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fix: make HTSLIB_TABIX more modular
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parent
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commit
5e71dc94d6
4 changed files with 43 additions and 14 deletions
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@ -5,7 +5,7 @@ params.options = [:]
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def options = initOptions(params.options)
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process HTSLIB_TABIX {
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tag "$vcf"
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tag "$tab"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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@ -19,7 +19,7 @@ process HTSLIB_TABIX {
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}
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input:
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path vcf
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path tab
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output:
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path("*.tbi") , emit: tbi
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@ -28,8 +28,8 @@ process HTSLIB_TABIX {
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script:
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def software = getSoftwareName(task.process)
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"""
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tabix -p vcf $vcf
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tabix $options.args $tab
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echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/(.*\$//' > ${software}.version.txt
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"""
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}
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}
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@ -32,10 +32,10 @@ params:
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Instead of directly downloading Singularity images for use with Singularity,
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force the workflow to pull and convert Docker containers instead.
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input:
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- vcf:
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- tab:
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type: file
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description: vcf.gz file
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pattern: "*.{vcf.gz}"
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description: TAB-delimited genome file
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pattern: "*"
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output:
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- tbi:
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type: file
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@ -2,8 +2,18 @@
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nextflow.enable.dsl = 2
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include { HTSLIB_TABIX } from '../../../../software/htslib/tabix/main.nf' addParams( options: [:] )
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include { HTSLIB_TABIX as TABIX_BED } from '../../../../software/htslib/tabix/main.nf' addParams( options: ['args': '-p bed'] )
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include { HTSLIB_TABIX as TABIX_GFF } from '../../../../software/htslib/tabix/main.nf' addParams( options: ['args': '-p gff'] )
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include { HTSLIB_TABIX as TABIX_VCF } from '../../../../software/htslib/tabix/main.nf' addParams( options: ['args': '-p vcf'] )
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workflow test_htslib_tabix {
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HTSLIB_TABIX ( file("${launchDir}/tests/data/vcf/test.vcf.gz", checkIfExists: true) )
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}
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workflow test_htslib_tabix_bed {
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TABIX_BED ( file("${launchDir}/tests/data/bed/B.bed.gz", checkIfExists: true) )
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}
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workflow test_htslib_tabix_gff {
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TABIX_GFF ( file("${launchDir}/tests/data/gff/a.gff3.gz", checkIfExists: true) )
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}
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workflow test_htslib_tabix_vcf {
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TABIX_VCF ( file("${launchDir}/tests/data/vcf/test.vcf.gz", checkIfExists: true) )
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}
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@ -1,8 +1,27 @@
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- name: htslib tabix
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command: nextflow run ./tests/software/htslib/tabix -entry test_htslib_tabix -c tests/config/nextflow.config
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- name: htslib tabix bed
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command: nextflow run ./tests/software/htslib/tabix -entry test_htslib_tabix_bed -c tests/config/nextflow.config
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tags:
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- htslib
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- htslib_tabix
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- bed
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files:
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- path: output/htslib/test.vcf.gz.tbi
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- path: output/tabix/B.bed.gz.tbi
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md5sum: 6d657159c283200109f2ed082296f853
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- name: htslib tabix gff
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command: nextflow run ./tests/software/htslib/tabix -entry test_htslib_tabix_gff -c tests/config/nextflow.config
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tags:
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- htslib
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- htslib_tabix
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- gff
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files:
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- path: output/tabix/a.gff3.gz.tbi
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md5sum: 77f666b63da45c6af8a394ab5642602e
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- name: htslib tabix vcf
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command: nextflow run ./tests/software/htslib/tabix -entry test_htslib_tabix_vcf -c tests/config/nextflow.config
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tags:
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- htslib
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- htslib_tabix
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- vcf
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files:
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- path: output/tabix/test.vcf.gz.tbi
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md5sum: a03f56d3e968f32256ffb9f6b7d01812
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