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Merge branch 'master' into bump/picard

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Matthias De Smet 2022-04-29 09:48:15 +02:00 committed by GitHub
commit e263f267a7
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3 changed files with 5 additions and 5 deletions
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4
modules/minimap2/align/main.nf
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@ -27,8 +27,8 @@ process MINIMAP2_ALIGN {
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}" def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}"
def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf" def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf"
def cigar_paf = cigar_paf_format && !sam_format ? "-c" : '' def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
def set_cigar_bam = cigar_bam && sam_format ? "-L" : '' def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
""" """
minimap2 \\ minimap2 \\
$args \\ $args \\

3
modules/picard/collectwgsmetrics/main.nf
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@ -8,7 +8,7 @@ process PICARD_COLLECTWGSMETRICS {
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }" 'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam), path(bai) tuple val(meta), path(bam)
path fasta path fasta
output: output:
@ -36,6 +36,7 @@ process PICARD_COLLECTWGSMETRICS {
--OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\ --OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\
--REFERENCE_SEQUENCE $fasta --REFERENCE_SEQUENCE $fasta
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
picard: \$(picard CollectWgsMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:) picard: \$(picard CollectWgsMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)

3
tests/modules/picard/collectwgsmetrics/main.nf
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@ -6,8 +6,7 @@ include { PICARD_COLLECTWGSMETRICS } from '../../../../modules/picard/collectwgs
workflow test_picard_collectwgsmetrics { workflow test_picard_collectwgsmetrics {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
] ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)