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round the < to ( to make markdown work for meta.yml (#1395)

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* round the < to ( to make markdown work for meta.yml

* changing md5sums and stub output so it doesnt trigger the empty file linting error
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Lasse Folkersen 2022-03-16 13:29:11 +01:00 committed by GitHub
parent 73aaecbc3a
commit df60a58426
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3 changed files with 29 additions and 29 deletions
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18
modules/ascat/main.nf
View file

@ -137,15 +137,15 @@ process ASCAT {
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.cnvs.txt
touch ${prefix}.purityploidy.txt
touch ${prefix}.segments.txt
touch Tumour.ASCATprofile.png
touch Tumour.ASPCF.png
touch Tumour.germline.png
touch Tumour.rawprofile.png
touch Tumour.sunrise.png
touch Tumour.tumour.png
echo stub > ${prefix}.cnvs.txt
echo stub > ${prefix}.purityploidy.txt
echo stub > ${prefix}.segments.txt
echo stub > Tumour.ASCATprofile.png
echo stub > Tumour.ASPCF.png
echo stub > Tumour.germline.png
echo stub > Tumour.rawprofile.png
echo stub > Tumour.sunrise.png
echo stub > Tumour.tumour.png
echo 'ASCAT:' > versions.yml
echo ' ascat: 3.0.0' >> versions.yml

22
modules/ascat/meta.yml
View file

@ -15,23 +15,23 @@ input:
- args:
type: map
description: |
Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters must be set between quotes. <optional> parameters can be removed from the map, if they are not set. For default values, please check the documentation above.
Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters must be set between quotes. (optional) parameters can be removed from the map, if they are not set. For default values, please check the documentation above.
```
{
[
"gender": "XX",
"genomeVersion": "hg19"
"purity": <optional>,
"ploidy": <optional>,
"gc_files": <optional>,
"minCounts": <optional>,
"chrom_names": <optional>,
"min_base_qual": <optional>,
"min_map_qual": <optional>,
"ref_fasta": <optional>,
"skip_allele_counting_tumour": <optional>,
"skip_allele_counting_normal": <optional>
"purity": (optional),
"ploidy": (optional),
"gc_files": (optional),
"minCounts": (optional),
"chrom_names": (optional),
"min_base_qual": (optional),
"min_map_qual": (optional),
"ref_fasta": (optional),
"skip_allele_counting_tumour": (optional),
"skip_allele_counting_normal": (optional)
]
}
```

18
tests/modules/ascat/test.yml
View file

@ -4,22 +4,22 @@
- ascat
files:
- path: output/ascat/Tumour.ASCATprofile.png
md5sum: d41d8cd98f00b204e9800998ecf8427e
md5sum: f50b84b1db4b83ba62ec1deacc69c260
- path: output/ascat/Tumour.ASPCF.png
md5sum: d41d8cd98f00b204e9800998ecf8427e
md5sum: f50b84b1db4b83ba62ec1deacc69c260
- path: output/ascat/Tumour.germline.png
md5sum: d41d8cd98f00b204e9800998ecf8427e
md5sum: f50b84b1db4b83ba62ec1deacc69c260
- path: output/ascat/Tumour.rawprofile.png
md5sum: d41d8cd98f00b204e9800998ecf8427e
md5sum: f50b84b1db4b83ba62ec1deacc69c260
- path: output/ascat/Tumour.sunrise.png
md5sum: d41d8cd98f00b204e9800998ecf8427e
md5sum: f50b84b1db4b83ba62ec1deacc69c260
- path: output/ascat/Tumour.tumour.png
md5sum: d41d8cd98f00b204e9800998ecf8427e
md5sum: f50b84b1db4b83ba62ec1deacc69c260
- path: output/ascat/test.cnvs.txt
md5sum: d41d8cd98f00b204e9800998ecf8427e
md5sum: f50b84b1db4b83ba62ec1deacc69c260
- path: output/ascat/test.purityploidy.txt
md5sum: d41d8cd98f00b204e9800998ecf8427e
md5sum: f50b84b1db4b83ba62ec1deacc69c260
- path: output/ascat/test.segments.txt
md5sum: d41d8cd98f00b204e9800998ecf8427e
md5sum: f50b84b1db4b83ba62ec1deacc69c260
- path: output/ascat/versions.yml
md5sum: 1af20694ec11004c4f8bc0c609b06386