change tumoronly to tumor_only

Clinical-Genomics · Aug 20, 2021 · d21ac02 · d21ac02
1 parent 6f44a90
commit d21ac02
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Showing 3 changed files with 15 additions and 15 deletions.
diff --git a/BALSAMIC/commands/report/deliver.py b/BALSAMIC/commands/report/deliver.py
@@ -97,12 +97,12 @@ def deliver(context, sample_config, analysis_type, rules_to_deliver,
         "vep_somatic",
         "vep_germline",
         "vep_stat",
-        "bcftools_filter_vardict_tumoronly",
+        "bcftools_filter_vardict_tumor_only",
         "bcftools_filter_vardict_tumor_normal",
-        "bcftools_filter_tnscope_tumoronly",
+        "bcftools_filter_tnscope_tumor_only",
         "bcftools_filter_tnscope_tumor_normal",
         "bcftools_filter_manta",
-        "bcftools_intersect_tumoronly",
+        "bcftools_intersect_tumor_only",
         "genmod_score_vardict",
         "mergeBam_tumor",
         "mergeBam_normal",

diff --git a/BALSAMIC/snakemake_rules/annotation/varcaller_filter_tumor_only.rule b/BALSAMIC/snakemake_rules/annotation/varcaller_filter_tumor_only.rule
@@ -2,14 +2,14 @@
 # coding: utf-8
 # NGS filters for various scenarios
 
-rule bcftools_filter_vardict_tumoronly:
+rule bcftools_filter_vardict_tumor_only:
   input:
     vcf = vep_dir + "{var_type}.somatic.{case_name}.vardict.all.vcf.gz",
   output:
     vcf_filtered = vep_dir + "{var_type}.somatic.{case_name}.vardict.all.filtered.vcf.gz",
     vcf_pass = vep_dir + "{var_type}.somatic.{case_name}.vardict.all.filtered.pass.vcf.gz",
   benchmark:
-    Path(benchmark_dir, 'bcftools_filter_vardict_tumoronly_' + "{var_type}.somatic.{case_name}.tsv").as_posix()
+    Path(benchmark_dir, 'bcftools_filter_vardict_tumor_only_' + "{var_type}.somatic.{case_name}.tsv").as_posix()
   singularity:
     Path(singularity_image, config["bioinfo_tools"].get("bcftools") + ".sif").as_posix()
   params:
@@ -23,7 +23,7 @@ rule bcftools_filter_vardict_tumoronly:
     pop_freq = [VARDICT.pop_freq.tag_value, VARDICT.pop_freq.filter_name],
     case_name =  '{case_name}'
   threads:
-    get_threads(cluster_config, 'bcftools_filter_vardict_tumoronly')
+    get_threads(cluster_config, 'bcftools_filter_vardict_tumor_only')
   message:
     "Filtering vardict tumor-only annotated variants using bcftools on {params.case_name}"
   shell:

diff --git a/BALSAMIC/snakemake_rules/annotation/varcaller_wgs_filter_tumor_only.rule b/BALSAMIC/snakemake_rules/annotation/varcaller_wgs_filter_tumor_only.rule
@@ -2,14 +2,14 @@
 # coding: utf-8
 # NGS filters for various scenarios
 
-rule bcftools_filter_tnscope_tumoronly:
+rule bcftools_filter_tnscope_tumor_only:
   input:
     vcf = vep_dir + "{var_type}.somatic.{case_name}.tnscope.all.vcf.gz",
     wgs_calling_file = config["reference"]["wgs_calling_interval"]
   output:
     vcf_filtered = vep_dir + "{var_type}.somatic.{case_name}.tnscope_isec.filtered.vcf.gz",
   benchmark:
-    Path(benchmark_dir, 'bcftools_filter_tnscope_tumoronly_' + "{var_type}.somatic.{case_name}.tsv").as_posix()
+    Path(benchmark_dir, 'bcftools_filter_tnscope_tumor_only_' + "{var_type}.somatic.{case_name}.tsv").as_posix()
   singularity:
     Path(singularity_image,config[ "bioinfo_tools" ].get("bcftools") + ".sif").as_posix()
   params:
@@ -24,7 +24,7 @@ rule bcftools_filter_tnscope_tumoronly:
     sor = [SENTIEON_CALLER.sor.tag_value, SENTIEON_CALLER.sor.filter_name],
     case_name = '{case_name}'
   threads: 
-    get_threads(cluster_config, 'bcftools_filter_tnscope_tumoronly')
+    get_threads(cluster_config, 'bcftools_filter_tnscope_tumor_only')
   message:
     "Filtering wgs tumor-only tnscope annotated variants using bcftools on {params.case_name}"
   shell:
@@ -47,14 +47,14 @@ bcftools view -f PASS --threads {threads} --regions-file {input.wgs_calling_file
 tabix -p vcf -f {output.vcf_filtered};
     """
 
