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nextflow.config
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nextflow.config
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docker.enabled = true
params {
reads = false
reads_folder = false
reads_extension = "fastq"
reads_prefix = "*"
bam = false
bai = false
intervals = false
skip_fastqc = false
skip_multiqc = false
skip_structural_variants = false
outdir = "./results"
// Params for the Read Group Line to be added to bam file; taken from nf-core DeepVariant.
rgid=4
rglb="lib1"
rgpl="illumina"
rgpu="unit1"
rgsm=20
}
/*
* -----------------------------------------------------
* Example Nextflow config file for using AWS-iGenomes
* -----------------------------------------------------
* Copy and paste the reference types that your pipeline needs.
* You can use the following code in your pipeline to get the paths:
*
* params.gtf = params.genome ? params.genomes[ params.genome ].gtf ?: false : false
* if (params.gtf) {
* Channel.fromPath(params.gtf)
* .ifEmpty { exit 1, "GTF annotation file not found: ${params.gtf}" }
* .into { my_gtf_channel }
* }
*
* The user can then specify --genome [key] or --gtf [path]
*
* If the references are synced to your local cluster, you can use a parallel config
* file for local files.
* For a working example of this, see https://github.com/SciLifeLab/NGI-RNAseq
*
* NB: Not all available references are listed here! eg. AbundantSequences,
* individual Chromosomes, SmallRNA, Variation and others.
*/
params {
// Command-line genome key
genome = false
// illumina iGenomes reference file paths on UPPMAX
genomes {
'hg19' {
fasta = 's3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa'
fai = 's3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa.fai'
dict = 's3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.dict'
dbsnp_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/hg19/dbsnp_138.hg19.vcf.gz'
dbsnp_idx_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/hg19/dbsnp_138.hg19.vcf.idx.gz'
golden_indel_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/hg19/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz'
golden_indel_idx_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/hg19/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.idx.gz'
hapmap_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/hg19/hapmap_3.3.hg19.sites.vcf.gz'
hapmap_idx_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/hg19/hapmap_3.3.hg19.sites.vcf.idx.gz'
omni_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/hg19/1000G_omni2.5.hg19.sites.vcf.gz'
omni_idx_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/hg19/1000G_omni2.5.hg19.sites.vcf.idx.gz'
phase1_snps_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/hg19/1000G_phase1.snps.high_confidence.hg19.sites.vcf.gz'
phase1_snps_idx_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/hg19/1000G_phase1.snps.high_confidence.hg19.sites.vcf.idx.gz'
bwa_index_amb = 's3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa.amb'
bwa_index_ann = 's3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa.ann'
bwa_index_bwt = 's3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa.bwt'
bwa_index_pac = 's3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa.pac'
bwa_index_sa = 's3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa.sa'
}
'GRCh37' {
fasta = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta'
fai = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta.fai'
dict = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.dict'
dbsnp_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf'
dbsnp_idx_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf.idx'
golden_indel_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.b37.vcf'
golden_indel_idx_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.b37.vcf.idx'
hapmap_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/b37/hapmap_3.3.b37.vcf.gz'
hapmap_idx_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/b37/hapmap_3.3.b37.vcf.idx.gz'
omni_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/1000G_omni2.5.b37.vcf.gz'
omni_idx_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/1000G_omni2.5.b37.vcf.idx.gz'
phase1_snps_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/1000G_phase1.indels.b37.vcf'
phase1_snps_idx_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/1000G_phase1.indels.b37.vcf.idx'
bwa_index_amb = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.amb'
bwa_index_ann = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.ann'
bwa_index_bwt = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.bwt'
bwa_index_pac = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.pac'
bwa_index_sa = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Sequence/BWAIndex/human_g1k_v37_decoy.fasta.sa'
}
'GRCh37chr20' {
fasta = 'chr20_testdata/human_g1k_v37_chr20.fasta'
fai = 'chr20_testdata/human_g1k_v37_chr20.fasta.fai'
dict = 'chr20_testdata/human_g1k_v37_chr20.dict'
dbsnp_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf'
dbsnp_idx_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf.idx'
golden_indel_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.b37.vcf'
golden_indel_idx_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.b37.vcf.idx'
hapmap_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/b37/hapmap_3.3.b37.vcf.gz'
hapmap_idx_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/b37/hapmap_3.3.b37.vcf.idx.gz'
omni_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/1000G_omni2.5.b37.vcf.gz'
omni_idx_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/1000G_omni2.5.b37.vcf.idx.gz'
phase1_snps_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/1000G_phase1.indels.b37.vcf'
phase1_snps_idx_gz = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/1000G_phase1.indels.b37.vcf.idx'
bwa_index_amb = 'chr20_testdata/human_g1k_v37_chr20.fasta.amb'
bwa_index_ann = 'chr20_testdata/human_g1k_v37_chr20.fasta.ann'
bwa_index_bwt = 'chr20_testdata/human_g1k_v37_chr20.fasta.bwt'
bwa_index_pac = 'chr20_testdata/human_g1k_v37_chr20.fasta.pac'
bwa_index_sa = 'chr20_testdata/human_g1k_v37_chr20.fasta.sa'
}
}
}