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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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7
modules/elprep/split/main.nf
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@ -11,7 +11,7 @@ process ELPREP_SPLIT {
tuple val(meta), path(bam) tuple val(meta), path(bam)
output: output:
tuple val(meta), path("**.{bam,sam}"), emit: bam tuple val(meta), path("output/**.{bam,sam}"), emit: bam
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:
@ -20,7 +20,7 @@ process ELPREP_SPLIT {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
meta.single_end ? args += " --single-end": "" def single_end = meta.single_end ? " --single-end": ""
""" """
# create directory and move all input so elprep can find and merge them before splitting # create directory and move all input so elprep can find and merge them before splitting
@ -31,8 +31,9 @@ process ELPREP_SPLIT {
elprep split \\ elprep split \\
input \\ input \\
. \\ output/ \\
$args \\ $args \\
$single_end \\
--nr-of-threads $task.cpus \\ --nr-of-threads $task.cpus \\
--output-prefix $prefix --output-prefix $prefix

6
tests/modules/elprep/split/test.yml
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@ -4,7 +4,7 @@
- elprep - elprep
- elprep/split - elprep/split
files: files:
- path: output/elprep/splits/test-group00001.bam - path: output/elprep/output/splits/test-group00001.bam
- path: output/elprep/splits/test-unmapped.bam - path: output/elprep/output/splits/test-unmapped.bam
- path: output/elprep/test-spread.bam - path: output/elprep/output/test-spread.bam
- path: output/elprep/versions.yml - path: output/elprep/versions.yml