Merge main into branch

uclahs-cds · Sep 25, 2023 · 16346a3 · 16346a3
2 parents 745a5ec + a860454
commit 16346a3
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 - Fix blarchive compression log output directory
+- Delay readcount compression until original file is no longer needed
 
 ## [7.0.0-rc.1] - 2023-08-28
 

diff --git a/module/somaticsniper.nf b/module/somaticsniper.nf
@@ -55,8 +55,12 @@ workflow somaticsniper {
         generate_ReadCount_bam_readcount(params.reference,create_ReadCountPosition_SomaticSniper.out.snp_positions, tumor_bam, tumor_index)
         filter_FalsePositive_SomaticSniper(apply_TumorIndelFilter_SomaticSniper.out.vcf_tumor, generate_ReadCount_bam_readcount.out.readcount)
         call_HighConfidenceSNV_SomaticSniper(filter_FalsePositive_SomaticSniper.out.fp_pass)
-        compress_file_blarchive(generate_ReadCount_bam_readcount.out.readcount
-            .map{ it -> ['readcount', it] })
+        // combining to delay compression until after filtering step
+        compress_file_blarchive(
+            generate_ReadCount_bam_readcount.out.readcount
+                .combine(filter_FalsePositive_SomaticSniper.out.fp_pass.collect())
+                .map{ it -> ['readcount', it[0]] }
+            )
         // rename_samples_BCFtools needs bgzipped input
         compress_index_VCF_hc(call_HighConfidenceSNV_SomaticSniper.out.hc
             .map{ it -> ['SNV', it] })