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main->develop #23

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merged 11 commits into from
Aug 8, 2023
Merged

main->develop #23

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a296e03
Merge branch 'release/1.1.1'
rhshah May 18, 2023
2ededa9
Merge branch 'release/1.1.2'
rhshah May 18, 2023
cc582ab
Merge branch 'release/1.1.3'
rhshah May 23, 2023
cd2f695
updating nucleo_aggregate_visualize.cwl
carmelinacharalambous Jul 20, 2023
7ef8f9f
before publish
rhshah Aug 8, 2023
a7e2d5e
fixing release version
rhshah Aug 8, 2023
a84075b
Merge pull request #20 from msk-access/cci_cwlscci_cwls
rhshah Aug 8, 2023
f8ee1bf
Merge pull request #21 from msk-access/main
rhshah Aug 8, 2023
19c8d99
updating working version
carmelinacharalambous Aug 8, 2023
bd1f169
point to release branches
rhshah Aug 8, 2023
7c550ca
Merge branch 'release/1.1.4'
rhshah Aug 8, 2023
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2 changes: 1 addition & 1 deletion cwl-commandlinetools
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Submodule cwl-commandlinetools updated 4 files
+0 −0 cci_utils/0.3.1/example_inputs.yaml
+1 −1 cci_utils/0.3.1/general_stats_parse.cwl
+1 −1 docs/cci_utils/general_stats_parse_0.3.1.md
+8 −19 requirements.txt
2 changes: 1 addition & 1 deletion cwl_subworkflows
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Submodule cwl_subworkflows updated 5 files
+1 −1 command_line_tools
+20 −2 vardict_workflow/run_processed_vardict.cwl
+29 −2 vardict_workflow/run_processed_vardict__packed.cwl
+8 −2 variant_annotation/variant_annotation.cwl
+14 −2 variant_annotation/variant_annotation__packed.cwl
3 changes: 2 additions & 1 deletion generate_aggregate.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -207,6 +207,7 @@ steps:
- id: output
source: output
- id: omaf
default: true
source: omaf
- id: generic_counting
source: generic_counting
Expand Down Expand Up @@ -262,7 +263,7 @@ steps:
source:
- qc_generator/collapsed_bam_stats_dir
- id: biometrics_extract_files_dir
source:
source:
- qc_generator/biometrics_extract_files_dir
- id: collapsed_bam_duplex_metrics_dir
source:
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2 changes: 1 addition & 1 deletion nucleo_aggregate_visualize.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -178,7 +178,7 @@ steps:
source: config
out:
- id: aggregate_parsed_stats
run: cwl-commandlinetools/cci_utils/0.3.0/general_stats_parse.cwl
run: cwl-commandlinetools/cci_utils/0.3.1/general_stats_parse.cwl
label: general_stats_parse
'sbg:x': 870.1131591796875
'sbg:y': 520.0625
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3 changes: 2 additions & 1 deletion nucleo_qc.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -230,6 +230,7 @@ steps:
- id: output
source: output
- id: omaf
default: true
source: omaf
- id: generic_counting
source: generic_counting
Expand Down Expand Up @@ -294,7 +295,7 @@ steps:
source:
- qc_generator/collapsed_bam_duplex_metrics_dir
- id: biometrics_extract_files_dir
source:
source:
- qc_generator/biometrics_extract_files_dir
- id: samples-json
source: samples-json
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