Merge pull request #66 from ramsainanduri/mosdepth_bug

Fixed mosdepth input channel bug when bedfile is not provided

CHANGELOG.md

@@ -22,6 +22,7 @@ Initial release of genomic-medicine-sweden/skierfe, created with the [nf-core](h
 
 - Fix input file validation [#67](https://github.com/genomic-medicine-sweden/skierfe/pull/67)
 - 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`
 

workflows/skierfe.nf

@@ -14,7 +14,7 @@ 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'}