dockstore-cgpwgs
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cancerit
Dockstore implementation of CGP core WGS analysis
I have been using the docker image of cgpwgs v2.1.0 and it's been working great for more than 50 samples. However, I'm getting this issue for one sample when running...
Hello, I am trying to run ascatNGS in a native docker environment with the following input: sudo docker run -it --rm \ --user 7793:7796 \ --env HOME=/var/spool/results \ -v /gpfs/analyses/kat/WGS_Tools/acatNgs/ref:/var/spool/ref...
The listing of files for GRCh37d5 on the wiki is missing: ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/qcGenotype_GRCh37d5.tar.gz On this section: https://github.com/cancerit/dockstore-cgpwgs/wiki/Reference-archives#human-grch37
we attempted to replicate brass results using the implementation in `analysisWGS.sh` on pcawg samples, but we are unfortunately getting very different results for some of the samples. Take for example...
I am running CGPWGS on a large number of samples (around 800 pairs). In case of 27 the pipeline finished without an error, but caveman snps.ids.vcf.gz contains only a header....
Hi, We noted that when the pipeline breaks, intermediate files are left in the output folder. To restart the analysis the output dir needs to be deleted. Have you considered...
https://github.com/cancerit/dockstore-cgpwgs/blob/develop/examples/cgpwgs/bam_bai.json is missing references to a .bas file
First of all thank you for the great work with the cgpwgs pipeline. We have been using version 2.0.1 and consider moving to 2.1.0 now, mainly due to the ASCAT/Caveman...
dockstore-cgpwgs-2.1.0 falls over on mouse bam files mapped using dockstore-cgpmap-3.0.4 giving these errors: No flagList found in flag.vcf.config.WGS.ini for section MUS MUSCULUS_WGS FLAGLIST. No flagging will be done. at /opt/wtsi-cgp/bin/cgpFlagCaVEMan.pl...
