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fix output glob (#1551)

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Matthias De Smet 2022-04-22 12:50:17 +02:00 committed by GitHub
parent 538dbac98b
commit b1749445d7
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2 changed files with 9 additions and 8 deletions
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11
modules/elprep/split/main.nf
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@ -11,16 +11,16 @@ process ELPREP_SPLIT {
tuple val(meta), path(bam)
output:
tuple val(meta), path("**.{bam,sam}"), emit: bam
tuple val(meta), path("output/**.{bam,sam}"), emit: bam
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
meta.single_end ? args += " --single-end": ""
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def single_end = meta.single_end ? " --single-end": ""
"""
# create directory and move all input so elprep can find and merge them before splitting
@ -31,8 +31,9 @@ process ELPREP_SPLIT {
elprep split \\
input \\
. \\
output/ \\
$args \\
$single_end \\
--nr-of-threads $task.cpus \\
--output-prefix $prefix

6
tests/modules/elprep/split/test.yml
View file

@ -4,7 +4,7 @@
- elprep
- elprep/split
files:
- path: output/elprep/splits/test-group00001.bam
- path: output/elprep/splits/test-unmapped.bam
- path: output/elprep/test-spread.bam
- path: output/elprep/output/splits/test-group00001.bam
- path: output/elprep/output/splits/test-unmapped.bam
- path: output/elprep/output/test-spread.bam
- path: output/elprep/versions.yml