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Updates for Biometrics and Genral Parse Stat
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rhshah committed Jun 18, 2024
1 parent 6477880 commit e7a9ace
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2 changes: 1 addition & 1 deletion cwl-commandlinetools
Submodule cwl-commandlinetools updated 45 files
+161 −0 biometrics_extract/0.2.15/biometrics_extract.cwl
+24 −0 biometrics_extract/0.2.15/example_inputs.yaml
+1 −1 biometrics_extract/README.md
+155 −0 biometrics_genotype/0.2.15/biometrics_genotype.cwl
+12 −0 biometrics_genotype/0.2.15/example_inputs.yaml
+1 −1 biometrics_genotype/README.md
+123 −0 biometrics_major/0.2.15/biometrics_major.cwl
+11 −0 biometrics_major/0.2.15/example_inputs.yaml
+1 −1 biometrics_major/README.md
+130 −0 biometrics_minor/0.2.15/biometrics_minor.cwl
+11 −0 biometrics_minor/0.2.15/example_inputs.yaml
+1 −1 biometrics_minor/README.md
+110 −0 biometrics_sexmismatch/0.2.15/biometrics_sexmismatch.cwl
+10 −0 biometrics_sexmismatch/0.2.15/example_inputs.yaml
+1 −1 biometrics_sexmismatch/README.md
+1 −1 cci_utils/0.3.1/general_stats_parse.cwl
+9 −32 docs/SUMMARY.md
+76 −0 docs/biometrics/biometrics_extract_0.2.15.md
+60 −0 docs/biometrics/biometrics_genotype_0.2.15.md
+56 −0 docs/biometrics/biometrics_major_0.2.15.md
+56 −0 docs/biometrics/biometrics_minor_0.2.15.md
+56 −0 docs/biometrics/biometrics_sexmismatch_0.2.15.md
+1 −1 docs/cci_utils/general_stats_parse_0.3.1.md
+1 −1 docs/postprocessing_variant_calls/maf_annotated_by_bed_0.2.2.md
+60 −0 docs/postprocessing_variant_calls/maf_annotated_by_tsv_0.2.3.md
+57 −0 docs/postprocessing_variant_calls/maf_filter_cmoch_0.2.3.md
+57 −0 docs/postprocessing_variant_calls/maf_tag_cmoch_0.2.3.md
+20 −2 oncokb_annotator_3.2.2/oncokb_annotator_3-2-2.cwl
+3 −0 postprocessing_variant_calls/0.2.2/container/README.md
+20 −3 postprocessing_variant_calls/0.2.2/maf_annotated_by_bed/maf_annotated_by_bed.cwl
+3 −0 postprocessing_variant_calls/0.2.3/container/README.md
+42 −0 postprocessing_variant_calls/0.2.3/maf_annotated_by_bed/README.md
+4 −0 postprocessing_variant_calls/0.2.3/maf_annotated_by_bed/example_inputs.yaml
+92 −0 postprocessing_variant_calls/0.2.3/maf_annotated_by_bed/maf_annotated_by_bed.cwl
+60 −0 postprocessing_variant_calls/0.2.3/maf_annotated_by_tsv/README.md
+9 −0 postprocessing_variant_calls/0.2.3/maf_annotated_by_tsv/example_input.txt
+103 −0 postprocessing_variant_calls/0.2.3/maf_annotated_by_tsv/maf_annotated_by_tsv.cwl
+57 −0 postprocessing_variant_calls/0.2.3/maf_filter_cmoch/README.md
+4 −0 postprocessing_variant_calls/0.2.3/maf_filter_cmoch/example_input.txt
+88 −0 postprocessing_variant_calls/0.2.3/maf_filter_cmoch/maf_filter_cmoch.cwl
+57 −0 postprocessing_variant_calls/0.2.3/maf_tag_cmoch/README.md
+4 −0 postprocessing_variant_calls/0.2.3/maf_tag_cmoch/example_input.txt
+88 −0 postprocessing_variant_calls/0.2.3/maf_tag_cmoch/maf_tag_cmoch.cwl
+1 −1 snpsift_annotate_5.0/snpsift_annotate_5-0.cwl
+19 −7 vcf2maf_1.6.21/vcf2maf_1.6.21.cwl
2 changes: 1 addition & 1 deletion nucleo_aggregate_visualize.cwl
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/0.3.1/general_stats_parse.cwl
run: cwl-commandlinetools/cci_utils/0.3.2/general_stats_parse.cwl
label: general_stats_parse
'sbg:x': 870.1131591796875
'sbg:y': 520.0625
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