fix: delivery rules (#1619)

fix delivery of files

Author: mathiasbio

BALSAMIC/constants/rules.py

@@ -210,13 +210,15 @@
     "svdb_merge_tumor_normal",
     "bcftools_filter_sv_research",
     "bcftools_filter_sv_clinical",
-    "tiddit_sv_tumor_only",
-    "tiddit_sv_tumor_normal",
+    "tiddit_sv_tumor_normal_wgs",
+    "tiddit_sv_tumor_only_wgs",
     # CNVs
     "delly_cnv_tumor_only",
     "delly_cnv_tumor_normal",
-    "ascat_tumor_normal",
-    "cnvpytor_tumor_only",
+    "delly_cnv_tumor_normal_wgs",
+    "delly_cnv_tumor_only_wgs",
+    "ascat_tumor_normal_wgs",
+    "cnvpytor_tumor_only_wgs",
     "vcf2cytosure_convert_tumor_only",
     "vcf2cytosure_convert_tumor_normal",
     "cnvkit_segment_CNV_research",

BALSAMIC/constants/workflow_profile/config.yaml

@@ -377,7 +377,7 @@ set-resources:
     mem_mb: min(230000, 20000 * attempt)
   bcftools_filter_tnscope_research_tumor_only:
     runtime: 280
-    mem_mb: 2min(230000, 0000 * attempt)
+    mem_mb: min(230000, 20000 * attempt)
   bcftools_filter_TNscope_umi_clinical_tumor_only:
     runtime: 280
     mem_mb: min(230000, 5000 * attempt)

BALSAMIC/snakemake_rules/annotation/varcaller_filter_tumor_only_wgs.rule

@@ -23,7 +23,7 @@ rule bcftools_filter_tnscope_research_tumor_only:
     "Filtering WGS tumor-only tnscope annotated research variants using bcftools for {params.case_name}"
   shell:
     """
-grep -v '^@' {input.wgs_calling_file} > {input.wgs_calling_file}.bed
+grep -v '^@' {input.wgs_calling_file} > {input.wgs_calling_file}.bed ;
 
 bcftools view --threads {threads} --regions-file {input.wgs_calling_file}.bed {input.vcf_snv_research} | \
 bcftools filter --threads {threads} --include 'INFO/GNOMADAF_popmax <= {params.pop_freq[0]} || INFO/GNOMADAF_popmax == \".\"' --soft-filter '{params.pop_freq[1]}' --mode '+' | \

BALSAMIC/snakemake_rules/variant_calling/somatic_cnv_tumor_normal_tga.rule

@@ -291,7 +291,7 @@ rule delly_cnv_tumor_normal:
         rd_delly = vcf_dir + "CNV.somatic." + config["analysis"]["case_id"] + ".dellycnv.cov.gz",
         namemap= vcf_dir + "CNV.somatic." + config["analysis"]["case_id"] + ".dellycnv.sample_name_map",
     benchmark:
-        benchmark_dir + 'delly_cnv_tumor_only_' + config["analysis"]["case_id"] + ".tsv"
+        benchmark_dir + 'delly_cnv_tumor_normal_' + config["analysis"]["case_id"] + ".tsv"
     singularity:
         Path(singularity_image, config["bioinfo_tools"].get("delly") + ".sif").as_posix(),
     params: