diff --git a/modules/local/samplesheet_check/main.nf b/modules/local/samplesheet_check/main.nf index f0437a6..4fb60f8 100644 --- a/modules/local/samplesheet_check/main.nf +++ b/modules/local/samplesheet_check/main.nf @@ -3,7 +3,7 @@ // MIT: https://github.com/nf-core/rnaseq/blob/master/LICENSE // // Changes: -// Added channel permissible_target_assemblies +// Added channel permissible_target_assemblies process SAMPLESHEET_CHECK { tag "$samplesheet" @@ -37,4 +37,4 @@ process SAMPLESHEET_CHECK { python: \$(python --version | sed 's/Python //g') END_VERSIONS """ -} \ No newline at end of file +} diff --git a/modules/local/validate_params.nf b/modules/local/validate_params.nf index f6ce18a..460ce80 100644 --- a/modules/local/validate_params.nf +++ b/modules/local/validate_params.nf @@ -1,6 +1,6 @@ def validateParams(params) { validateFastaTags(params) - + if (!params['repeat_annotator']) { error "Error: repeat_annotator must be either 'repeatmodeler' or 'edta'" } @@ -8,7 +8,7 @@ def validateParams(params) { if ( !(params['repeat_annotator'] in ['repeatmodeler', 'edta']) ) { error "Error: repeat_annotator must be either 'repeatmodeler' or 'edta'" } - + validateTETags(params) validateTEFastaCorrespondence(params) @@ -67,7 +67,7 @@ def validateTEFastaCorrespondence(params) { if(!params["te_libraries"]) { return } - + def listOfTETuples = params["te_libraries"] def listOfFastaTuples = params["target_assemblies"] @@ -84,7 +84,7 @@ def validateTEFastaCorrespondence(params) { def validateRiboDBManifest(params) { if (params.remove_ribo_rna) { file_ribo_db = file(params.ribo_database_manifest, checkIfExists: true) - + if (file_ribo_db.isEmpty()) {exit 1, "File provided with --ribo_database_manifest is empty: ${file_ribo_db.getName()}!"} } } @@ -101,4 +101,4 @@ def validateLiftoffXrefs(params) { def isNotListOfLists(thisOne, subListSize) { return (!(thisOne instanceof List) || thisOne.isEmpty() || thisOne.any { !(it instanceof List) || it.size() != subListSize }) -} \ No newline at end of file +}