add pipeline level tests #1661
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -3,4 +3,8 @@ config { | |
| workDir ".nf-test" | ||
| configFile "conf/test.config" | ||
| profile "test" | ||
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| plugins { | ||
| load "[email protected]" | ||
| } | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| csv/*.csv | ||
| multiqc/multiqc_data/gatk_base_recalibrator.txt | ||
| multiqc/multiqc_data/multiqc.log | ||
| multiqc/multiqc_data/multiqc_data.json | ||
| multiqc/multiqc_data/multiqc_general_stats.txt | ||
| multiqc/multiqc_data/multiqc_picard_dups.txt | ||
| multiqc/multiqc_data/multiqc_sources.txt | ||
| multiqc/multiqc_report.html | ||
| pipeline_info/*.{html,json,txt,yml} | ||
| preprocessing/**/*.{md,recal}.{cram,cram.crai,table} | ||
| reports/fastqc/**/*_fastqc.{html,zip} | ||
| reports/markduplicates/**/*.md.cram.metrics | ||
| variant_calling/**/*.vcf.{gz,gz.tbi} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,176 @@ | ||
| { | ||
| "Run with profile test": { | ||
| "content": [ | ||
| 23, | ||
| { | ||
| "BCFTOOLS_STATS": { | ||
| "bcftools": 1.2 | ||
| }, | ||
| "BWAMEM1_MEM": { | ||
| "bwa": "0.7.18-r1243-dirty", | ||
| "samtools": 1.2 | ||
| }, | ||
| "FASTQC": { | ||
| "fastqc": "0.12.1" | ||
| }, | ||
| "GATK4_APPLYBQSR": { | ||
| "gatk4": "4.5.0.0" | ||
| }, | ||
| "GATK4_BASERECALIBRATOR": { | ||
| "gatk4": "4.5.0.0" | ||
| }, | ||
| "GATK4_MARKDUPLICATES": { | ||
| "gatk4": "4.5.0.0", | ||
| "samtools": "1.19.2" | ||
| }, | ||
| "INDEX_CRAM": { | ||
| "samtools": 1.2 | ||
| }, | ||
| "MOSDEPTH": { | ||
| "mosdepth": "0.3.8" | ||
| }, | ||
| "SAMTOOLS_STATS": { | ||
| "samtools": 1.2 | ||
| }, | ||
| "STRELKA_SINGLE": { | ||
| "strelka": "2.9.10" | ||
| }, | ||
| "VCFTOOLS_TSTV_COUNT": { | ||
| "vcftools": "0.1.16" | ||
| }, | ||
| "Workflow": { | ||
| "nf-core/sarek": "v3.5.0dev" | ||
| } | ||
| }, | ||
| [ | ||
| "csv", | ||
| "markduplicates.csv", | ||
| "markduplicates_no_table.csv", | ||
| "recalibrated.csv", | ||
| "variantcalled.csv", | ||
| "multiqc", | ||
| "multiqc_data", | ||
| "gatk_base_recalibrator.txt", | ||
| "mosdepth_cov_dist.txt", | ||
| "mosdepth_cumcov_dist.txt", | ||
| "mosdepth_perchrom.txt", | ||
| "multiqc.log", | ||
| "multiqc_bcftools_stats.txt", | ||
| "multiqc_citations.txt", | ||
| "multiqc_data.json", | ||
| "multiqc_fastqc.txt", | ||
| "multiqc_general_stats.txt", | ||
| "multiqc_picard_dups.txt", | ||
| "multiqc_samtools_stats.txt", | ||
| "multiqc_software_versions.txt", | ||
| "multiqc_sources.txt", | ||
| "picard_histogram.txt", | ||
| "picard_histogram_1.txt", | ||
| "picard_histogram_2.txt", | ||
| "vcftools_tstv_by_count.txt", | ||
| "vcftools_tstv_by_qual.txt", | ||
| "multiqc_plots", | ||
| "multiqc_report.html", | ||
| "pipeline_info", | ||
| "nf_core_sarek_software_mqc_versions.yml", | ||
| "preprocessing", | ||
| "markduplicates", | ||
| "test", | ||
| "test.md.cram", | ||
| "test.md.cram.crai", | ||
| "recal_table", | ||
| "test", | ||
| "test.recal.table", | ||
| "recalibrated", | ||
| "test", | ||
| "test.recal.cram", | ||
| "test.recal.cram.crai", | ||
| "reference", | ||
| "reports", | ||
| "bcftools", | ||
| "strelka", | ||
| "test", | ||
|
There was a problem hiding this comment. why are folder names showing up several times here? There was a problem hiding this comment. so it's actually like a tree arborescence but flat, so any duplicate name is actually in a different location |
||
| "test.strelka.variants.bcftools_stats.txt", | ||
| "fastqc", | ||
| "test-test_L1", | ||
| "test-test_L1_1_fastqc.html", | ||
| "test-test_L1_1_fastqc.zip", | ||
| "test-test_L1_2_fastqc.html", | ||
| "test-test_L1_2_fastqc.zip", | ||
