qbic-pipelines / pipeline-docs Goto Github PK

Should be --target_bed and not --targetBED

Dear all,

there are some broken lins in the exomeseq.md, when referencing the sarek input documentation and the variant calling docs. The links https://github.com/nf-core/sarek/blob/master/docs/input.md and https://github.com/nf-core/sarek/blob/dev/docs/variant_calling are not valid anymore. I guess it should rather point to Sarek Usage Docs now?

Potentially, this issue also occurs in other parts of the docs..

Best,
Marie

Error:

java.io.FileNotFoundException: /nfsmounts/container/.nfcore-cageseq-1.0.0.img.lock (Read-only file system) 

Usually, this mean that the container pulling failed or the container is corrupted.

Solution:

Navigate to

/nfsmounts/containers

and remove the existing container.
Re-run your pipeline.

The master branch contains changes not present in the dev branch:

https://github.com/qbic-pipelines/pipeline-docs/blob/master/docs/markdown/exomeseq.md#running-the-pipeline-with-a-non-igenomes-genome

They look like they should stay there though. For me this setup is a bit confusing now. Intuitively I would merge into dev, which is then eventually released into master. In the past that apparently didn't always happen. I guess 2 scenarios could be used:

1. Protect master branch to only allow merges from dev. Everyone would then merge their PRs into dev for a release. That would include more overhead to make releases every once in a while and changes won't directly appear on the website.
2. Remove dev branch completely and everyone just directly merges into master from their fork. Is there a reason to keep the dev branch?
3. Keep both branches, but note in the README where to open PRs to