From 4e0a2ebb85a29dde36e94640d54fc21ad6e26c96 Mon Sep 17 00:00:00 2001 From: Ram Nanduri Date: Thu, 4 Apr 2024 12:28:21 +0200 Subject: [PATCH 1/2] Fixed mosdepth input channel bug when bedfile is not provided --- workflows/skierfe.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/skierfe.nf b/workflows/skierfe.nf index 038574fd..3bad4b53 100644 --- a/workflows/skierfe.nf +++ b/workflows/skierfe.nf @@ -12,7 +12,7 @@ ch_extra_snfs = params.extra_snfs ? Channel.fromSamplesheet('extra_snfs' ch_extra_gvcfs = params.extra_gvcfs ? Channel.fromSamplesheet('extra_gvcfs', immutable_meta: false) : Channel.empty() ch_tandem_repeats = params.tandem_repeats ? Channel.fromPath(params.tandem_repeats).collect() : Channel.value([]) ch_bed = params.bed ? Channel.fromPath(params.bed).map{ [ it.getSimpleName(), it]}.collect() : Channel.empty() -ch_input_bed = params.bed ? Channel.fromPath(params.bed).map{ [ it.getSimpleName(), it]}.collect() : Channel.value([]) +ch_input_bed = params.bed ? Channel.fromPath(params.bed).map{ [ it.getSimpleName(), it]}.collect() : Channel.value([[],[]]) // This should be able to in schema? if (params.split_fastq < 250 & params.split_fastq > 0 ) { exit 1, '--split_fastq must be 0 or >= 250'} From 1d02941a466ba5c553780ea6a6c750b9eefdd3ca Mon Sep 17 00:00:00 2001 From: Ram Nanduri Date: Fri, 5 Apr 2024 13:28:12 +0200 Subject: [PATCH 2/2] Updated CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8501543c..f0ab359a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,7 @@ Initial release of genomic-medicine-sweden/skierfe, created with the [nf-core](h ### `Fixed` - Fix BCFTools merge module inputs [#43](https://github.com/genomic-medicine-sweden/skierfe/pull/43) +- Fix Mosdepth input channel when run without a bed file [#66](https://github.com/genomic-medicine-sweden/skierfe/pull/66) ### `Dependencies`