From 678f1de3f180fdf0bbaec973186f2265cbe49105 Mon Sep 17 00:00:00 2001 From: Sam Nicholls Date: Thu, 14 May 2026 17:18:57 +0000 Subject: [PATCH] Use value channels for refs crossing samples --- .gitlab-ci.yml | 3 ++- subworkflows/transcriptome.nf | 4 ++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index f920a93..f88ffb8 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -135,7 +135,8 @@ docker-run: NF_WORKFLOW_OPTS: "--fastq test_data/smoke/de --sample_sheet test_data/smoke/sample_sheet_de.csv --ref_genome test_data/smoke/reference.fa --ref_annotation test_data/smoke/annotation.gtf --de_analysis --reference_level control --covariates batch" AFTER_NEXTFLOW_CMD: > test -f ${CI_PROJECT_NAME}/de_analysis/condition_treated_vs_control/results_dge.tsv && - test -f ${CI_PROJECT_NAME}/de_analysis/condition_treated_vs_control/results_dtu_transcript.tsv + test -f ${CI_PROJECT_NAME}/de_analysis/condition_treated_vs_control/results_dtu_transcript.tsv && + [ "$(find ${CI_PROJECT_NAME}/samples -type f -name 'gene_counts.tsv' | wc -l)" -eq 4 ] - if: $MATRIX_NAME == "invalid_mode" variables: NF_BEFORE_SCRIPT: ":" diff --git a/subworkflows/transcriptome.nf b/subworkflows/transcriptome.nf index 7d7f738..4b9d380 100644 --- a/subworkflows/transcriptome.nf +++ b/subworkflows/transcriptome.nf @@ -211,8 +211,8 @@ workflow transcriptome_analysis { log.warn(stdoutput.trim()) } } - analysis_annotation = prepared_reference_annotation.annotation - analysis_reference = prepared_reference_annotation.reference + analysis_annotation = prepared_reference_annotation.annotation.first() + analysis_reference = prepared_reference_annotation.reference.first() joint_bambu = runJointBambu( alignments