| "test-test_L2", | ||
| "test-test_L2_1_fastqc.html", | ||
| "test-test_L2_1_fastqc.zip", | ||
| "test-test_L2_2_fastqc.html", | ||
| "test-test_L2_2_fastqc.zip", | ||
| "markduplicates", | ||
| "test", | ||
| "test.md.cram.metrics", | ||
| "mosdepth", | ||
| "test", | ||
| "test.md.mosdepth.global.dist.txt", | ||
| "test.md.mosdepth.region.dist.txt", | ||
| "test.md.mosdepth.summary.txt", | ||
| "test.md.regions.bed.gz", | ||
| "test.md.regions.bed.gz.csi", | ||
| "test.recal.mosdepth.global.dist.txt", | ||
| "test.recal.mosdepth.region.dist.txt", | ||
| "test.recal.mosdepth.summary.txt", | ||
| "test.recal.regions.bed.gz", | ||
| "test.recal.regions.bed.gz.csi", | ||
| "samtools", | ||
| "test", | ||
| "test.md.cram.stats", | ||
| "test.recal.cram.stats", | ||
| "vcftools", | ||
| "strelka", | ||
| "test", | ||
| "test.strelka.variants.FILTER.summary", | ||
| "test.strelka.variants.TsTv.count", | ||
| "test.strelka.variants.TsTv.qual", | ||
| "variant_calling", | ||
| "strelka", | ||
| "test", | ||
| "test.strelka.genome.vcf.gz", | ||
| "test.strelka.genome.vcf.gz.tbi", | ||
| "test.strelka.variants.vcf.gz", | ||
| "test.strelka.variants.vcf.gz.tbi" | ||
| ], | ||
| [ | ||
| "mosdepth_cov_dist.txt:md5,eadafaa5473dd49daadb7b4696c6b7f9", | ||
| "mosdepth_cumcov_dist.txt:md5,8d0d7cb485a7bffb07da17b28f827120", | ||
| "mosdepth_perchrom.txt:md5,264db67a99d2c90ea7b075e33c201b77", | ||
| "multiqc_bcftools_stats.txt:md5,103ba59d44fc60e9308e64bbd0d0e504", | ||
| "multiqc_citations.txt:md5,4660dd5d8757841ed75dca3a90d21617", | ||
| "multiqc_fastqc.txt:md5,bde0d0bffa62228b33fb68b7e25b6ff8", | ||
| "multiqc_samtools_stats.txt:md5,0f1e4c6c497d9a952765f9f3068ea4b9", | ||
| "multiqc_software_versions.txt:md5,2c9d16da278a231b0dc4c4cb5c08e626", | ||
| "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", | ||
| "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", | ||
| "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", | ||
| "vcftools_tstv_by_count.txt:md5,327f731f65de167c7cfcbb30a5f04079", | ||
| "vcftools_tstv_by_qual.txt:md5,911bc05c5169149dbb0b068f65b4274a", | ||
| "test.strelka.variants.bcftools_stats.txt:md5,86bd4938eed920d36f3f5937102a2967", | ||
| "test.md.mosdepth.global.dist.txt:md5,b61e1acee11a6ddf7ce3232a5948a6a0", | ||
| "test.md.mosdepth.region.dist.txt:md5,1a382f98d488d2ae3df83a0d87caafc1", | ||
| "test.md.mosdepth.summary.txt:md5,839108358878ada89e1eaddf6e0541ba", | ||
| "test.md.regions.bed.gz:md5,6fdaec99e739dc0f47fe55dd64dfe93e", | ||
| "test.md.regions.bed.gz.csi:md5,5f9c60279af78e3aeafc96a8c11fb35f", | ||
| "test.recal.mosdepth.global.dist.txt:md5,b61e1acee11a6ddf7ce3232a5948a6a0", | ||
| "test.recal.mosdepth.region.dist.txt:md5,1a382f98d488d2ae3df83a0d87caafc1", | ||
| "test.recal.mosdepth.summary.txt:md5,839108358878ada89e1eaddf6e0541ba", | ||
| "test.recal.regions.bed.gz:md5,6fdaec99e739dc0f47fe55dd64dfe93e", | ||
| "test.recal.regions.bed.gz.csi:md5,5f9c60279af78e3aeafc96a8c11fb35f", | ||
| "test.md.cram.stats:md5,c4dc6487d0b8b8a74c26ea1ef4e17f6f", | ||
| "test.recal.cram.stats:md5,38bcc10d0464b259551db3b5356610ca", | ||
| "test.strelka.variants.FILTER.summary:md5,ad417bc96d31223f61170987975d8128", | ||
| "test.strelka.variants.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a", | ||
| "test.strelka.variants.TsTv.qual:md5,bc68ae4e688e9fb772b457069e604883" | ||
| ] | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.0", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-10-01T10:33:51.201431" | ||
| } | ||
| } | ||
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why are these not stable?
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because they contain the full path and not the relative one, I need to sort this out