From b5828f47c17c41ce3a4c70b863c99207e3f6d37c Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 12 Dec 2024 14:51:44 +0000 Subject: [PATCH] Fix subworkflow imports for bam_dedup_umi (#7209) --- subworkflows/nf-core/bam_dedup_umi/main.nf | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/subworkflows/nf-core/bam_dedup_umi/main.nf b/subworkflows/nf-core/bam_dedup_umi/main.nf index fcaa6f2ea79..d091a5824fa 100644 --- a/subworkflows/nf-core/bam_dedup_umi/main.nf +++ b/subworkflows/nf-core/bam_dedup_umi/main.nf @@ -2,13 +2,14 @@ // BAM deduplication with UMI processing // -include { BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE as BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_TRANSCRIPTOME } from '../../../subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse' -include { BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS as BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME } from '../../../subworkflows/nf-core/bam_dedup_stats_samtools_umitools' -include { BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE as BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME } from '../../../subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse' -include { BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS as BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME } from '../../../subworkflows/nf-core/bam_dedup_stats_samtools_umitools' -include { BAM_SORT_STATS_SAMTOOLS } from '../../../subworkflows/nf-core/bam_sort_stats_samtools' -include { UMITOOLS_PREPAREFORRSEM } from '../../../modules/nf-core/umitools/prepareforrsem' -include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' +include { BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE as BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_TRANSCRIPTOME } from '../bam_dedup_stats_samtools_umicollapse' +include { BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS as BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME } from '../bam_dedup_stats_samtools_umitools' +include { BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE as BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME } from '../bam_dedup_stats_samtools_umicollapse' +include { BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS as BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME } from '../bam_dedup_stats_samtools_umitools' +include { BAM_SORT_STATS_SAMTOOLS } from '../bam_sort_stats_samtools' + +include { UMITOOLS_PREPAREFORRSEM } from '../../../modules/nf-core/umitools/prepareforrsem' +include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' workflow BAM_DEDUP_UMI { take: