Explore Workflows

Wrapper to run bam indexing on all bams before submitting for samples fillout Also includes steps to pre-filter some maf input files NOTE: each sample in a sample_group must have a .bam file, and there must be a minumum of 1 .maf file amoungst samples in the same sample_group this means that for each sample in the sample_group, a .bam is required but a .maf is optional as long as one sample in the group has a .maf this also means that singleton sample groups, or a sample group with only one sample, MUST include a .maf file; singletons cannot lack a .maf NOTE: all .maf files must be valid, at a minimum they must have a header and at least one variant if a sample has no variants in its .maf file, or has an empty .maf file, then it should NOT have a maf_file entry associated with it

https://github.com/mskcc/pluto-cwl.git

Path: cwl/samples_fillout_index_batch_workflow.cwl

Branch/Commit ID: master

https://github.com/ebi-wp/webservice-cwl.git

Path: workflows/workflow-fasta-pratt.cwl

Branch/Commit ID: master

https://git.astron.nl/RD/LINC.git

Path: workflows/linc_target.cwl

Branch/Commit ID: master

https://github.com/mightqxc/panda-atm.git

Path: test_workflow.cwl

Branch/Commit ID: master

https://github.com/ska-sa/den.git

Path: cwl/main.cwl

Branch/Commit ID: master

https://github.com/NCGM-genome/WGSpipeline.git

Path: Workflows/germline-gpu-v4.2.0.cwl

Branch/Commit ID: main

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/subworkflows/bwa_mem.cwl

Branch/Commit ID: 3bb03c9b

https://github.com/eosc-lofar/presto-cwl.git

Path: birds.cwl

Branch/Commit ID: visualise

https://github.com/ChrisMaherLab/PACT.git

Path: subworkflows/strelka_and_post_processing.cwl

Branch/Commit ID: master

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/scatter-wf1.cwl

Branch/Commit ID: main