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[09/0eb606] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[dc/460b62] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/3fc9d7] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[c4/7d5fd4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[57/195f6e] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[9d/0ba5d1] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[1c/2abfbb] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[ee/ba02e4] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[b9/0f85cb] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[19/70962f] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[90/4d1486] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[a6/50142d] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[41/801c12] process > NFCORE_RNASEQ:RNASEQ:STRING... [100%] 5 of 5 ✔\n", - "[b5/1066ee] process > NFCORE_RNASEQ:RNASEQ:SUBREA... [100%] 5 of 5 ✔\n", - "[ba/3fe174] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [100%] 5 of 5 ✔\n", - "[d1/3bf954] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... [100%] 5 of 5 ✔\n", - "[ee/396753] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[e5/1b69c6] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[18/7476ba] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[72/0f1ad5] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[39/92f97c] process > NFCORE_RNASEQ:RNASEQ:QUALIM... [100%] 5 of 5 ✔\n", - "[93/ee7586] process > NFCORE_RNASEQ:RNASEQ:DUPRAD... [100%] 5 of 5 ✔\n", - "[bf/b249b6] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[a9/78a120] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[be/279ad8] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[cd/4a48c2] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[5d/e95635] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[33/efe883] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[f7/a302cd] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[bc/8d3eae] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[4d/d2edfb] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[7a/6718e8] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[0b/f4bcf2] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/35bff4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[b1/faaa94] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[12/163264] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[17/662343] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[e3/e99594] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... [100%] 1 of 1 ✔\n", - "[6b/d2ebb3] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [ 0%] 0 of 1\n", - "\n", - "executor > local (196)\n", - "[bf/cd0d9d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[5c/bbd5f9] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[f3/460f93] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[0f/d33896] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[77/49b796] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[8d/6b59d1] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[d6/908096] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[30/e7d2c8] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[c5/6c2904] process > NFCORE_RNASEQ:RNASEQ:INPUT_... [100%] 1 of 1 ✔\n", - "[77/317e3a] process > NFCORE_RNASEQ:RNASEQ:CAT_FA... [100%] 2 of 2 ✔\n", - "[43/d93bf3] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[6a/24ca0d] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[5e/cf9ba9] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[d5/6397d1] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[27/85c96b] process > NFCORE_RNASEQ:RNASEQ:BBMAP_... [100%] 5 of 5 ✔\n", - "[51/fa5357] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[71/ba06f7] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[ed/974851] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[33/60bf71] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[6a/4c51fc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[4a/d5e328] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[52/39a759] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[09/0eb606] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[dc/460b62] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/3fc9d7] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[c4/7d5fd4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[57/195f6e] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[9d/0ba5d1] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[1c/2abfbb] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[ee/ba02e4] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[b9/0f85cb] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[19/70962f] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[90/4d1486] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[a6/50142d] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[41/801c12] process > NFCORE_RNASEQ:RNASEQ:STRING... [100%] 5 of 5 ✔\n", - "[b5/1066ee] process > NFCORE_RNASEQ:RNASEQ:SUBREA... [100%] 5 of 5 ✔\n", - "[ba/3fe174] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [100%] 5 of 5 ✔\n", - "[d1/3bf954] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... [100%] 5 of 5 ✔\n", - "[ee/396753] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[e5/1b69c6] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[18/7476ba] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[72/0f1ad5] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[39/92f97c] process > NFCORE_RNASEQ:RNASEQ:QUALIM... [100%] 5 of 5 ✔\n", - "[93/ee7586] process > NFCORE_RNASEQ:RNASEQ:DUPRAD... [100%] 5 of 5 ✔\n", - "[bf/b249b6] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[a9/78a120] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[be/279ad8] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[cd/4a48c2] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[5d/e95635] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[33/efe883] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[f7/a302cd] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[bc/8d3eae] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[4d/d2edfb] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[7a/6718e8] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[0b/f4bcf2] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/35bff4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[b1/faaa94] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[12/163264] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[17/662343] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[e3/e99594] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... [100%] 1 of 1 ✔\n", - "[6b/d2ebb3] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [100%] 1 of 1 ✔\n", - "-[nf-core/rnaseq] Pipeline completed successfully with skipped sampl(es)-\n", - "-[nf-core/rnaseq] Please check MultiQC report: 1/5 samples failed strandedness check.-\n", - "\n", - "executor > local (196)\n", - "[bf/cd0d9d] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[5c/bbd5f9] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[f3/460f93] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[0f/d33896] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[77/49b796] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[8d/6b59d1] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[d6/908096] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[30/e7d2c8] process > NFCORE_RNASEQ:RNASEQ:PREPAR... [100%] 1 of 1 ✔\n", - "[c5/6c2904] process > NFCORE_RNASEQ:RNASEQ:INPUT_... [100%] 1 of 1 ✔\n", - "[77/317e3a] process > NFCORE_RNASEQ:RNASEQ:CAT_FA... [100%] 2 of 2 ✔\n", - "[43/d93bf3] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[6a/24ca0d] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 2 of 2 ✔\n", - "[5e/cf9ba9] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[d5/6397d1] process > NFCORE_RNASEQ:RNASEQ:FASTQ_... [100%] 5 of 5 ✔\n", - "[27/85c96b] process > NFCORE_RNASEQ:RNASEQ:BBMAP_... [100%] 5 of 5 ✔\n", - "[51/fa5357] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[71/ba06f7] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[ed/974851] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[33/60bf71] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[6a/4c51fc] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[4a/d5e328] process > NFCORE_RNASEQ:RNASEQ:ALIGN_... [100%] 5 of 5 ✔\n", - "[52/39a759] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[09/0eb606] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[dc/460b62] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/3fc9d7] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[c4/7d5fd4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[57/195f6e] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[9d/0ba5d1] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[1c/2abfbb] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[ee/ba02e4] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[b9/0f85cb] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[19/70962f] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[90/4d1486] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[a6/50142d] process > NFCORE_RNASEQ:RNASEQ:BAM_MA... [100%] 5 of 5 ✔\n", - "[41/801c12] process > NFCORE_RNASEQ:RNASEQ:STRING... [100%] 5 of 5 ✔\n", - "[b5/1066ee] process > NFCORE_RNASEQ:RNASEQ:SUBREA... [100%] 5 of 5 ✔\n", - "[ba/3fe174] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [100%] 5 of 5 ✔\n", - "[d1/3bf954] process > NFCORE_RNASEQ:RNASEQ:BEDTOO... [100%] 5 of 5 ✔\n", - "[ee/396753] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[e5/1b69c6] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[18/7476ba] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[72/0f1ad5] process > NFCORE_RNASEQ:RNASEQ:BEDGRA... [100%] 5 of 5 ✔\n", - "[39/92f97c] process > NFCORE_RNASEQ:RNASEQ:QUALIM... [100%] 5 of 5 ✔\n", - "[93/ee7586] process > NFCORE_RNASEQ:RNASEQ:DUPRAD... [100%] 5 of 5 ✔\n", - "[bf/b249b6] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[a9/78a120] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[be/279ad8] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[cd/4a48c2] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[5d/e95635] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[33/efe883] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[f7/a302cd] process > NFCORE_RNASEQ:RNASEQ:BAM_RS... [100%] 5 of 5 ✔\n", - "[bc/8d3eae] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 5 of 5 ✔\n", - "[4d/d2edfb] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[7a/6718e8] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[0b/f4bcf2] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[a8/35bff4] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[b1/faaa94] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[12/163264] process > NFCORE_RNASEQ:RNASEQ:QUANTI... [100%] 1 of 1 ✔\n", - "[17/662343] process > NFCORE_RNASEQ:RNASEQ:DESEQ2... [100%] 1 of 1 ✔\n", - "[e3/e99594] process > NFCORE_RNASEQ:RNASEQ:CUSTOM... [100%] 1 of 1 ✔\n", - "[6b/d2ebb3] process > NFCORE_RNASEQ:RNASEQ:MULTIQ... [100%] 1 of 1 ✔\n", - "-[nf-core/rnaseq] Pipeline completed successfully with skipped sampl(es)-\n", - "-[nf-core/rnaseq] Please check MultiQC report: 1/5 samples failed strandedness check.-\n", - "Completed at: 06-Dec-2023 12:23:05\n", - "Duration : 13m 49s\n", - "CPU hours : 0.7\n", - "Succeeded : 196\n", - "\n", - "\n" - ] - } - ], - "source": [ - "!nextflow run nf-core/rnaseq -r 3.11.2 -profile test,docker --outdir rna-seq-results -name \"lamin_{run.uid}\"" - ] - }, - { - "cell_type": "markdown", - "id": "58eea7fc", - "metadata": {}, - "source": [ - "Here, we passed the LaminDB run id to nextflow so that we can query it from within nextflow." - ] - }, - { - "cell_type": "markdown", - "id": "fb81c953", - "metadata": {}, - "source": [ - "## Register outputs" - ] - }, - { - "cell_type": "markdown", - "id": "e02898d4", - "metadata": {}, - "source": [ - "### QC" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "id": "7140018a-9ef7-4136-a595-37b514c66a81", - "metadata": {}, - "outputs": [], - "source": [ - "multiqc_file = ln.File(\"rna-seq-results/multiqc/star_salmon/multiqc_report.html\")\n", - "multiqc_file.save()" - ] - }, - { - "cell_type": "markdown", - "id": "a588717f", - "metadata": {}, - "source": [ - ":::{dropdown} How would I register all QC files?\n", - "\n", - "```python\n", - "multiqc_results = ln.File.from_dir(\"rna-seq-results/multiqc/\")\n", - "ln.save(multiqc_results)\n", - "```\n", - "\n", - ":::" - ] - }, - { - "cell_type": "markdown", - "id": "6f107ee9", - "metadata": {}, - "source": [ - "### Count matrix" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "id": "b8ed9118-1fd1-47a7-a825-736f78a7d111", - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "❗ file has more than one suffix (path.suffixes), using only last suffix: '.tsv' - if you want your file format to be recognized, make an issue: https://github.com/laminlabs/lamindb/issues/new\n" - ] - } - ], - "source": [ - "count_matrix = ln.File(\"rna-seq-results/salmon/salmon.merged.gene_counts.tsv\")\n", - "count_matrix.save()" - ] - }, - { - "cell_type": "markdown", - "id": "429bf863", - "metadata": {}, - "source": [ - "## Track Nextflow ID" - ] - }, - { - "cell_type": "markdown", - "id": "7afa797c", - "metadata": {}, - "source": [ - "Let us look at the nextflow logs:" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "id": "11538f9b", - "metadata": { - "tags": [] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "TIMESTAMP \tDURATION\tRUN NAME \tSTATUS\tREVISION ID\tSESSION ID \tCOMMAND \n", - "2023-12-05 14:21:02\t3m 59s \tflamin_1 \tOK \t00ec8d4096 \tb187d9dc-7074-4da5-91f1-d5abe704614b\tnextflow run 'https://github.com/labsyspharm/mcmicro' --in exemplar-001 --start-at illumination --stop-at registration -name flamin_1 \n", - "2023-12-06 09:16:44\t23m 55s \tlamin_tMP8mHQQhvF9adI0u1T3\tOK \t5671b65af9 \t76fbcdf1-5ff6-493b-8493-0519f36fde65\tnextflow run nf-core/rnaseq -r 3.11.2 -profile test,docker --outdir rna-seq-results -name lamin_tMP8mHQQhvF9adI0u1T3 \n", - "2023-12-06 10:31:23\t27.8s \telegant_stallman \tOK \t00ec8d4096 \tb8be7888-793a-454b-914b-013146026055\tnextflow run labsyspharm/mcmicro/exemplar.nf --name exemplar-001 \n", - "2023-12-06 10:32:17\t29.1s \tinfallible_brown \tOK \t00ec8d4096 \t8f90f51d-e93d-4a95-9ce7-fd392ee4325b\tnextflow run labsyspharm/mcmicro/exemplar.nf --name exemplar-001 \n", - "2023-12-06 10:36:21\t30.5s \tmodest_lovelace \tOK \t00ec8d4096 \t8f90f51d-e93d-4a95-9ce7-fd392ee4325b\tnextflow run labsyspharm/mcmicro/exemplar.nf --name exemplar-001 -resume \n", - "2023-12-06 