🔧 do not rename reheadered vcfs

kids-first · Nov 7, 2024 · dc7c16e · dc7c16e
1 parent c7c0fd5
commit dc7c16e
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Showing 5 changed files with 5 additions and 5 deletions.
diff --git a/sub_workflows/kfdrc_lancet_sub_wf.cwl b/sub_workflows/kfdrc_lancet_sub_wf.cwl
@@ -94,7 +94,7 @@ steps:
       input_vcf: sort_merge_lancet_vcf/merged_vcf
       output_filename:
         valueFrom: |
-          $(inputs.input_vcf.basename.replace(".vcf", ".reheadered.vcf"))
+          $(inputs.input_vcf.basename)
       new_normal_name: input_normal_name
       new_tumor_name: input_tumor_name
       old_normal_name: old_normal_name

diff --git a/sub_workflows/kfdrc_manta_sub_wf.cwl b/sub_workflows/kfdrc_manta_sub_wf.cwl
@@ -57,7 +57,7 @@ steps:
       input_vcf: manta/output_sv
       output_filename:
         valueFrom: |
-          $(inputs.input_vcf.basename.replace(".vcf", ".reheadered.vcf"))
+          $(inputs.input_vcf.basename)
       new_normal_name: input_normal_name
       new_tumor_name: input_tumor_name
       old_normal_name: old_normal_name

diff --git a/sub_workflows/kfdrc_mutect2_sub_wf.cwl b/sub_workflows/kfdrc_mutect2_sub_wf.cwl
@@ -139,7 +139,7 @@ steps:
       input_vcf: filter_mutect2_vcf/filtered_vcf
       output_filename:
         valueFrom: |
-          $(inputs.input_vcf.basename.replace(".vcf", ".reheadered.vcf"))
+          $(inputs.input_vcf.basename)
       new_normal_name: input_normal_name
       new_tumor_name: input_tumor_name
       old_normal_name: old_normal_name

diff --git a/sub_workflows/kfdrc_strelka2_sub_wf.cwl b/sub_workflows/kfdrc_strelka2_sub_wf.cwl
@@ -95,7 +95,7 @@ steps:
       input_vcf: merge_strelka2_vcf/merged_vcf
       output_filename:
         valueFrom: |
-          $(inputs.input_vcf.basename.replace(".vcf", ".reheadered.vcf"))
+          $(inputs.input_vcf.basename)
       new_normal_name: input_normal_name
       new_tumor_name: input_tumor_name
       old_normal_name:

diff --git a/sub_workflows/kfdrc_vardict_sub_wf.cwl b/sub_workflows/kfdrc_vardict_sub_wf.cwl
@@ -101,7 +101,7 @@ steps:
       input_vcf: sort_merge_vardict_vcf/merged_vcf
       output_filename:
         valueFrom: |
-          $(inputs.input_vcf.basename.replace(".vcf", ".reheadered.vcf"))
+          $(inputs.input_vcf.basename)
       new_normal_name: input_normal_name
       new_tumor_name: input_tumor_name
       old_normal_name: old_normal_name