From 77145db2b1ebb095a8ef8319298bc2a60c827425 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 12 Oct 2023 19:46:01 +0100 Subject: [PATCH] Fix channel issues after updating nf-core/modules --- subworkflows/local/align_star/main.nf | 4 ++-- subworkflows/local/prepare_genome/main.nf | 2 +- workflows/rnaseq.nf | 6 +++--- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/align_star/main.nf b/subworkflows/local/align_star/main.nf index 479ed2379..1dba0c085 100644 --- a/subworkflows/local/align_star/main.nf +++ b/subworkflows/local/align_star/main.nf @@ -9,8 +9,8 @@ include { BAM_SORT_STATS_SAMTOOLS } from '../../nf-core/bam_sort_stats_samtools' workflow ALIGN_STAR { take: reads // channel: [ val(meta), [ reads ] ] - index // channel: /path/to/star/index/ - gtf // channel: /path/to/genome.gtf + index // channel: [ val(meta), [ index ] ] + gtf // channel: [ val(meta), [ gtf ] ] star_ignore_sjdbgtf // boolean: when using pre-built STAR indices do not re-extract and use splice junctions from the GTF file seq_platform // string : sequencing platform seq_center // string : sequencing center diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index 200957cda..eceb2c1ce 100644 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -191,7 +191,7 @@ workflow PREPARE_GENOME { ch_star_index = STAR_GENOMEGENERATE_IGENOMES ( ch_fasta, ch_gtf ).index ch_versions = ch_versions.mix(STAR_GENOMEGENERATE_IGENOMES.out.versions) } else { - ch_star_index = STAR_GENOMEGENERATE ( ch_fasta, ch_gtf ).index + ch_star_index = STAR_GENOMEGENERATE ( ch_fasta.map { [ [:], it ] }, ch_gtf.map { [ [:], it ] } ).index.map { it[1] } ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions) } } diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf index f2dd49a0b..955a727c3 100755 --- a/workflows/rnaseq.nf +++ b/workflows/rnaseq.nf @@ -382,8 +382,8 @@ workflow RNASEQ { if (!params.skip_alignment && params.aligner == 'star_salmon') { ALIGN_STAR ( ch_filtered_reads, - PREPARE_GENOME.out.star_index, - PREPARE_GENOME.out.gtf, + PREPARE_GENOME.out.star_index.map { [ [:], it ] }, + PREPARE_GENOME.out.gtf.map { [ [:], it ] }, params.star_ignore_sjdbgtf, '', params.seq_center ?: '', @@ -729,7 +729,7 @@ workflow RNASEQ { if (!params.skip_qualimap) { QUALIMAP_RNASEQ ( ch_genome_bam, - PREPARE_GENOME.out.gtf + PREPARE_GENOME.out.gtf.map { [ [:], it ] } ) ch_qualimap_multiqc = QUALIMAP_RNASEQ.out.results ch_versions = ch_versions.mix(QUALIMAP_RNASEQ.out.versions.first())