updated modules

dbmi-bgm · Aug 23, 2022 · d5df94b · d5df94b
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/cgap-pipeline-SNV-germline b/cgap-pipeline-SNV-germline
diff --git a/cgap-pipeline-SV-germline b/cgap-pipeline-SV-germline
diff --git a/cgap-pipeline-base b/cgap-pipeline-base
+2 −4		dockerfiles/sv_germline_granite/scripts/SV_cytoband.py
+1 −1		portal_objects/workflows/workflow_manta_vcf-check.json
+69 −0		cwl/gatk_liftover.cwl
+43 −0		cwl/preprocess_liftover.cwl
+61 −0		cwl/workflow_gatk_liftover.cwl
+33 −0		dockerfiles/gatk_picard/Dockerfile
+39 −0		dockerfiles/granite/Dockerfile
+82 −0		dockerfiles/granite/scripts/preprocess_liftover.py
+ −		dockerfiles/granite/scripts/test/files/liftover_vcf_chr_missing_in.vcf.gz
+135 −0		dockerfiles/granite/scripts/test/files/liftover_vcf_correct_out.vcf
+ −		dockerfiles/granite/scripts/test/files/liftover_vcf_non_standard_chrom_in.vcf.gz
+ −		dockerfiles/granite/scripts/test/files/liftover_vcf_two_samples_in.vcf.gz
+94 −0		dockerfiles/granite/scripts/test/test_preprocess_liftover.py
+13 −1		portal_objects/file_reference.json
+36 −0		portal_objects/software.json
+160 −0		portal_objects/workflows/workflow_liftovervcf.json