From fb7117c65c0f9673a871ef906c1fd4837027421d Mon Sep 17 00:00:00 2001 From: Luca Beltrame Date: Wed, 18 Jan 2023 13:43:35 +0100 Subject: [PATCH] Fix typo preventing the use of UMI processing with HISAT2 BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME was mistakenly written as BAM_DEDUP_STATS_SAMTOOLS_UMI_UMITOOLS_GENOME, causing the workflow to error out in case the UMI option was set when using HISAT2. Fixes #929. --- workflows/rnaseq.nf | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf index c22c8688c..6dc57e72d 100755 --- a/workflows/rnaseq.nf +++ b/workflows/rnaseq.nf @@ -522,19 +522,19 @@ workflow RNASEQ { // SUBWORKFLOW: Remove duplicate reads from BAM file based on UMIs // if (params.with_umi) { - BAM_DEDUP_STATS_SAMTOOLS_UMI_UMITOOLS_GENOME ( + BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME ( ch_genome_bam.join(ch_genome_bam_index, by: [0]), params.umitools_dedup_stats ) - ch_genome_bam = BAM_DEDUP_STATS_SAMTOOLS_UMI_UMITOOLS_GENOME.out.bam - ch_genome_bam_index = BAM_DEDUP_STATS_SAMTOOLS_UMI_UMITOOLS_GENOME.out.bai - ch_samtools_stats = BAM_DEDUP_STATS_SAMTOOLS_UMI_UMITOOLS_GENOME.out.stats - ch_samtools_flagstat = BAM_DEDUP_STATS_SAMTOOLS_UMI_UMITOOLS_GENOME.out.flagstat - ch_samtools_idxstats = BAM_DEDUP_STATS_SAMTOOLS_UMI_UMITOOLS_GENOME.out.idxstats + ch_genome_bam = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.bam + ch_genome_bam_index = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.bai + ch_samtools_stats = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.stats + ch_samtools_flagstat = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.flagstat + ch_samtools_idxstats = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.idxstats if (params.bam_csi_index) { - ch_genome_bam_index = BAM_DEDUP_STATS_SAMTOOLS_UMI_UMITOOLS_GENOME.out.csi + ch_genome_bam_index = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.csi } - ch_versions = ch_versions.mix(BAM_DEDUP_STATS_SAMTOOLS_UMI_UMITOOLS_GENOME.out.versions) + ch_versions = ch_versions.mix(BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.versions) } }