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(parent: 7a447e0) | patch
Add cwl and docker files
authorJiayong Li <jli@curii.com>
Fri, 9 Dec 2022 21:03:13 +0000 (21:03 +0000)
committerJiayong Li <jli@curii.com>
Fri, 9 Dec 2022 21:03:13 +0000 (21:03 +0000)
commit93917ecafad9e6d811daf600ccf53991b1cbc86e
tree9004f2b8c8b9d4aae5fea16770c3f65c7e4cfdfbtree | snapshot
parent7a447e0c90a4da2e2851abb078df2b233728f6b1commit | diff
Add cwl and docker files

refs #19785

Arvados-DCO-1.1-Signed-off-by: Jiayong Li <jli@curii.com>
206 files changed:
.licenseignore diff | blob | history
cwl/annotation/annotate-wf.cwl [new file with mode: 0644] blob
cwl/annotation/bcftools-concat.cwl [new file with mode: 0644] blob
cwl/annotation/getcount.cwl [new file with mode: 0644] blob
cwl/annotation/getfiles.cwl [new file with mode: 0644] blob
cwl/annotation/preprocess.cwl [new file with mode: 0644] blob
cwl/annotation/snpeff-bcftools-annotate.cwl [new file with mode: 0644] blob
cwl/annotation/src/getcount.sh [new file with mode: 0755] blob
cwl/annotation/src/totalcounts.sh [new file with mode: 0755] blob
cwl/annotation/totalcounts.cwl [new file with mode: 0644] blob
cwl/annotation/yml/annotate-wf-A-PRHS-PR000971-BL-COL-47620BL1.yml [new file with mode: 0644] blob
cwl/annotation/yml/preprocess-test.yml [new file with mode: 0644] blob
cwl/annotation/yml/snpeff-bcftools-annotate-annotation_chr19.yml [new file with mode: 0644] blob
cwl/annotation/yml/snpeff-bcftools-annotate-annotation_chr19_new.yml [new file with mode: 0644] blob
cwl/annotation/yml/snpeff-bcftools-annotate-annotation_chr22.yml [new file with mode: 0644] blob
cwl/comparevcf/change-GT.cwl [new file with mode: 0644] blob
cwl/comparevcf/comparevcf-original-lightning-wf.cwl [new file with mode: 0644] blob
cwl/comparevcf/rtg-vcfeval.cwl [new file with mode: 0644] blob
cwl/comparevcf/src/change-GT.sh [new file with mode: 0755] blob
cwl/comparevcf/src/concatenate.sh [new file with mode: 0755] blob
cwl/comparevcf/yml/comparevcf-original-lightning-wf-A-PRHS-PR000971-BL-COL-47620BL1.yml [new file with mode: 0644] blob
cwl/gvcf2fasta/append-sampleid.cwl [new file with mode: 0644] blob
cwl/gvcf2fasta/bcftools-consensus.cwl [new file with mode: 0644] blob
cwl/gvcf2fasta/concat-get_bed_varonlyvcf.cwl [new file with mode: 0644] blob
cwl/gvcf2fasta/fixvcf-get_bed_varonlyvcf.cwl [new file with mode: 0644] blob
cwl/gvcf2fasta/get_bed_varonlyvcf.cwl [new file with mode: 0644] blob
cwl/gvcf2fasta/getfiles.cwl [new file with mode: 0644] blob
cwl/gvcf2fasta/gvcf2fasta-wf.cwl [new file with mode: 0644] blob
cwl/gvcf2fasta/gvcf2fasta_nonrefvcf-imputation-wf.cwl [new file with mode: 0644] blob
cwl/gvcf2fasta/gvcf2fasta_nonrefvcf-wf.cwl [new file with mode: 0644] blob
cwl/gvcf2fasta/gvcf2fasta_splitvcf-imputation-wf.cwl [new file with mode: 0644] blob
cwl/gvcf2fasta/gvcf2fasta_splitvcf-wf.cwl [new file with mode: 0644] blob
cwl/gvcf2fasta/gvcf2fasta_splitvcftar-wf.cwl [new file with mode: 0644] blob
cwl/gvcf2fasta/scatter-gvcf2fasta-wf.cwl [new file with mode: 0644] blob
cwl/gvcf2fasta/scatter-gvcf2fasta_nonrefvcf-wf.cwl [new file with mode: 0644] blob
cwl/gvcf2fasta/scatter-gvcf2fasta_splitvcf-imputation-wf.cwl [new file with mode: 0644] blob
cwl/gvcf2fasta/scatter-gvcf2fasta_splitvcf-wf.cwl [new file with mode: 0644] blob
