bio-cwl-tools

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Create a script that can be used (via a github action?) to automatically generate a complete `.dockstore.yml` that contains entries for all tools in the repo. This would be a...

svonworl

https://github.com/galaxyproject/tpv-shared-database/blob/main/tools.yml Do a single sweep of existing tools, and add to the checklist for new contributions

mr-c

in `bio-cwl-tools/subread/featureCounts.cwl`

kafeenstra

- cellranger * cellranger-aggr.cwl * cellranger-arc-aggr.cwl * cellranger-arc-count.cwl * cellranger-arc-mkref.cwl * cellranger-count.cwl * cellranger-mkref.cwl * cellranger-reanalyze.cwl - gat * gat-run.cwl - gffread * gffread.cwl - gsea * gseapy.cwl - haltools...

michael-kotliar

Update BWA tools with correct secondaryFiles

5

`bwa` identifies an indexed database by base name but the actual DB consists of 5 files with extensions `amb`, `ann`, `bwt`, `pac` and `sa`. This means that for such a...

pvanheus

The structure of the repository

7

Here we need to decide the structure of the this repository. As it was agreed, every tool should be placed in a separate directory. The questions are: - should we...

michael-kotliar

Add snp-sites tool

1

Add a tool for [snp-sites](http://sanger-pathogens.github.io/snp-sites/)

pvanheus

https://github.com/truwl/biocondastats/blob/main/top100.tsv Generated from Jeremy's tool.

swzCuroverse

added WDL2CWL conversion examples

3

This is my pull request for WDL2CWL conversion example. Will fix https://github.com/common-workflow-library/bio-cwl-tools/issues/79

ambarishK

A call for a bio-cwl-tools team

9

At the moment I have a number of PRs open against this repository, and I have opened a [discussion](https://cwl.discourse.group/t/moving-bio-cwl-tools-forward/213/2) on moving this repository forward. I would like to see a...

pvanheus