diff --git a/subworkflows/local/hicstuff_sub.nf b/subworkflows/local/hicstuff_sub.nf index 3f49999601013b356c25b19ad04b6753ed0d8d80..f4ace144c9c0c85821be1de12974368649497b4a 100644 --- a/subworkflows/local/hicstuff_sub.nf +++ b/subworkflows/local/hicstuff_sub.nf @@ -9,8 +9,7 @@ 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 { SAMTOOLS_SORT as SAMTOOLS_SORT1} from '../../modules/nf-core/custom/samtools/sort/main' -include { SAMTOOLS_SORT as SAMTOOLS_SORT2} from '../../modules/nf-core/custom/samtools/sort/main' +include { SAMTOOLS_SORT } from '../../modules/nf-core/custom/samtools/sort/main' include { SAMTOOLS_SORT_N } from '../../modules/nf-core/custom/samtools_n/sort/main' include { FILTER_PAIR } from '../../modules/nf-core/custom/filterbam/main' include { SAMTOOLS_INDEX } from '../../modules/nf-core/custom/samtools/index/main' @@ -67,13 +66,13 @@ workflow HICSTUFF_SUB { error "Error: filter_pcr and filter_pcr_picard can't both be true at the same time! Set one of them false in the config file" } else if (params.filter_pcr_picard){ - SAMTOOLS_SORT1( + SAMTOOLS_SORT( BOWTIE2_ALIGNMENT.out.bam ) PICARD_MARKDUPLICATES( - SAMTOOLS_SORT1.out.bam, + SAMTOOLS_SORT.out.bam, fasta.collect(), index.collect() )