Merge pull request #18 from BIGslu/dev_kadm

Allowing skipping of picard step
BIGslu · Feb 10, 2025 · 0439f61 · 0439f61
2 parents 30a5cc1 + 990af80
commit 0439f61
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Showing 2 changed files with 6 additions and 5 deletions.
diff --git a/Snakefile_step2 b/Snakefile_step2
@@ -17,10 +17,11 @@ COUNT = expand("result/4_count/{sample}_feature_counts.tsv", sample=SAMPLES)
 
 rule all:
     input:
-        TRIM1 + TRIM2 + QC_trim_html + QC_trim_zip + BAM + BAM2 + BAI + FLAGSTAT + PICARD + COUNT,
+        TRIM1 + TRIM2 + QC_trim_html + QC_trim_zip + BAM + BAM2 + BAI + FLAGSTAT +
+        (PICARD if config["picard"] else []) + COUNT,
         'result/5_combined/combined_feature_counts.tsv',
         'result/5_combined/combined_flagstat.tsv',
-        'result/5_combined/combined_picard.tsv',
+        *( ['result/5_combined/combined_picard.tsv'] if config["picard"] else [] ),
         'log/benchmark/STAR_index.benchmark.txt',
         'log/benchmark/STAR_load.benchmark.txt'
 

diff --git a/Snakefile_step2_single b/Snakefile_step2_single
@@ -14,14 +14,14 @@ COUNT = expand("result/4_count/{sample}_feature_counts.tsv", sample=SAMPLES)
 
 rule all:
     input:
-        TRIM1 + QC_trim_html + QC_trim_zip + BAM + BAM2 + FLAGSTAT + PICARD + COUNT,
+        TRIM1 + QC_trim_html + QC_trim_zip + BAM + BAM2 + FLAGSTAT +
+        (PICARD if config["picard"] else []) + COUNT,
         'result/5_combined/combined_feature_counts.tsv',
         'result/5_combined/combined_flagstat.tsv',
-        'result/5_combined/combined_picard.tsv',
+        *( ['result/5_combined/combined_picard.tsv'] if config["picard"] else [] ),
         'log/benchmark/STAR_index.benchmark.txt',
         'log/benchmark/STAR_load.benchmark.txt'
 
-
 ##----------------------------------------##
 ## 1. Adapter removal & quality filtering ##
 ##----------------------------------------##