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Merge branch 'master' into diamond-update

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James A. Fellows Yates 2022-04-29 10:28:38 +02:00 committed by GitHub
commit 983d61763d
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3 changed files with 10 additions and 11 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 ?: "${meta.id}"
def input_reads = meta.single_end ? "$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 cigar_paf = cigar_paf_format && !sam_format ? "-c" : ''
def set_cigar_bam = cigar_bam && sam_format ? "-L" : ''
def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
"""
minimap2 \\
$args \\

14
modules/picard/collectwgsmetrics/main.nf
View file

@ -2,13 +2,13 @@ process PICARD_COLLECTWGSMETRICS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam), path(bai)
tuple val(meta), path(bam)
path fasta
output:
@ -32,9 +32,9 @@ process PICARD_COLLECTWGSMETRICS {
-Xmx${avail_mem}g \\
CollectWgsMetrics \\
$args \\
INPUT=$bam \\
OUTPUT=${prefix}.CollectWgsMetrics.coverage_metrics \\
REFERENCE_SEQUENCE=$fasta
-INPUT $bam \\
-OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\
-REFERENCE_SEQUENCE $fasta
cat <<-END_VERSIONS > versions.yml
"${task.process}":

3
tests/modules/picard/collectwgsmetrics/main.nf
View file

@ -6,8 +6,7 @@ include { PICARD_COLLECTWGSMETRICS } from '../../../../modules/picard/collectwgs
workflow test_picard_collectwgsmetrics {
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_bai'], checkIfExists: true)
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)