diff --git a/subworkflows/local/hicstuff_sub.nf b/subworkflows/local/hicstuff_sub.nf index 92c5181f3cd31a16a88655d79637a5f29891d58d..ad0332d0b6b899020f17097d8af9e0f76bfbfaf5 100644 --- a/subworkflows/local/hicstuff_sub.nf +++ b/subworkflows/local/hicstuff_sub.nf @@ -8,7 +8,7 @@ include { BUILD_MATRIX_COOL_ALT } from '../../modules/local/hicstuff/build_matri include { FILTER_EVENT } from '../../modules/local/hicstuff/filter_event' include { DISTANCE_LAW } from '../../modules/local/hicstuff/distance_law' include { FILTER_PCR } from '../../modules/local/hicstuff/filter_pcr' -include { GATK4_MARKDUPLICATES } from '../../modules/nf-core/custom/gatk4/markduplicates/main' +include { GATK4_MARKDUPLICATES } from '../../modules/nf-core/custom/markduplicates/main' include { SAMTOOLS_SORT } from '../../modules/nf-core/custom/samtools/sort/main' include { SAMTOOLS_INDEX } from '../../modules/nf-core/custom/samtools/index/main' @@ -89,7 +89,7 @@ workflow HICSTUFF_SUB { .map { meta1, bam1, meta2, bam2 -> meta1.id == meta2.id && meta1.chunk == meta2.chunk && meta1.mates == "R1" && meta2.mates == "R2" ? [ meta1, bam1, meta2, bam2 ] : null - }, + }.view(), FRAGMENT_ENZYME.out.info_contigs.collect(), digestion, fasta.collect()