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moved error catching from workflow to subworkflow utils #1122

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moved error catching from workflow to subworkflow utils #1122

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7d8e848
moved error catching from workflow to subworkflow utils
ilight1542 Mar 24, 2025
e59a923
adjusted adapterlist param check reference
ilight1542 Mar 24, 2025
3fa5c83
added params. to adapter list
ilight1542 Mar 24, 2025
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7 changes: 5 additions & 2 deletions subworkflows/local/utils_nfcore_eager_pipeline/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -210,8 +210,11 @@ def validateInputParameters() {
genomeExistsError()
if ( !params.fasta && !params.fasta_sheet ) { exit 1, "[nf-core/eager] ERROR: Neither FASTA file --fasta nor reference sheet --fasta_sheet have been provided."}
if ( params.fasta && params.fasta_sheet ) { exit 1, "[nf-core/eager] ERROR: A FASTA file --fasta and a reference sheet --fasta_sheet have been provided. These parameters are mutually exclusive."}
if ( params.preprocessing_adapterlist && params.preprocessing_skipadaptertrim ) { log.warn("[nf-core/eager] WARNING: --preprocessing_skipadaptertrim will override --preprocessing_adapterlist. Adapter trimming will be skipped!") }
if ( params.deduplication_tool == 'dedup' && ! params.preprocessing_excludeunmerged ) { exit 1, "[nf-core/eager] ERROR: Dedup can only be used on collapsed (i.e. merged) PE reads. For all other cases, please set --deduplication_tool to 'markduplicates'."}
if (params.preprocessing_adapterlist && !params.preprocessing_skipadaptertrim) {
if (params.preprocessing_tool == 'adapterremoval' && !(params.preprocessing_adapterlist.extension == 'txt') ) { exit 1, ("[nf-core/eager] ERROR: AdapterRemoval2 adapter list requires a `.txt` format and extension. Check input: --preprocessing_adapterlist ${params.preprocessing_adapterlist}") }
if (params.preprocessing_tool == 'fastp' && !params.preprocessing_adapterlist.extension.matches(".*(fa|fasta|fna|fas)") ) { exit 1, ("[nf-core/eager] ERROR: fastp adapter list requires a `.fasta` format and extension (or fa, fas, fna). Check input: --preprocessing_adapterlist ${params.preprocessing_adapterlist}") }
} else if (params.preprocessing_adapterlist && params.preprocessing_skipadaptertrim ) { log.warn("[nf-core/eager] WARNING: --preprocessing_skipadaptertrim will override --preprocessing_adapterlist. Adapter trimming will be skipped!") }
if ( params.deduplication_tool == 'dedup' && ! params.preprocessing_excludeunmerged ) { exit 1, ("[nf-core/eager] ERROR: Dedup can only be used on collapsed (i.e. merged) PE reads. For all other cases, please set --deduplication_tool to 'markduplicates'.") }
if ( params.bamfiltering_retainunmappedgenomicbam && params.bamfiltering_mappingquality > 0 ) { exit 1, ("[nf-core/eager] ERROR: You cannot both retain unmapped reads and perform quality filtering, as unmapped reads have a mapping quality of 0. Pick one or the other functionality.") }
if ( params.bamfiltering_generatefastq && params.run_bamfiltering ) { exit 1, ("[nf-core/eager] ERROR: --bamfiltering_generatefastq will NOT generate a fastq file unless BAM filtering is turned on with `--run_bamfiltering`") }
if ( params.genotyping_source == 'trimmed' && ! params.run_trim_bam ) { exit 1, ("[nf-core/eager] ERROR: --genotyping_source cannot be 'trimmed' unless BAM trimming is turned on with `--run_trim_bam`.") }
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9 changes: 0 additions & 9 deletions workflows/eager.nf
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Expand Up @@ -90,15 +90,6 @@ workflow EAGER {
// Preprocessing
adapterlist = params.preprocessing_skipadaptertrim ? [] : params.preprocessing_adapterlist ? file(params.preprocessing_adapterlist, checkIfExists: true) : []

if (params.preprocessing_adapterlist && !params.preprocessing_skipadaptertrim) {
if (params.preprocessing_tool == 'adapterremoval' && !(adapterlist.extension == 'txt')) {
error("[nf-core/eager] ERROR: AdapterRemoval2 adapter list requires a `.txt` format and extension. Check input: --preprocessing_adapterlist ${params.preprocessing_adapterlist}")
}
if (params.preprocessing_tool == 'fastp' && !adapterlist.extension.matches(".*(fa|fasta|fna|fas)")) {
error("[nf-core/eager] ERROR: fastp adapter list requires a `.fasta` format and extension (or fa, fas, fna). Check input: --preprocessing_adapterlist ${params.preprocessing_adapterlist}")
}
}

//
// MODULE: Convert input BAMs back to FastQ
//
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