kfukuta/wf-transcriptomes-v202
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Merge branch 'de-validation-ndr-fixes' into 'dev'

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Fix DE validation gating and per-sample NDR

See merge request epi2melabs/workflows/wf-transcriptomes!238
This commit is contained in:
Chris Wright 2026-05-06 08:16:28 +00:00
commit 265b462cc6
2 changed files with 5 additions and 2 deletions
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5
subworkflows/differential_expression.nf
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@ -31,6 +31,7 @@ process runDifferentialAnalysis {
path transcript_rds path transcript_rds
path gene_rds path gene_rds
path sample_sheet path sample_sheet
path validation_token
output: output:
path "de_analysis", emit: dir path "de_analysis", emit: dir
script: script:
@ -55,8 +56,8 @@ workflow differential_expression {
gene_rds gene_rds
sample_sheet sample_sheet
main: main:
checkExperimentDesign(sample_sheet) validated = checkExperimentDesign(sample_sheet)
results = runDifferentialAnalysis(transcript_rds, gene_rds, sample_sheet) results = runDifferentialAnalysis(transcript_rds, gene_rds, sample_sheet, validated.ok)
emit: emit:
dir = results.dir dir = results.dir
} }

2
subworkflows/transcriptome.nf
View File

@ -209,6 +209,7 @@ process runPerSampleBambu {
tuple val(meta), path("${meta.alias}/bambu_genes.rds"), emit: gene_rds tuple val(meta), path("${meta.alias}/bambu_genes.rds"), emit: gene_rds
tuple val(meta), path("${meta.alias}/transcript_metadata.tsv"), emit: transcript_metadata tuple val(meta), path("${meta.alias}/transcript_metadata.tsv"), emit: transcript_metadata
script: script:
String ndr_arg = params.ndr != null ? "--ndr ${params.ndr}" : ""
""" """
supeRglue bambu \ supeRglue bambu \
--bam_path "${bam}" \ --bam_path "${bam}" \
@ -217,6 +218,7 @@ process runPerSampleBambu {
--genome "${reference}" \ --genome "${reference}" \
--transcriptome_mode "${params.transcriptome_mode}" \ --transcriptome_mode "${params.transcriptome_mode}" \
--threads ${task.cpus} \ --threads ${task.cpus} \
${ndr_arg} \
--out_dir "${meta.alias}" --out_dir "${meta.alias}"
""" """
} }