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https://github.com/MillironX/nf-core_modules.git
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MD finally supports cram output (#2019)
* MD finally supports cram output * publish crai file * fix test output * fix mv * figure out if contains breaks stuff * remove variable checksum * add contains check * remove variable checksum Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
This commit is contained in:
FriederikeHanssen
GitHub
parent
5e7b1ef9a5
commit
e726b1730d
5 changed files with 81 additions and 17 deletions
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@ -9,20 +9,25 @@ process GATK4_MARKDUPLICATES {
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input:
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tuple val(meta), path(bam)
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path fasta
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path fasta_fai
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output:
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tuple val(meta), path("*.bam") , emit: bam
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tuple val(meta), path("*.bai") , optional:true, emit: bai
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tuple val(meta), path("*cram"), emit: cram, optional: true
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tuple val(meta), path("*bam"), emit: bam, optional: true
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tuple val(meta), path("*.crai"), emit: crai, optional: true
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tuple val(meta), path("*.bai"), emit: bai, optional: true
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tuple val(meta), path("*.metrics"), emit: metrics
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path "versions.yml" , emit: versions
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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prefix = task.ext.prefix ?: "${meta.id}"
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def input_list = bam.collect{"--INPUT $it"}.join(' ')
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def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
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def avail_mem = 3
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if (!task.memory) {
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@ -33,11 +38,17 @@ process GATK4_MARKDUPLICATES {
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"""
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gatk --java-options "-Xmx${avail_mem}g" MarkDuplicates \\
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$input_list \\
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--OUTPUT ${prefix}.bam \\
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--OUTPUT ${prefix} \\
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--METRICS_FILE ${prefix}.metrics \\
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--TMP_DIR . \\
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${reference} \\
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$args
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if [[ ${prefix} == *.cram ]]; then
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mv ${prefix}.bai ${prefix}.crai
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fi
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
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@ -26,6 +26,14 @@ input:
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type: file
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description: Sorted BAM file
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pattern: "*.{bam}"
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- fasta:
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type: file
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description: Fasta file
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pattern: "*.{fasta}"
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- fasta_fai:
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type: file
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description: Fasta index file
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pattern: "*.{fai}"
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output:
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- meta:
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@ -41,6 +49,18 @@ output:
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type: file
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description: Marked duplicates BAM file
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pattern: "*.{bam}"
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- cram:
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type: file
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description: Marked duplicates CRAM file
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pattern: "*.{cram}"
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- bai:
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type: file
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description: BAM index file
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pattern: "*.{bam.bai}"
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- crai:
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type: file
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description: CRAM index file
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pattern: "*.{cram.crai}"
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- metrics:
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type: file
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description: Duplicate metrics file generated by GATK
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@ -3,13 +3,14 @@
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nextflow.enable.dsl = 2
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include { GATK4_MARKDUPLICATES } from '../../../../modules/gatk4/markduplicates/main.nf'
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include { GATK4_MARKDUPLICATES as GATK4_MARKDUPLICATES_CRAM } from '../../../../modules/gatk4/markduplicates/main.nf'
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workflow test_gatk4_markduplicates {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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]
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GATK4_MARKDUPLICATES ( input )
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GATK4_MARKDUPLICATES ( input, [], [] )
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}
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workflow test_gatk4_markduplicates_multiple_bams {
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@ -18,5 +19,16 @@ workflow test_gatk4_markduplicates_multiple_bams {
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
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] ]
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GATK4_MARKDUPLICATES ( input )
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GATK4_MARKDUPLICATES ( input, [], [] )
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}
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workflow test_gatk4_markduplicates_multiple_cram_output {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
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] ]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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GATK4_MARKDUPLICATES_CRAM ( input, fasta, fai )
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}
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@ -4,6 +4,12 @@ process {
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withName: GATK4_MARKDUPLICATES {
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ext.args = '--CREATE_INDEX true'
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ext.prefix = { "${meta.id}.bam" }
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}
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withName: GATK4_MARKDUPLICATES_CRAM {
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ext.args = '--CREATE_INDEX true'
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ext.prefix = { "${meta.id}.cram" }
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}
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}
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@ -1,25 +1,40 @@
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- name: gatk4 markduplicates test_gatk4_markduplicates
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command: nextflow run tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates -c tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicates/nextflow.config
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command: nextflow run ./tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicates/nextflow.config
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tags:
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- gatk4
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- gatk4/markduplicates
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files:
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- path: output/gatk4/test.bai
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md5sum: c8f7a9e426c768577f88f59cb1336bf3
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md5sum: 4ac375b5288501c832bc3e4773f06d39
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- path: output/gatk4/test.bam
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md5sum: 58533ddab47f7ac07f7b10e7f4aac234
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- path: output/gatk4/test.metrics
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- path: output/gatk4/versions.yml
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md5sum: c1a0d25c5f65514e72aa490326557a88
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- path: output/gatk4/test.bam.metrics
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- name: gatk4 markduplicates test_gatk4_markduplicates_multiple_bams
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command: nextflow run tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates_multiple_bams -c tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicates/nextflow.config
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command: nextflow run ./tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates_multiple_bams -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicates/nextflow.config
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tags:
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- gatk4
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- gatk4/markduplicates
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files:
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- path: output/gatk4/test.bai
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md5sum: bad71df9c876e72a5bc0a3e0fd755f92
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md5sum: 832fbc6b3c3266d024fc7131ffd1b45d
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- path: output/gatk4/test.bam
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md5sum: 112580c24b43331950f24f9adea30788
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- path: output/gatk4/test.metrics
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- path: output/gatk4/versions.yml
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md5sum: 36909e80bde1aa547fae6382fd35764d
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- path: output/gatk4/test.bam.metrics
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contains:
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- "testN"
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- "2820"
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- name: gatk4 markduplicates test_gatk4_markduplicates_multiple_cram_output
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command: nextflow run ./tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates_multiple_cram_output -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicates/nextflow.config
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tags:
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- gatk4
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- gatk4/markduplicates
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files:
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- path: output/gatk4/test.cram
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- path: output/gatk4/test.cram.crai
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md5sum: 53a329f0828210e317ad81b0e6ca4bc5
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- path: output/gatk4/test.cram.metrics
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contains:
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- "testN"
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- "2820"
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