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Copy quantification GTF to project-level results root (once, not per-sample) #42

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Merged
mtinti merged 1 commit into from
Jan 28, 2026
Merged

Copy quantification GTF to project-level results root (once, not per-sample) #42

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8 changes: 7 additions & 1 deletion rules/results.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -355,7 +355,9 @@ rule copy_results_all:
copy_fastq = config.get("copy_fastq", False),
copy_bam = config.get("copy_bam", False),
cleanup_processing = str(config.get("cleanup_processing", False)).lower(),
reference_dir = get_processing_path("reference")
reference_dir = get_processing_path("reference"),
gtf_file = config["processing_gtf_file"],
results_root = get_results_path()
log:
get_results_path("logs/copy_results_all.log")
shell:
Expand All @@ -379,6 +381,10 @@ rule copy_results_all:
echo "Timestamp: $(date)" >> {log}
echo "All individual copy operations completed successfully" >> {log}

# Copy GTF file used for quantification to results root
echo "Copying GTF file used for quantification" >> {log}
cp {params.gtf_file} {params.results_root}/ 2>> {log}

# Remove reference directory if cleanup is enabled
if [ "{params.cleanup_processing}" = "true" ]; then
if [ -d "{params.reference_dir}" ]; then
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