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https://github.com/MillironX/nf-core_modules.git
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Merge branch 'master' into diamond-update
This commit is contained in:
commit
983d61763d
3 changed files with 10 additions and 11 deletions
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@ -27,8 +27,8 @@ process MINIMAP2_ALIGN {
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def prefix = task.ext.prefix ?: "${meta.id}"
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def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}"
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def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf"
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def cigar_paf = cigar_paf_format && !sam_format ? "-c" : ''
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def set_cigar_bam = cigar_bam && sam_format ? "-L" : ''
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def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
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def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
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"""
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minimap2 \\
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$args \\
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@ -2,13 +2,13 @@ process PICARD_COLLECTWGSMETRICS {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
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conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
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'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
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'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(bam), path(bai)
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tuple val(meta), path(bam)
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path fasta
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output:
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@ -32,9 +32,9 @@ process PICARD_COLLECTWGSMETRICS {
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-Xmx${avail_mem}g \\
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CollectWgsMetrics \\
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$args \\
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INPUT=$bam \\
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OUTPUT=${prefix}.CollectWgsMetrics.coverage_metrics \\
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REFERENCE_SEQUENCE=$fasta
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-INPUT $bam \\
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-OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\
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-REFERENCE_SEQUENCE $fasta
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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@ -6,8 +6,7 @@ include { PICARD_COLLECTWGSMETRICS } from '../../../../modules/picard/collectwgs
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workflow test_picard_collectwgsmetrics {
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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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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
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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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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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