kfukuta/wf-transcriptomes-v202
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Merge branch 'unbreak-multisample' into 'dev'

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Use value channels for refs crossing samples

See merge request epi2melabs/workflows/wf-transcriptomes!257
This commit is contained in:
Sam Nicholls 2026-05-14 17:18:57 +00:00
commit a08e23849d
2 changed files with 4 additions and 3 deletions
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3
.gitlab-ci.yml
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@ -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: ":"

4
subworkflows/transcriptome.nf
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@ -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