10:47:06\t2m 4s \tlamin_WviO6YTCwKBIrtbFZKYg\tOK \t00ec8d4096 \t4ea66f86-0355-42ab-b59b-bb18a1a51fba\tnextflow run 'https://github.com/labsyspharm/mcmicro' --in exemplar-001 --start-at illumination --stop-at registration -name lamin_WviO6YTCwKBIrtbFZKYg\n", - "2023-12-06 10:53:29\t29.3s \tmaniac_bernard \tOK \t00ec8d4096 \t68012528-4de5-465f-9425-07ff34f96202\tnextflow run labsyspharm/mcmicro/exemplar.nf --name exemplar-001 \n", - "2023-12-06 10:58:12\t1m 57s \tlamin_hx3Udnfc7MauAdK8NZo3\tOK \t00ec8d4096 \t890f38fa-e0c9-4106-a892-34b078ed48e1\tnextflow run 'https://github.com/labsyspharm/mcmicro' --in exemplar-001 --start-at illumination --stop-at registration -name lamin_hx3Udnfc7MauAdK8NZo3\n", - "2023-12-06 11:52:16\t15m 31s \tlamin_ne4lhXyvOSU3F0LcdKGK\tOK \t5671b65af9 \t25f7caac-5474-4c50-8234-6bb0f3e8e1c8\tnextflow run nf-core/rnaseq -r 3.11.2 -profile test,docker --outdir rna-seq-results -name lamin_ne4lhXyvOSU3F0LcdKGK \n", - "2023-12-06 12:09:16\t13m 50s \tlamin_Bcs8m6VxzFM42qhCD4VF\tOK \t5671b65af9 \t09eedc66-747d-4d00-a014-1150acabe45a\tnextflow run nf-core/rnaseq -r 3.11.2 -profile test,docker --outdir rna-seq-results -name lamin_Bcs8m6VxzFM42qhCD4VF \n" - ] - } - ], - "source": [ - "!nextflow log" - ] - }, - { - "cell_type": "markdown", - "id": "36e4afc3", - "metadata": {}, - "source": [ - "Let us add the information about the session ID to our `run` record:" - ] - }, - { - "cell_type": "code", - "execution_count": 11, - "id": "4c14e053", - "metadata": {}, - "outputs": [], - "source": [ - "nextflow_id = getoutput(f\"nextflow log | awk '/{run.id}/{{print $8}}'\")\n", - "run.reference = nextflow_id\n", - "run.reference_type = \"nextflow_id\"\n", - "run.save()" - ] - }, - { - "cell_type": "markdown", - "id": "dd98074b", - "metadata": {}, - "source": [ - "## Link biological entities" - ] - }, - { - "cell_type": "markdown", - "id": "22c88eed-61e0-4d12-96bb-ea4e10f476c0", - "metadata": {}, - "source": [ - "To make the count matrix queryable by biological entities (genes, experimental metadata, etc.), we can now proceed with: {doc}`docs:bulkrna`" - ] - }, - { - "cell_type": "markdown", - "id": "9f607150", - "metadata": {}, - "source": [ - "## Visualize" - ] - }, - { - "cell_type": "markdown", - "id": "54595d81", - "metadata": {}, - "source": [ - "View data lineage:" - ] - }, - { - "cell_type": "code", - "execution_count": 12, - "id": "ba83bfee-5cb8-4520-9a32-0deccd47ff34", - "metadata": {}, - "outputs": [ - { - "data": { - "image/svg+xml": [ - "\n", - "\n", - "\n", - "\n", - "\n", - "\n", - "file_MMLLAnPZeLjEmJ68bJVB\n", - "\n", - "\n", - "\n", - "file_14TTurTS6A67gyc8Pwsu\n", - "\n", - "📄 test-datasets/samplesheet/v3.10/samplesheet_test.csv\n", - "uid=14TTurTS6A67gyc8Pwsu\n", - 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" - ], - "text/plain": [ - " uid handle name updated_at\n", - "id \n", - "1 I5DPZdiE zethson None 2023-12-06 11:09:01.191310+00:00" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "ln.view()" - ] - }, - { - "cell_type": "markdown", - "id": "ad06a7e1", - "metadata": {}, - "source": [ - "Clean up the test instance:" - ] - }, - { - "cell_type": "code", - "execution_count": 14, - "id": "5f3f95a8", - "metadata": { - "tags": [ - "hide-output" - ] - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "💡 deleting instance zethson/nextflow-bulkrna\n", - "✅ deleted instance settings file: /home/zeth/.lamin/instance--zethson--nextflow-bulkrna.env\n", - "❗ You are running 3.11.5\n", - "Only python versions 3.8~3.10 are currently tested, use at your own risk.\n", - "✅ instance cache deleted\n", - "✅ deleted '.lndb' sqlite file\n", - "❗ consider manually deleting your stored data: /home/zeth/PycharmProjects/nextflow-lamin-usecases/docs\n" - ] - } - ], - "source": [ - "!lamin delete --force nextflow-bulkrna" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3 (ipykernel)", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.11.5" - }, - "nbproject": { - "id": "8124Vtle6ZrO", - "parent": null, - "pypackage": null, - "time_init": "2023-07-24T13:06:04.795992+00:00", - "user_handle": null, - "user_id": null, - "user_name": null, - "version": "0" - } - }, - "nbformat": 4, - "nbformat_minor": 5 -} diff --git a/noxfile.py b/noxfile.py index 5c1518c..a788831 100644 --- a/noxfile.py +++ b/noxfile.py @@ -17,9 +17,11 @@ def lint(session: nox.Session) -> None: @nox.session() def build(session): session.run( + "uv", "pip", "install", - "lamindb @ git+https://github.com/laminlabs/lamindb", + "--system", + "lamindb[aws,jupyter,bionty]", ) session.run(*"pip install -e .[dev]".split()) login_testuser1(session) diff --git a/pyproject.toml b/pyproject.toml index 3cac8d8..8b7ac5e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -27,7 +27,7 @@ dev = [ [tool.ruff] src = ["nextflow_lamin"] -line-length = 88 +line-length = 120 select = [ "F", # Errors detected by Pyflakes "E", # Error detected by Pycodestyle