kfukuta/wf-transcriptomes-v202
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Merge branch 'unnecessary-igv' into 'dev'

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Publish refs for IGV only when necessary [CW-7280]

See merge request epi2melabs/workflows/wf-transcriptomes!306
This commit is contained in:
Sam Nicholls 2026-05-27 12:24:08 +00:00
commit 9cba80832d
1 changed files with 23 additions and 19 deletions
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42
main.nf
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@ -294,28 +294,31 @@ workflow {
pipeline_run = wf(processed_samples, sample_sheet, ref_genome, ref_annotation)
results = pipeline_run.results
reference_basename = file(params.ref_genome).getName()
if (params.igv) {
results = results
.concat(ref_genome.map { fasta, faidx -> [fasta, "igv_reference"] })
.concat(ref_genome.map { fasta, faidx -> [faidx, "igv_reference"] })
// TODO lib/ref should be responsible for writing NEW outputs to a location of our choosing
// until then, we'll handle emission here. we'll emit (path:str, to_publish:bool) tuples for ref-related files
// and pass those to both igv_ref_paths and results (for publishing)
is_compressed = params.ref_genome.toLowerCase().endsWith("gz")
if (is_compressed) {
// ref files are directly publish into output
igv_files = Channel.of("${reference_basename}")
igv_index_paths = prepared_reference.ref_gzidx.map {
fasta, faidx, gzidx -> "${faidx.getName()}"
}
.concat(prepared_reference.ref_gzidx.map {
fasta, faidx, gzidx -> "${gzidx.getName()}"
})
ref_files = prepared_reference.ref_gzidx | flatten | map {
boolean to_publish = it.toString().startsWith("${workflow.workDir}")
[it, to_publish]
}
} else {
igv_files = Channel.of("igv_reference/${reference_basename}")
igv_index_paths = ref_genome.map { fasta, faidx -> "igv_reference/${faidx.getName()}"}
ref_files = ref_genome | flatten | map {
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
.map { meta, bam, bai, stat -> [
meta.src_xam ?: "${meta.alias},samples/${meta.alias}/alignment/reads.bam",
@ -331,8 +334,7 @@ workflow {
(paths instanceof List ? paths : [paths]).collect { path -> "${alias},samples/${alias}/mods/${path.name}" }
}
igv_files = igv_files
.concat(igv_index_paths)
igv_files = igv_ref_paths
.concat(igv_alignment_paths)
.concat(igv_bigwigs)
.collectFile(name: "igv-files.txt", newLine: true, sort: false)
@ -344,7 +346,9 @@ workflow {
[:],
false
)
results = results.concat(igv_conf.map { [it, null] })
results = results
.concat(publish_ref_paths)
.concat(igv_conf.map { [it, null] })
}
publishResults(results)
}