cwl/gvcf2fasta/scatter-gvcf2fasta_splitvcftar-wf.cwl [new file with mode: 0644] blob
cwl/gvcf2fasta/src/bcftools-consensus.sh [new file with mode: 0755] blob
cwl/gvcf2fasta/src/concat-get_bed_varonlyvcf.sh [new file with mode: 0755] blob
cwl/gvcf2fasta/src/fixvcf-get_bed_varonlyvcf.sh [new file with mode: 0755] blob
cwl/gvcf2fasta/src/untar-concat.sh [new file with mode: 0755] blob
cwl/gvcf2fasta/untar-concat-get_bed_varonlyvcf.cwl [new file with mode: 0644] blob
cwl/gvcf2fasta/yml/bcftools-consensus-A-IIAA-IA000196-BL-NCR-14AD66938_phased_imputed.yml [new file with mode: 0644] blob
cwl/gvcf2fasta/yml/bcftools-consensus-test-newadni.yml [new file with mode: 0644] blob
cwl/gvcf2fasta/yml/bcftools-consensus-test-varonly.yml [new file with mode: 0644] blob
cwl/gvcf2fasta/yml/bcftools-consensus-test.yml [new file with mode: 0644] blob
cwl/gvcf2fasta/yml/concat-get_bed_varonlyvcf-A-WCAP-WC001544-BL-COL-49161BL1.yml [new file with mode: 0644] blob
cwl/gvcf2fasta/yml/get_bed_varonlyvcf-test.yml [new file with mode: 0644] blob
cwl/gvcf2fasta/yml/gvcf2fasta-wf-test-newadni.yml [new file with mode: 0644] blob
cwl/gvcf2fasta/yml/gvcf2fasta-wf-test.yml [new file with mode: 0644] blob
cwl/gvcf2fasta/yml/gvcf2fasta-wf-test37.yml [new file with mode: 0644] blob
cwl/gvcf2fasta/yml/gvcf2fasta_nonrefvcf-imputation-wf-A-PRHS-PR000971-BL-COL-47620BL1.yml [new file with mode: 0644] blob
cwl/gvcf2fasta/yml/gvcf2fasta_nonrefvcf-wf-A-PRHS-PR000971-BL-COL-47620BL1.yml [new file with mode: 0644] blob
cwl/gvcf2fasta/yml/gvcf2fasta_splitvcf-imputation-wf-A-IIAA-IA000196-BL-NCR-14AD66938.yml [new file with mode: 0644] blob
cwl/gvcf2fasta/yml/gvcf2fasta_splitvcf-imputation-wf-A-WCAP-WC001544-BL-COL-49161BL1.yml [new file with mode: 0644] blob
cwl/gvcf2fasta/yml/gvcf2fasta_splitvcf-wf-A-WCAP-WC001544-BL-COL-49161BL1.yml [new file with mode: 0644] blob
cwl/gvcf2fasta/yml/gvcf2fasta_splitvcftar-wf-test.yml [new file with mode: 0644] blob
cwl/gvcf2fasta/yml/scatter-gvcf2fasta-wf-16gvcf.yml [new file with mode: 0644] blob
cwl/gvcf2fasta/yml/scatter-gvcf2fasta-wf-test.yml [new file with mode: 0644] blob
cwl/gvcf2fasta/yml/scatter-gvcf2fasta_splitvcf-imputation-wf-100test.yml [new file with mode: 0644] blob
cwl/gvcf2fasta/yml/untar-concat-get_bed_varonlyvcf-test.yml [new file with mode: 0644] blob
cwl/imputation/bcftools-concat.cwl [new file with mode: 0644] blob
cwl/imputation/beagle.cwl [new file with mode: 0644] blob
cwl/imputation/bedtools-intersect.cwl [new file with mode: 0644] blob
cwl/imputation/bedtools-subtract.cwl [new file with mode: 0644] blob
cwl/imputation/get-imputedvcf.cwl [new file with mode: 0644] blob
cwl/imputation/get-phasedvcf.cwl [new file with mode: 0644] blob
cwl/imputation/imputation-wf.cwl [new file with mode: 0644] blob
cwl/imputation/match-ref-map-chr.cwl [new file with mode: 0644] blob
cwl/imputation/merge-phased-imputed-wf.cwl [new file with mode: 0644] blob
cwl/imputation/rtg-vcffilter-bedtools-intersect.cwl [new file with mode: 0644] blob
cwl/imputation/rtg-vcffilter.cwl [new file with mode: 0644] blob
cwl/imputation/rtg-vcfmerge.cwl [new file with mode: 0644] blob
cwl/imputation/scatter-beagle-wf.cwl [new file with mode: 0644] blob
cwl/imputation/yml/imputation-A-PRHS-PR000971-BL-COL-47620BL1.yml [new file with mode: 0644] blob
