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Restore IGV [CW-7234]

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Natalia Garcia 2026-05-18 09:41:49 +00:00
parent 855fbb69b2
commit 4dfd5f06e7
1 changed files with 46 additions and 38 deletions
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@ -228,42 +228,6 @@ workflow pipeline {
.concat(transcriptome.joint_sqanti_dir.map { [it, "cohort"] }) .concat(transcriptome.joint_sqanti_dir.map { [it, "cohort"] })
.concat(transcriptome.sample_sqanti_dirs.map { meta, sqanti_dir -> [sqanti_dir, "samples/${meta.alias}"] }) .concat(transcriptome.sample_sqanti_dirs.map { meta, sqanti_dir -> [sqanti_dir, "samples/${meta.alias}"] })
reference_basename = file(params.ref_genome).getName()
if (params.igv) {
//todo ???
//results = results
// .concat(transcriptome.reference.map { [it, "igv_reference"] })
// .concat(transcriptome.reference_fai.map { [it, "igv_reference"] })
// .concat(transcriptome.reference_gzi.map { [it, "igv_reference"] })
results = Channel.empty()
//igv_index_paths = transcriptome.reference_fai
// .map { "igv_reference/${it.getName()}" }
// .concat(transcriptome.reference_gzi.map { "igv_reference/${it.getName()}" })
igv_index_paths = Channel.empty()
igv_alignment_paths = reads
.map { meta, bam, bai, stat -> [
meta.src_xam ?: "cohort/alignments/${meta.alias}/reads.bam",
meta.src_xai ?: "cohort/alignments/${meta.alias}/reads.bam.bai"
] }
.flatten()
igv_files = Channel.of("igv_reference/${reference_basename}")
.concat(igv_index_paths)
.concat(igv_alignment_paths)
.collectFile(name: "igv-files.txt", newLine: true, sort: false)
igv_conf = configure_igv(
igv_files,
"",
[displayMode: "SQUISHED", colorBy: "strand"],
[:],
false
)
results = results.concat(igv_conf.map { [it, null] })
}
if (params.de_analysis) { if (params.de_analysis) {
results = results.concat(de_dir.map { [it, null] }) results = results.concat(de_dir.map { [it, null] })
} }
@ -351,11 +315,55 @@ workflow {
throw new Exception("No samples with reads were available for transcriptome analysis.") throw new Exception("No samples with reads were available for transcriptome analysis.")
} }
processed_samples = analysis_samples processed_samples = analysis_samples
pipeline_run = pipeline(processed_samples, sample_sheet, ref_genome, ref_annotation) pipeline_run = pipeline(processed_samples, sample_sheet, ref_genome, ref_annotation)
publishResults(pipeline_run.results) results = pipeline_run.results
reference_basename = file(params.ref_genome).getName()
if (params.igv) {
results = results
.concat(ref_genome.map { fasta, faidx -> [fasta, "igv_reference"] })
.concat(ref_genome.map { fasta, faidx -> [faidx, "igv_reference"] })
is_compressed = params.ref_genome.toLowerCase().endsWith("gz")
if (is_compressed) {
// ref files are directly publish into output
igv_files = Channel.of("${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()}"
})
} else {
igv_files = Channel.of("igv_reference/${reference_basename}")
igv_index_paths = ref_genome.map { fasta, faidx -> "igv_reference/${faidx.getName()}"}
}
igv_alignment_paths = processed_samples
.map { meta, bam, bai, stat -> [
meta.src_xam ?: "${meta.alias},cohort/alignments/${meta.alias}/reads.bam",
meta.src_xai ?: "${meta.alias},cohort/alignments/${meta.alias}/reads.bam.bai"
] }
.flatten()
igv_files = igv_files
.concat(igv_index_paths)
.concat(igv_alignment_paths)
.collectFile(name: "igv-files.txt", newLine: true, sort: false)
igv_conf = configure_igv(
igv_files,
"",
[displayMode: "SQUISHED", colorBy: "strand"],
[:],
false
)
results = results.concat(igv_conf.map { [it, null] })
}
publishResults(results)
} }