diff --git a/conf/modules.config b/conf/modules.config index 5b451d38..1c2c3360 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -307,6 +307,13 @@ process { ext.args = { "-k2,2 -nr -S${task.memory.mega - 100}M -T ." } } + // + // KMER + // + withName: CAT_CAT { + ext.prefix = { "${meta.id}_merged.fasta.gz" } + } + withName: FASTK_FASTK { ext.args = "-k31 -t -P." } diff --git a/subworkflows/local/kmer.nf b/subworkflows/local/kmer.nf index e0f7992e..9e498a0f 100755 --- a/subworkflows/local/kmer.nf +++ b/subworkflows/local/kmer.nf @@ -47,17 +47,9 @@ workflow KMER { ch_versions = ch_versions.mix( CAT_CAT.out.versions.first() ) // - // LOGIC: PRODUCE MERGED READS - // - CAT_CAT.out.file_out - .map{ meta, reads -> - reads.getName().endsWith('gz') ? [meta, reads.getParent().toString() + '/' + reads.getBaseName().toString() + '.fa.gz'] : [meta, reads.getParent().toString() + '/' + reads.getBaseName().toString() + '.fa'] - } - .set{ ch_reads_merged } - // MODULE: COUNT KMERS // - FASTK_FASTK( ch_reads_merged ) + FASTK_FASTK( CAT_CAT.out.file_out ) ch_versions = ch_versions.mix( FASTK_FASTK.out.versions.first() ) //