cwl/imputation/yml/rtg-vcffilter-A-PRHS-PR000971-BL-COL-47620BL1.yml [new file with mode: 0644] blob
cwl/imputation/yml/rtg-vcffilter-test.yml [new file with mode: 0644] blob
cwl/lightning/batch-dirs.cwl [new file with mode: 0644] blob
cwl/lightning/fasta2numpy-multi-wf.cwl [new file with mode: 0644] blob
cwl/lightning/fasta2numpy-wf.cwl [new file with mode: 0644] blob
cwl/lightning/genreadme.cwl [new file with mode: 0644] blob
cwl/lightning/imputation-gvcf2fasta-fasta2numpy-wf.cwl [new file with mode: 0644] blob
cwl/lightning/libray2numpy-wf.cwl [new file with mode: 0644] blob
cwl/lightning/lightning-anno2vcf.cwl [new file with mode: 0644] blob
cwl/lightning/lightning-choose-samples.cwl [new file with mode: 0644] blob
cwl/lightning/lightning-import.cwl [new file with mode: 0644] blob
cwl/lightning/lightning-plot.cwl [new file with mode: 0644] blob
cwl/lightning/lightning-slice-numpy-anno2vcf-wf.cwl [new file with mode: 0644] blob
cwl/lightning/lightning-slice-numpy-onehot.cwl [new file with mode: 0644] blob
cwl/lightning/lightning-slice-numpy-pca.cwl [new file with mode: 0644] blob
cwl/lightning/lightning-slice-numpy.cwl [new file with mode: 0644] blob
cwl/lightning/lightning-slice.cwl [new file with mode: 0644] blob
cwl/lightning/lightning-tiling-stats.cwl [new file with mode: 0644] blob
cwl/lightning/make-arrays.cwl [new file with mode: 0644] blob
cwl/lightning/make-fastadirs.cwl [new file with mode: 0644] blob
cwl/lightning/make-libname.cwl [new file with mode: 0644] blob
cwl/lightning/readme.md [new file with mode: 0644] blob
cwl/lightning/src/genreadme.py [new file with mode: 0755] blob
cwl/lightning/stage-output.cwl [new file with mode: 0644] blob
cwl/lightning/yml/fasta2numpy-multi-wf-0831_0315.yml [new file with mode: 0644] blob
cwl/lightning/yml/fasta2numpy-multi-wf-0831_0315_ADNI.yml [new file with mode: 0644] blob
cwl/lightning/yml/fasta2numpy-multi-wf-A-PRHS-PR000971-BL-COL-47620BL1.yml [new file with mode: 0644] blob
cwl/lightning/yml/fasta2numpy-multi-wf-public.yml [new file with mode: 0644] blob
cwl/lightning/yml/fasta2numpy-multi-wf-test.yml [new file with mode: 0644] blob
cwl/lightning/yml/fasta2numpy-multi-wf-testonehot.yml [new file with mode: 0644] blob
cwl/lightning/yml/fasta2numpy-wf-0831_0315.yml [new file with mode: 0644] blob
cwl/lightning/yml/fasta2numpy-wf-100test.yml [new file with mode: 0644] blob
cwl/lightning/yml/imputation-gvcf2fasta-fasta2numpy-wf-100test.yml [new file with mode: 0644] blob
cwl/lightning/yml/lightning-export-numpy-merged.yml [new file with mode: 0644] blob
cwl/lightning/yml/lightning-import-ref37.yml [new file with mode: 0644] blob
cwl/lightning/yml/lightning-import-ref38.yml [new file with mode: 0644] blob
cwl/lightning/yml/lightning-import-testdata.yml [new file with mode: 0644] blob
cwl/lightning/yml/lightning-merge-testdata_ref38.yml [new file with mode: 0644] blob
cwl/lightning/yml/lightning-slice-numpy-anno2vcf-wf-0831_0315.yml [new file with mode: 0644] blob
cwl/lightning/yml/lightning-slice-numpy-anno2vcf-wf-test.yml [new file with mode: 0644] blob
cwl/lightning/yml/lightning-slice-numpy-onehot-A-ADC.yml [new file with mode: 0644] blob
cwl/lightning/yml/lightning-slice-numpy-onehot-A-CUHS.yml [new file with mode: 0644] blob
cwl/lightning/yml/lightning-slice-numpy-onehot-A-IIAA.yml [new file with mode: 0644] blob
