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nf-core_modules/modules/strelka/germline/main.nf

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Strelka germline (#340) * nf-core template created * boilerplate and sarek_dsl2 code merged * adding an option to give it args * bai got away * seperating vcf files and vcf index files into seperate streams * some minor spacefixes * adding standard information about the module * removing typos * some basic tests based on tiddit tests * removed the bed parameter, should be provided via options.args instead * removing typos * adding indexed bam file instead * Adding changing out fasta with reference to deal with empty fasta input * adding the correct fasta * removing the empty test * adding the correct data to the testoutput and removing the md5sum since it constantly changes * adding target_bed to input * adding info on target bed * adding target bed to test * adding more files to the test * adding meta for target bed test * adding a test for target_bed * typo * fixing pytest with master
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// Import generic module functions
Bulk update modules to use versions.yml (#739) * New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-27 08:41:24 +00:00
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
Strelka germline (#340) * nf-core template created * boilerplate and sarek_dsl2 code merged * adding an option to give it args * bai got away * seperating vcf files and vcf index files into seperate streams * some minor spacefixes * adding standard information about the module * removing typos * some basic tests based on tiddit tests * removed the bed parameter, should be provided via options.args instead * removing typos * adding indexed bam file instead * Adding changing out fasta with reference to deal with empty fasta input * adding the correct fasta * removing the empty test * adding the correct data to the testoutput and removing the md5sum since it constantly changes * adding target_bed to input * adding info on target bed * adding target bed to test * adding more files to the test * adding meta for target bed test * adding a test for target_bed * typo * fixing pytest with master
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params.options = [:]
options = initOptions(params.options)
process STRELKA_GERMLINE {
tag "$meta.id"
label 'process_high'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
Update functions.nf to be more flexible for publishing by meta keys (#423) * Update functions.nf * Replace saveAs line in module main script * Add spacing for ECLint
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
Strelka germline (#340) * nf-core template created * boilerplate and sarek_dsl2 code merged * adding an option to give it args * bai got away * seperating vcf files and vcf index files into seperate streams * some minor spacefixes * adding standard information about the module * removing typos * some basic tests based on tiddit tests * removed the bed parameter, should be provided via options.args instead * removing typos * adding indexed bam file instead * Adding changing out fasta with reference to deal with empty fasta input * adding the correct fasta * removing the empty test * adding the correct data to the testoutput and removing the md5sum since it constantly changes * adding target_bed to input * adding info on target bed * adding target bed to test * adding more files to the test * adding meta for target bed test * adding a test for target_bed * typo * fixing pytest with master
2021-03-24 05:07:29 +00:00
conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/strelka:2.9.10--0"
} else {
container "quay.io/biocontainers/strelka:2.9.10--0"
}
input:
tuple val(meta), path(bam), path(bai)
Re-organise all test data (#354) * Re-organise all test data * Fix ECLint * Fix ECLint agaaainn * Now is not the time EClint
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path fasta
path fai
path target_bed
Strelka germline (#340) * nf-core template created * boilerplate and sarek_dsl2 code merged * adding an option to give it args * bai got away * seperating vcf files and vcf index files into seperate streams * some minor spacefixes * adding standard information about the module * removing typos * some basic tests based on tiddit tests * removed the bed parameter, should be provided via options.args instead * removing typos * adding indexed bam file instead * Adding changing out fasta with reference to deal with empty fasta input * adding the correct fasta * removing the empty test * adding the correct data to the testoutput and removing the md5sum since it constantly changes * adding target_bed to input * adding info on target bed * adding target bed to test * adding more files to the test * adding meta for target bed test * adding a test for target_bed * typo * fixing pytest with master
2021-03-24 05:07:29 +00:00
output:
Modules TLC (#551) * Modules TLC * Fix all the tests
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tuple val(meta), path("*variants.vcf.gz") , emit: vcf
tuple val(meta), path("*variants.vcf.gz.tbi"), emit: vcf_tbi
tuple val(meta), path("*genome.vcf.gz") , emit: genome_vcf
tuple val(meta), path("*genome.vcf.gz.tbi") , emit: genome_vcf_tbi
Bulk update modules to use versions.yml (#739) * New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-27 08:41:24 +00:00
path "versions.yml" , emit: version
