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fix command line, fix meta.yml

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This commit is contained in:
Matthias De Smet 2022-04-19 15:31:39 +02:00
parent b35264e919
commit 07982d6cb1
2 changed files with 9 additions and 5 deletions
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5
modules/bamtools/split/main.nf
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@ -23,7 +23,10 @@ process BAMTOOLS_SPLIT {
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def input_list = bam.collect{"-in $it"}.join(' ') def input_list = bam.collect{"-in $it"}.join(' ')
if (bam_list) { if (bam_list) {
input += " -list $bam_list" input_list += " -list $bam_list"
}
if (!args.contains("-stub")) {
args += " -stub ${prefix}"
} }
""" """

9
tests/modules/bamtools/split/test.yml
View file

@ -1,10 +1,11 @@
- name: bamtools split test_bamtools_split - name: bamtools split test_bamtools_split
command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config command: nextflow run tests/modules/bamtools/split -entry test_bamtools_split -c tests/config/nextflow.config
tags: tags:
- bamtools/split
- bamtools - bamtools
- bamtools/split
files: files:
- path: output/bamtools/test.paired_end.sorted.REF_chr22.bam - path: output/bamtools/test.REF_chr22.bam
md5sum: b7dc50e0edf9c6bfc2e3b0e6d074dc07 md5sum: b7dc50e0edf9c6bfc2e3b0e6d074dc07
- path: output/bamtools/test.paired_end.sorted.REF_unmapped.bam - path: output/bamtools/test.REF_unmapped.bam
md5sum: e0754bf72c51543b2d745d96537035fb md5sum: e0754bf72c51543b2d745d96537035fb
- path: output/bamtools/versions.yml