diff --git a/modules/ascat/main.nf b/modules/ascat/main.nf index 1d2bd96f..35f262dd 100644 --- a/modules/ascat/main.nf +++ b/modules/ascat/main.nf @@ -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 diff --git a/modules/ascat/meta.yml b/modules/ascat/meta.yml index 949afd6a..b44862a1 100644 --- a/modules/ascat/meta.yml +++ b/modules/ascat/meta.yml @@ -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. 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": , - "ploidy": , - "gc_files": , - "minCounts": , - "chrom_names": , - "min_base_qual": , - "min_map_qual": , - "ref_fasta": , - "skip_allele_counting_tumour": , - "skip_allele_counting_normal": + "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) ] } ``` diff --git a/tests/modules/ascat/test.yml b/tests/modules/ascat/test.yml index e46c66b4..668e8823 100644 --- a/tests/modules/ascat/test.yml +++ b/tests/modules/ascat/test.yml @@ -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