Strelka germline (#340) * nf-core template created * boilerplate and sarek_dsl2 code merged * adding an option to give it args * bai got away * seperating vcf files and vcf index files into seperate streams * some minor spacefixes * adding standard information about the module * removing typos * some basic tests based on tiddit tests * removed the bed parameter, should be provided via options.args instead * removing typos * adding indexed bam file instead * Adding changing out fasta with reference to deal with empty fasta input * adding the correct fasta * removing the empty test * adding the correct data to the testoutput and removing the md5sum since it constantly changes * adding target_bed to input * adding info on target bed * adding target bed to test * adding more files to the test * adding meta for target bed test * adding a test for target_bed * typo * fixing pytest with master
2021-03-24 05:07:29 +00:00
script:
def software = getSoftwareName(task.process)
Modules TLC (#551) * Modules TLC * Fix all the tests
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def regions = params.target_bed ? "--exome --callRegions ${target_bed}" : ""
Strelka germline (#340) * nf-core template created * boilerplate and sarek_dsl2 code merged * adding an option to give it args * bai got away * seperating vcf files and vcf index files into seperate streams * some minor spacefixes * adding standard information about the module * removing typos * some basic tests based on tiddit tests * removed the bed parameter, should be provided via options.args instead * removing typos * adding indexed bam file instead * Adding changing out fasta with reference to deal with empty fasta input * adding the correct fasta * removing the empty test * adding the correct data to the testoutput and removing the md5sum since it constantly changes * adding target_bed to input * adding info on target bed * adding target bed to test * adding more files to the test * adding meta for target bed test * adding a test for target_bed * typo * fixing pytest with master
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"""
Re-organise all test data (#354) * Re-organise all test data * Fix ECLint * Fix ECLint agaaainn * Now is not the time EClint
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configureStrelkaGermlineWorkflow.py \\
--bam $bam \\
--referenceFasta $fasta \\
Modules TLC (#551) * Modules TLC * Fix all the tests
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$regions \\
Re-organise all test data (#354) * Re-organise all test data * Fix ECLint * Fix ECLint agaaainn * Now is not the time EClint
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$options.args \\
Strelka germline (#340) * nf-core template created * boilerplate and sarek_dsl2 code merged * adding an option to give it args * bai got away * seperating vcf files and vcf index files into seperate streams * some minor spacefixes * adding standard information about the module * removing typos * some basic tests based on tiddit tests * removed the bed parameter, should be provided via options.args instead * removing typos * adding indexed bam file instead * Adding changing out fasta with reference to deal with empty fasta input * adding the correct fasta * removing the empty test * adding the correct data to the testoutput and removing the md5sum since it constantly changes * adding target_bed to input * adding info on target bed * adding target bed to test * adding more files to the test * adding meta for target bed test * adding a test for target_bed * typo * fixing pytest with master
2021-03-24 05:07:29 +00:00
--runDir strelka
Re-organise all test data (#354) * Re-organise all test data * Fix ECLint * Fix ECLint agaaainn * Now is not the time EClint
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python strelka/runWorkflow.py -m local -j $task.cpus
Modules TLC (#551) * Modules TLC * Fix all the tests
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mv strelka/results/variants/genome.*.vcf.gz ${prefix}.genome.vcf.gz
mv strelka/results/variants/genome.*.vcf.gz.tbi ${prefix}.genome.vcf.gz.tbi
mv strelka/results/variants/variants.vcf.gz ${prefix}.variants.vcf.gz
mv strelka/results/variants/variants.vcf.gz.tbi ${prefix}.variants.vcf.gz.tbi
Re-organise all test data (#354) * Re-organise all test data * Fix ECLint * Fix ECLint agaaainn * Now is not the time EClint
2021-03-24 09:53:41 +00:00
Bulk update modules to use versions.yml (#739) * New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-27 08:41:24 +00:00
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
strelka: \$( configureStrelkaGermlineWorkflow.py --version )
END_VERSIONS
Strelka germline (#340) * nf-core template created * boilerplate and sarek_dsl2 code merged * adding an option to give it args * bai got away * seperating vcf files and vcf index files into seperate streams * some minor spacefixes * adding standard information about the module * removing typos * some basic tests based on tiddit tests * removed the bed parameter, should be provided via options.args instead * removing typos * adding indexed bam file instead * Adding changing out fasta with reference to deal with empty fasta input * adding the correct fasta * removing the empty test * adding the correct data to the testoutput and removing the md5sum since it constantly changes * adding target_bed to input * adding info on target bed * adding target bed to test * adding more files to the test * adding meta for target bed test * adding a test for target_bed * typo * fixing pytest with master
2021-03-24 05:07:29 +00:00
"""
}
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