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@rhshah
rhshah committed Jun 24, 2024
1 parent 038334c commit b60e4a0
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2 changes: 1 addition & 1 deletion command_line_tools
Submodule command_line_tools updated 221 files
2 changes: 1 addition & 1 deletion subworkflows
Submodule subworkflows updated 64 files
+41 −0 .github/workflows/codeql.yml
+5 −5 .github/workflows/pack_cwls.yml
+31 −0 .github/workflows/validate_cwls.yml
+1 −0 .gitignore
+656 −11 LICENSE
+173 −136 alignment/alignment__packed.cwl
+74 −0 athena_report/README.md
+115 −0 athena_report/athena_report.cwl
+885 −0 athena_report/athena_report__packed.cwl
+3 −0 athena_report/example_inputs.yaml
+12 −0 athena_report/example_inputs_juno.yaml
+12 −0 athena_report/example_inputs_juno_empty.yaml
+51 −0 bam_qc_stats/README.md
+57 −13 bam_qc_stats/bam_qc_stats.cwl
+317 −224 bam_qc_stats/bam_qc_stats__packed.cwl
+0 −6 base_quality_recalibration/base_quality_recalibration.cwl
+228 −219 base_quality_recalibration/base_quality_recalibration__packed.cwl
+1 −1 command_line_tools
+20 −9 docs/SUMMARY.md
+361 −300 fgbio_separate_bams/fgbio_separate_bams__packed.cwl
+43 −0 gbcms_genotyping/README.md
+51 −0 gbcms_genotyping/example_inputs.json
+316 −0 gbcms_genotyping/gbcms_genotyping.cwl
+714 −0 gbcms_genotyping/gbcms_genotyping__packed.cwl
+246 −230 indel_realignment/indel_realignment__packed.cwl
+129 −0 qc_collapsed_bam/README.md
+677 −0 qc_collapsed_bam/qc_collapsed_bam.cwl
+3,714 −0 qc_collapsed_bam/qc_collapsed_bam__packed.cwl
+539 −0 qc_collapsed_bam/qc_collapsed_bam_v2.0.cwl
+3,477 −0 qc_collapsed_bam/qc_collapsed_bam_v2.0__packed.cwl
+142 −0 qc_duplex_bam/README.md
+537 −0 qc_duplex_bam/qc_duplex_bam.cwl
+3,287 −0 qc_duplex_bam/qc_duplex_bam__packed.cwl
+508 −0 qc_duplex_bam/qc_duplex_bam_v2.0.cwl
+3,271 −0 qc_duplex_bam/qc_duplex_bam_v2.0__packed.cwl
+71 −0 qc_simplex_bam/README.md
+197 −0 qc_simplex_bam/qc_simplex_bam.cwl
+1,609 −0 qc_simplex_bam/qc_simplex_bam__packed.cwl
+135 −0 qc_simplex_bam/qc_simplex_bam_v2.0.cwl
+1,498 −0 qc_simplex_bam/qc_simplex_bam_v2.0__packed.cwl
+72 −0 qc_uncollapsed_bam/README.md
+294 −0 qc_uncollapsed_bam/qc_uncollapsed_bam.cwl
+2,404 −0 qc_uncollapsed_bam/qc_uncollapsed_bam__packed.cwl
+216 −0 qc_uncollapsed_bam/qc_uncollapsed_bam_v2.0.cwl
+2,261 −0 qc_uncollapsed_bam/qc_uncollapsed_bam_v2.0__packed.cwl
+3 −3 requirements.txt
+26 −0 vardict_workflow/README.md
+16 −0 vardict_workflow/example_inputs.yaml
+185 −0 vardict_workflow/run_processed_vardict.cwl
+2,755 −0 vardict_workflow/run_processed_vardict__packed.cwl
+103 −0 variant_annotation/README.md
+60 −0 variant_annotation/chipvar_processing.cwl
+380 −0 variant_annotation/chipvar_processing__packed.cwl
+5 −0 variant_annotation/example_inputs_chipvar.yaml
+28 −0 variant_annotation/example_inputs_variant_annotation.yaml
+353 −0 variant_annotation/variant_annotation.cwl
+1,644 −0 variant_annotation/variant_annotation__packed.cwl
+127 −0 variant_postprocessing/README.md
+165 −0 variant_postprocessing/variant_normalize_sort.cwl
+851 −0 variant_postprocessing/variant_normalize_sort__packed.cwl
+115 −0 variant_postprocessing/variant_sort.cwl
+597 −0 variant_postprocessing/variant_sort__packed.cwl
+165 −0 variant_postprocessing/variants_concat.cwl
+1,483 −0 variant_postprocessing/variants_concat__packed.cwl

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