cwl/lightning/yml/lightning-slice-numpy-onehot-ADNI.yml [new file with mode: 0644] blob
cwl/lightning/yml/lightning-slice-numpy-onehot-full.yml [new file with mode: 0644] blob
cwl/lightning/yml/lightning-slice-numpy-onehot-pvalue1e-8-full.yml [new file with mode: 0644] blob
cwl/lightning/yml/lightning-tiling-stats-ref37.yml [new file with mode: 0644] blob
cwl/preprocess/cgivar/bedtools-intersect.cwl [new file with mode: 0644] blob
cwl/preprocess/cgivar/cgatools-mkvcf.cwl [new file with mode: 0644] blob
cwl/preprocess/cgivar/cgatools-mkvcf.sh [new file with mode: 0755] blob
cwl/preprocess/cgivar/cgivar2vcfbed-wf.cwl [new file with mode: 0644] blob
cwl/preprocess/cgivar/fix_vcf.cwl [new file with mode: 0644] blob
cwl/preprocess/cgivar/fix_vcf.py [new file with mode: 0755] blob
cwl/preprocess/cgivar/getfiles.cwl [new file with mode: 0644] blob
cwl/preprocess/cgivar/gvcf_regions.cwl [new file with mode: 0644] blob
cwl/preprocess/cgivar/scatter-cgivar2vcfbed-wf.cwl [new file with mode: 0644] blob
cwl/preprocess/cgivar/yml/cgivar2vcfbed-wf-test.yml [new file with mode: 0644] blob
cwl/preprocess/cgivar/yml/scatter-cgivar2vcfbed-wf-367set.yml [new file with mode: 0644] blob
cwl/preprocess/chrmvcf/change_gt_M.js [new file with mode: 0644] blob
cwl/preprocess/chrmvcf/change_gt_chrM.js [new file with mode: 0644] blob
cwl/preprocess/chrmvcf/fixchrm-wf.cwl [new file with mode: 0644] blob
cwl/preprocess/chrmvcf/fixchrm.cwl [new file with mode: 0644] blob
cwl/preprocess/chrmvcf/getfiles.cwl [new file with mode: 0644] blob
cwl/preprocess/chrmvcf/yml/fixchrm-test.yml [new file with mode: 0644] blob
cwl/preprocess/chrmvcf/yml/fixchrm-wf-1kcgi.yml [new file with mode: 0644] blob
cwl/preprocess/chrmvcf/yml/fixchrm-wf-harvardpgpcgi.yml [new file with mode: 0644] blob
cwl/preprocess/chrmvcf/yml/fixchrm-wf-simons.yml [new file with mode: 0644] blob
cwl/preprocess/gvcf/filtercleangvcf-wf.cwl [new file with mode: 0644] blob
cwl/preprocess/gvcf/filtercleangvcf.cwl [new file with mode: 0644] blob
cwl/preprocess/gvcf/getfiles.cwl [new file with mode: 0644] blob
cwl/preprocess/gvcf/src/cleanvcf.py [new file with mode: 0755] blob
cwl/preprocess/gvcf/src/filter-gvcf [new file with mode: 0755] blob
cwl/preprocess/gvcf/yml/filtercleangvcf-test.yml [new file with mode: 0644] blob
cwl/preprocess/gvcf/yml/filtercleangvcf-wf-1kcgi.yml [new file with mode: 0644] blob
cwl/preprocess/gvcf/yml/filtercleangvcf-wf-vcfbed-test.yml [new file with mode: 0644] blob
cwl/preprocess/gvcf/yml/keepGQdot-test.yml [new file with mode: 0644] blob
cwl/preprocess/haploidvcf/change_gt.js [new file with mode: 0644] blob
cwl/preprocess/haploidvcf/fixgt-wf.cwl [new file with mode: 0644] blob
cwl/preprocess/haploidvcf/fixgt.cwl [new file with mode: 0644] blob
cwl/preprocess/haploidvcf/getfiles.cwl [new file with mode: 0644] blob
cwl/preprocess/haploidvcf/yml/fixgt-test.yml [new file with mode: 0644] blob
cwl/preprocess/haploidvcf/yml/fixgt-wf-pgpcanada.yml [new file with mode: 0644] blob
cwl/preprocess/nonrefvcf/fixnonref-wf.cwl [new file with mode: 0644] blob
cwl/preprocess/nonrefvcf/fixnonref.cwl [new file with mode: 0644] blob
cwl/preprocess/nonrefvcf/getfiles.cwl [new file with mode: 0644] blob
cwl/preprocess/nonrefvcf/yml/fixnonref-test.yml [new file with mode: 0644] blob