-rule bcftools_filter_tnhaplotyper_tumoronly:
+rule bcftools_filter_tnhaplotyper_tumor_only:
   input:
     vcf = vep_dir + "{var_type}.somatic.{case_name}.tnhaplotyper.all.vcf.gz",
     wgs_calling_file = config["reference"]["wgs_calling_interval"]
   output:
     vcf_filtered = vep_dir + "{var_type}.somatic.{case_name}.tnhaplotyper_isec.filtered.vcf.gz",
   benchmark:
-    Path(benchmark_dir, 'bcftools_filter_tnhaplotyper_tumoronly_' + "{var_type}.somatic.{case_name}.tsv").as_posix()
+    Path(benchmark_dir, 'bcftools_filter_tnhaplotyper_tumor_only_' + "{var_type}.somatic.{case_name}.tsv").as_posix()
   singularity:
     Path(singularity_image, config[ "bioinfo_tools" ].get("bcftools") + ".sif").as_posix()
   params:
@@ -68,7 +68,7 @@ rule bcftools_filter_tnhaplotyper_tumoronly:
     qss = [SENTIEON_CALLER.qss.tag_value, SENTIEON_CALLER.qss.filter_name],
     case_name = '{case_name}'
   threads: 
-    get_threads(cluster_config, 'bcftools_filter_tnhaplotyper_tumoronly')
+    get_threads(cluster_config, 'bcftools_filter_tnhaplotyper_tumor_only')
   message:
     "Filtering wgs tumor-only tnhaplotyper annotated variants using bcftools on {params.case_name}"
   shell:
@@ -90,15 +90,15 @@ bcftools view -f PASS --threads {threads} --regions-file {input.wgs_calling_file
 tabix -p vcf -f {output.vcf_filtered};
     """
 
-rule bcftools_intersect_tumoronly:
+rule bcftools_intersect_tumor_only:
   input:
     tnscope = vep_dir + "{var_type}.somatic.{case_name}.tnscope_isec.filtered.vcf.gz",
     tnhaplotyper = vep_dir + "{var_type}.somatic.{case_name}.tnhaplotyper_isec.filtered.vcf.gz"
   output:
     vcf_filtered = vep_dir + "{var_type}.somatic.{case_name}.tnscope.filtered.vcf.gz",
     vcf_pass = vep_dir + "{var_type}.somatic.{case_name}.tnscope.filtered.pass.vcf.gz",
   benchmark:
-    Path(benchmark_dir, 'bcftools_intersect_tumoronly_' + "{var_type}.somatic.{case_name}.tsv").as_posix()
+    Path(benchmark_dir, 'bcftools_intersect_tumor_only_' + "{var_type}.somatic.{case_name}.tsv").as_posix()
   singularity:
     Path(singularity_image,config[ "bioinfo_tools" ].get("bcftools") + ".sif").as_posix()
   params:
@@ -107,7 +107,7 @@ rule bcftools_intersect_tumoronly:
     housekeeper_id = {"id": config["analysis"]["case_id"], "tags": "clinical"},
     case_name = '{case_name}'
   threads: 
-    get_threads(cluster_config, 'bcftools_intersect_tumoronly')
+    get_threads(cluster_config, 'bcftools_intersect_tumor_only')
   message:
     "Retrieving common annotated variants between tnscope and tnhaplotyper using bcftools for {params.case_name}"
   shell: