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fix: picard sortsam (#605)

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* Add picard/sortsam module

* Fix container links

* Changes after code review

* Input meta in the right place

* Correct output file suffix

* Define only `bam` in output tuple
This commit is contained in:
James A. Fellows Yates 2021-07-21 15:34:21 +02:00 committed by GitHub
parent f43778b0e6
commit a0019d4175
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2 changed files with 3 additions and 3 deletions
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4
modules/picard/sortsam/main.nf
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@ -24,7 +24,7 @@ process PICARD_SORTSAM {
val sort_order val sort_order
output: output:
tuple val(meta), path("*.sorted.bam"), emit: bam tuple val(meta), path("*.bam"), emit: bam
path "*.version.txt" , emit: version path "*.version.txt" , emit: version
script: script:
@ -41,7 +41,7 @@ process PICARD_SORTSAM {
SortSam \\ SortSam \\
-Xmx${avail_mem}g \\ -Xmx${avail_mem}g \\
--INPUT $bam \\ --INPUT $bam \\
--OUTPUT ${prefix}.sorted.bam \\ --OUTPUT ${prefix}.bam \\
--SORT_ORDER $sort_order --SORT_ORDER $sort_order
echo \$(picard SortSam --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt echo \$(picard SortSam --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt

2
tests/modules/picard/sortsam/main.nf
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@ -2,7 +2,7 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { PICARD_SORTSAM } from '../../../../modules/picard/sortsam/main.nf' addParams( options: [:] ) include { PICARD_SORTSAM } from '../../../../modules/picard/sortsam/main.nf' addParams( options: [suffix:'.sorted'] )
workflow test_picard_sortsam { workflow test_picard_sortsam {