cwl/preprocess/nonrefvcf/yml/fixnonref-wf-1kgvcf.yml [new file with mode: 0644] blob
cwl/preprocess/nonrefvcf/yml/fixnonref-wf-ukpgp.yml [new file with mode: 0644] blob
cwl/preprocess/portablevcf/bcftools-annotate.cwl [new file with mode: 0644] blob
cwl/preprocess/portablevcf/bcftools-reheader.cwl [new file with mode: 0644] blob
cwl/preprocess/portablevcf/cat.cwl [new file with mode: 0644] blob
cwl/preprocess/portablevcf/getfiles.cwl [new file with mode: 0644] blob
cwl/preprocess/portablevcf/header [new file with mode: 0644] blob
cwl/preprocess/portablevcf/preprocess-portablevcf-wf.cwl [new file with mode: 0644] blob
cwl/preprocess/portablevcf/rtg-vcfeval.cwl [new file with mode: 0644] blob
cwl/preprocess/portablevcf/scatter-preprocess-portablevcf-wf.cwl [new file with mode: 0644] blob
cwl/preprocess/portablevcf/sort-clean.cwl [new file with mode: 0644] blob
cwl/preprocess/portablevcf/yml/bcftools-annotate-test.yml [new file with mode: 0644] blob
cwl/preprocess/portablevcf/yml/preprocess-portablevcf-wf.yml [new file with mode: 0644] blob
cwl/preprocess/portablevcf/yml/scatter-preprocess-portablevcf-wf.yml [new file with mode: 0644] blob
cwl/preprocess/portablevcf/yml/sort-clean.cwl [new file with mode: 0644] blob
cwl/preprocess/simons/filter-vcf.cwl [new file with mode: 0644] blob
cwl/preprocess/simons/getfiles.cwl [new file with mode: 0644] blob
cwl/preprocess/simons/make-bed.cwl [new file with mode: 0644] blob
cwl/preprocess/simons/make-vcf-bed-wf.cwl [new file with mode: 0644] blob
cwl/preprocess/simons/yml/filter-vcf-test.yml [new file with mode: 0644] blob
cwl/preprocess/simons/yml/make-bed-test.yml [new file with mode: 0644] blob
cwl/preprocess/simons/yml/make-vcf-bed-wf-simons.yml [new file with mode: 0644] blob
cwl/preprocess/splitvcf/concatvcf-wf.cwl [new file with mode: 0644] blob
cwl/preprocess/splitvcf/concatvcf.cwl [new file with mode: 0644] blob
cwl/preprocess/splitvcf/src/concatvcf.sh [new file with mode: 0755] blob
cwl/preprocess/splitvcf/yml/concatvcf-test.yml [new file with mode: 0644] blob
cwl/preprocess/splitvcf/yml/concatvcf-wf-test.yml [new file with mode: 0644] blob
cwl/preprocess/vcfbed/get-vcfbed.cwl [new file with mode: 0644] blob
cwl/preprocess/vcfbed/intersect-vcfbed.cwl [new file with mode: 0644] blob
cwl/preprocess/vcfbed/sort-bed.cwl [new file with mode: 0644] blob
cwl/preprocess/vcfbed/sort-vcf.cwl [new file with mode: 0644] blob
cwl/preprocess/vcfbed/src/convert-vcf-bed-to-gvcf [new file with mode: 0755] blob
cwl/preprocess/vcfbed/vcfbed2gvcf-wf-lite.cwl [new file with mode: 0644] blob
cwl/preprocess/vcfbed/vcfbed2gvcf-wf.cwl [new file with mode: 0644] blob
cwl/preprocess/vcfbed/vcfbed2gvcf.cwl [new file with mode: 0644] blob
cwl/preprocess/vcfbed/yml/single-bed.yml [new file with mode: 0644] blob
cwl/preprocess/vcfbed/yml/vcfbed2gvcf-wf-1kcgivcfbed.yml [new file with mode: 0644] blob
cwl/preprocess/vcfbed/yml/vcfbed2gvcf-wf-cgi-5samples.yml [new file with mode: 0644] blob
cwl/preprocess/vcfbed/yml/vcfbed2gvcf-wf-cgi.yml [new file with mode: 0644] blob
docker/beagle5.4/Dockerfile [new file with mode: 0644] blob
docker/cgivar2vcfbed/Dockerfile [new file with mode: 0644] blob
docker/lightning/Dockerfile [new file with mode: 0644] blob
docker/snpeff/Dockerfile [new file with mode: 0644] blob
docker/vcfutil/Dockerfile [new file with mode: 0644] blob