Comments (1)
Hi @dxkeac,
Thanks for your interest in our workflows. This repo contains all of the workflows utilized at our institution so it can be a bit confusing at first. The immuno.cwl you're looking for can be found here. The reason you're seeing so many cwl files in this repo is that a cwl workflow is made up of steps, which in itself can be other workflows or tool cwls. In case of the immuno.cwl it calls various other subworkflows, e.g. for alignment, variant & fusion calling, rnasq, hla typing, etc up to running pVACseq for neoepitope prediction. It's probably our most complex workflow. You might find our wiki documentation for this workflow helpful for starts.
Best,
Susanna
from analysis-workflows.
Related Issues (20)
- Update biscuit QC scripts in bisulfite pipeline
- add padding to germline exome target region intervals HOT 1
- Validate 2.0 workflows
- New step to sort a merged BAM in the rnaseq.cwl workflow
- strandedeness_check tool shouldn't use an ENTRYPOINT in its docker image HOT 1
- strandness check rnaseq docker image HOT 1
- Add jigv for pre-computed IGV views in a clean HTML format HOT 1
- update germline workflows to produce genome vcfs and genotyped vcf
- Add -m and -d options to vt decompose step to avoid splitting HOT 1
- Problem with merge_bams HOT 4
- Gather input files page has broken image links HOT 1
- Should we pass Omni to BQSR?
- Location of FASTQ files HOT 1
- Add cwltool requirement InlineJavascriptRequirement HOT 1
- Build HCC1395 test input for CNVKit
- Pangenome: ATAC-seq Pipeline
- Pangenome: RNA-seq Pipeline Requirements HOT 1
- germline docm filter needs a decompose step
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from analysis-workflows.