kfukuta/wf-transcriptomes-v202
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Publish refs for IGV only when necessary [CW-7280]

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This commit is contained in:
Sam Nicholls 2026-05-27 12:24:07 +00:00
parent d73b9a2721
commit 262f49944e
1 changed files with 23 additions and 19 deletions
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42
main.nf
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@ -293,28 +293,31 @@ workflow {
pipeline_run = wf(processed_samples, sample_sheet, ref_genome, ref_annotation) pipeline_run = wf(processed_samples, sample_sheet, ref_genome, ref_annotation)
results = pipeline_run.results results = pipeline_run.results
reference_basename = file(params.ref_genome).getName()
if (params.igv) { if (params.igv) {
results = results // TODO lib/ref should be responsible for writing NEW outputs to a location of our choosing
.concat(ref_genome.map { fasta, faidx -> [fasta, "igv_reference"] }) // until then, we'll handle emission here. we'll emit (path:str, to_publish:bool) tuples for ref-related files
.concat(ref_genome.map { fasta, faidx -> [faidx, "igv_reference"] }) // and pass those to both igv_ref_paths and results (for publishing)
is_compressed = params.ref_genome.toLowerCase().endsWith("gz") is_compressed = params.ref_genome.toLowerCase().endsWith("gz")
if (is_compressed) { if (is_compressed) {
// ref files are directly publish into output ref_files = prepared_reference.ref_gzidx | flatten | map {
igv_files = Channel.of("${reference_basename}") boolean to_publish = it.toString().startsWith("${workflow.workDir}")
igv_index_paths = prepared_reference.ref_gzidx.map { [it, to_publish]
fasta, faidx, gzidx -> "${faidx.getName()}" }
}
.concat(prepared_reference.ref_gzidx.map {
fasta, faidx, gzidx -> "${gzidx.getName()}"
})
} else { } else {
igv_files = Channel.of("igv_reference/${reference_basename}") ref_files = ref_genome | flatten | map {
igv_index_paths = ref_genome.map { fasta, faidx -> "igv_reference/${faidx.getName()}"} boolean to_publish = it.toString().startsWith("${workflow.workDir}")
[it, to_publish]
}
} }
// convert files set to_publish to their IGV location
igv_ref_paths = ref_files.map {
path, to_publish -> to_publish ? "reference/${path.getName()}" : path.toString()
}
publish_ref_paths = ref_files
.filter { it[1] } // select files set to_publish
.map { [ it[0], "reference" ] }
igv_alignment_paths = processed_samples igv_alignment_paths = processed_samples
.map { meta, bam, bai, stat -> [ .map { meta, bam, bai, stat -> [
meta.src_xam ?: "${meta.alias},samples/${meta.alias}/alignment/reads.bam", meta.src_xam ?: "${meta.alias},samples/${meta.alias}/alignment/reads.bam",
@ -330,8 +333,7 @@ workflow {
(paths instanceof List ? paths : [paths]).collect { path -> "${alias},samples/${alias}/mods/${path.name}" } (paths instanceof List ? paths : [paths]).collect { path -> "${alias},samples/${alias}/mods/${path.name}" }
} }
igv_files = igv_files igv_files = igv_ref_paths
.concat(igv_index_paths)
.concat(igv_alignment_paths) .concat(igv_alignment_paths)
.concat(igv_bigwigs) .concat(igv_bigwigs)
.collectFile(name: "igv-files.txt", newLine: true, sort: false) .collectFile(name: "igv-files.txt", newLine: true, sort: false)
@ -343,7 +345,9 @@ workflow {
[:], [:],
false false
) )
results = results.concat(igv_conf.map { [it, null] }) results = results
.concat(publish_ref_paths)
.concat(igv_conf.map { [it, null] })
} }
publishResults(results) publishResults(results)
} }