millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-12-22 11:08:17 +00:00
Code Issues Releases Packages Activity

Merge branch 'master' into bump/picard

Browse source
This commit is contained in:
Matthias De Smet 2022-04-29 09:48:15 +02:00 committed by GitHub
commit e263f267a7
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
3 changed files with 5 additions and 5 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

4
modules/minimap2/align/main.nf
View file

@ -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 \\

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

@ -8,7 +8,7 @@ process PICARD_COLLECTWGSMETRICS {
'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:
@ -36,6 +36,7 @@ process PICARD_COLLECTWGSMETRICS {
--OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\
--REFERENCE_SEQUENCE $fasta
cat <<-END_VERSIONS > versions.yml
"${task.process}":
picard: \$(picard CollectWgsMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)

1
tests/modules/picard/collectwgsmetrics/main.nf
View file

@ -7,7 +7,6 @@ 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)
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)