diff --git a/CHANGELOG.md b/CHANGELOG.md index a6a18bff..1c3b95cb 100644 --- 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 index 1fa95f31..e6a34f5f 100644 --- 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] })