From 415f7ba92baca42f8719cb9246f9a5895e04719a Mon Sep 17 00:00:00 2001 From: mtinti Date: Tue, 27 Jan 2026 11:59:00 +0000 Subject: [PATCH] Copy quantification GTF to results root --- rules/results.smk | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/rules/results.smk b/rules/results.smk index 2d5f79b..6ea5265 100644 --- a/rules/results.smk +++ b/rules/results.smk @@ -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: @@ -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