This thread is the designated place to ask questions about running the **pcawg-sanger-variant-caller** workflow.
Created by James Eddy jaeddy Hi @vipin
For running the workflow with `rabix`, you can try to modify `pcawg-sanger-variant-caller.cwl` to add this snippet of CWL
```YAML
arguments:
- position: 50
shellQuote: false
valueFrom: " && cp -r /var/spool/cwl/* ."
requirements:
- class: ShellCommandRequirement
- class: DockerRequirement
dockerPull: images.sbgenomics.com/bogdang/pcawg-sanger:1.0
```
in place of:
```YAML
requirements:
- class: DockerRequirement
dockerPull: quay.io/pancancer/pcawg-sanger-cgp-workflow:2.0.3
```
I had to change the docker image to add the `/var/spool/cwl` directory to the system. Since all outputs are created in that directory, the extension to the command line is added to make these files available in the workdir:
```shell
&& cp -r /var/spool/cwl/* .
```
Hi @bogdang,
I am interested in using your image for running the `pcawg-sanger-variant-caller` workflow with `rabix`. Could you please share me your docker image link?
Thanks!
Vipin Hey @Junjun
Similar to the Delly workflow, I had to edit the start.sh to run on rabix and CGC:
```
#!/usr/bin/env bash
set -o errexit
set -o pipefail
set -x
mkdir -p /var/spool/cwl
gosu root chmod a+wrx /tmp
gosu root chmod a+wrx /var/spool/cwl
export TMPDIR=/tmp
export HOME=/var/spool/cwl
env
gosu root bash -c "$*"
#allow cwltool to pick up the results created by seqware
gosu root chmod -R a+wrx /var/spool/cwl
```
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