From 779e3fe8a0d47c5e02c68f2e905fc00320b5ed58 Mon Sep 17 00:00:00 2001 From: Karthigayini Sivaprakasam Date: Mon, 7 Oct 2024 19:14:28 -0500 Subject: [PATCH 1/5] pv single filter version update --- vardict_workflow/run_processed_vardict.cwl | 76 +++++++++------------- 1 file changed, 32 insertions(+), 44 deletions(-) diff --git a/vardict_workflow/run_processed_vardict.cwl b/vardict_workflow/run_processed_vardict.cwl index 52502da..2c9dd54 100644 --- a/vardict_workflow/run_processed_vardict.cwl +++ b/vardict_workflow/run_processed_vardict.cwl @@ -10,8 +10,8 @@ inputs: type: File secondaryFiles: - .fai - 'sbg:x': 0 - 'sbg:y': 213.53125 + 'sbg:x': -79.38146209716797 + 'sbg:y': 249.81459045410156 - id: input_bam_case type: File secondaryFiles: @@ -28,12 +28,12 @@ inputs: 'sbg:y': 106.765625 - id: concat_output_name type: string - 'sbg:x': 513.37158203125 - 'sbg:y': 334.296875 + 'sbg:x': 740.790283203125 + 'sbg:y': 70.54559326171875 - id: stdout type: boolean - 'sbg:x': 513.37158203125 - 'sbg:y': 92.765625 + 'sbg:x': 847.7826538085938 + 'sbg:y': -11.541033744812012 - id: vardict_output_vcf_name type: string? 'sbg:x': 0 @@ -47,12 +47,6 @@ inputs: 'sbg:x': 227.29263305664062 'sbg:y': -49.30992126464844 outputs: - - id: txt - outputSource: - - pv_vardict_single_filter/txt - type: File - 'sbg:x': 759.164794921875 - 'sbg:y': 266.9140625 - id: concatenated_vcf outputSource: - variants_concat/concatenated_vcf @@ -65,18 +59,24 @@ outputs: type: File 'sbg:x': 397.9921875 'sbg:y': 590.5 - - id: single_filter_vcf + - id: txt + outputSource: + - pv_vardict_single_filter/txt + type: File + 'sbg:x': 501.0516662597656 + 'sbg:y': 446.3981628417969 + - id: vcf outputSource: - pv_vardict_single_filter/vcf type: File - 'sbg:x': 688.9921875 - 'sbg:y': 587.5 - - id: single_filter_vcf_complex + 'sbg:x': 667.1679077148438 + 'sbg:y': 454.6510925292969 + - id: vcf_complex outputSource: - pv_vardict_single_filter/vcf_complex type: File - 'sbg:x': 942.9921875 - 'sbg:y': 552.5 + 'sbg:x': 804.0721435546875 + 'sbg:y': 435.0933532714844 steps: - id: vardict in: @@ -109,30 +109,6 @@ steps: label: vardict 'sbg:x': 250.328125 'sbg:y': 185.53125 - - id: pv_vardict_single_filter - in: - - id: inputVCF - source: vardict/output - - id: tsampleName - source: sample_name - - id: alleledepth - default: 1 - - id: totalDepth - default: 20 - - id: tnRatio - default: 5 - - id: variantFraction - default: 0 - - id: minQual - default: 20 - out: - - id: txt - - id: vcf_complex - - id: vcf - run: >- - ../command_line_tools/postprocessing_variant_calls/0.1.5/pv_vardict_single_filter.cwl - 'sbg:x': 483 - 'sbg:y': 220 - id: variants_concat in: - id: fastaRef @@ -159,8 +135,20 @@ steps: - id: concatenated_vcf run: ../variant_postprocessing/variants_concat.cwl label: variants_concat - 'sbg:x': 759.164794921875 - 'sbg:y': 132.1484375 + 'sbg:x': 937.3206787109375 + 'sbg:y': 213.682373046875 + - id: pv_vardict_single_filter + in: + - id: inputVCF + source: vardict/output + out: + - id: txt + - id: vcf_complex + - id: vcf + run: >- + ../command_line_tools/postprocessing_variant_calls/0.2.3/pv_vardict_single_filter/pv_vardict_single_filter.cwl + 'sbg:x': 492.4954528808594 + 'sbg:y': 150.5911865234375 requirements: - class: SubworkflowFeatureRequirement $schemas: From 20364491049573e9670444f3ed57adfa871d8c78 Mon Sep 17 00:00:00 2001 From: Karthigayini Sivaprakasam Date: Mon, 7 Oct 2024 19:29:56 -0500 Subject: [PATCH 2/5] updating default values --- vardict_workflow/run_processed_vardict.cwl | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/vardict_workflow/run_processed_vardict.cwl b/vardict_workflow/run_processed_vardict.cwl index 2c9dd54..fd000ee 100644 --- a/vardict_workflow/run_processed_vardict.cwl +++ b/vardict_workflow/run_processed_vardict.cwl @@ -141,6 +141,18 @@ steps: in: - id: inputVCF source: vardict/output + - id: tsampleName + source: sample_name + - id: alleledepth + default: 1 + - id: totalDepth + default: 20 + - id: tnRatio + default: 1 + - id: variantFraction + default: 0.00005 + - id: minQual + default: 0 out: - id: txt - id: vcf_complex From 07344d6717931a016f6a3dfd6e5caca4fc117502 Mon Sep 17 00:00:00 2001 From: Karthigayini Sivaprakasam Date: Mon, 7 Oct 2024 19:36:25 -0500 Subject: [PATCH 3/5] renaming output Files --- vardict_workflow/run_processed_vardict.cwl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/vardict_workflow/run_processed_vardict.cwl b/vardict_workflow/run_processed_vardict.cwl index fd000ee..fd3bc65 100644 --- a/vardict_workflow/run_processed_vardict.cwl +++ b/vardict_workflow/run_processed_vardict.cwl @@ -65,13 +65,13 @@ outputs: type: File 'sbg:x': 501.0516662597656 'sbg:y': 446.3981628417969 - - id: vcf + - id: single_filter_vcf outputSource: - pv_vardict_single_filter/vcf type: File 'sbg:x': 667.1679077148438 'sbg:y': 454.6510925292969 - - id: vcf_complex + - id: single_filter_vcf_complex outputSource: - pv_vardict_single_filter/vcf_complex type: File From 8b7a39702349412131757fd2b7b0e23ca9c0a6a4 Mon Sep 17 00:00:00 2001 From: Karthigayini Sivaprakasam Date: Mon, 7 Oct 2024 20:37:24 -0500 Subject: [PATCH 4/5] Update command_line_tools --- command_line_tools | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/command_line_tools b/command_line_tools index 082f3a3..189f6c9 160000 --- a/command_line_tools +++ b/command_line_tools @@ -1 +1 @@ -Subproject commit 082f3a3177a845acfd717ad1783ae5b6a668095e +Subproject commit 189f6c974a9d825b54380e19b05ec3042a0d060e From e17a416da9bc097067249d7ea32b3c6345017106 Mon Sep 17 00:00:00 2001 From: Ronak Shah Date: Tue, 15 Oct 2024 11:37:34 -0400 Subject: [PATCH 5/5] Update command_line_tools --- command_line_tools | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/command_line_tools b/command_line_tools index 189f6c9..b8c66ac 160000 --- a/command_line_tools +++ b/command_line_tools @@ -1 +1 @@ -Subproject commit 189f6c974a9d825b54380e19b05ec3042a0d060e +Subproject commit b8c66acf773e623f94947a16f969dc6d53d434f9