Maxime U Garcia

No status is 0 - but contains tumor only sample error message

5

### Description of the bug The sample-sheet only contains tumor-samples, but the following tools, which were requested by the option "tools", expect at least one normal-sample : deepvariant, haplotypecaller while...

Try to simplify params.tools usage

1

## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...

Read data length does not match expected size - bytes read: 2756; expected: 16013759

1

### Description of the bug Issue with latest Nextflow release. This was a silent message before, it's now an error and fails the pipeline. ### Command used and terminal output...

WIP: transfer mutect2 SBWFs to modules repo

2

PRs are coming

I'll create an issue, and I'll update the metro map at a later date (before the release). I noticed some weird changes with the new version of the workflow, but...

### Description of feature We don't have patterns for most of the reference files, and that is a source of issue and confusion: https://github.com/nf-core/sarek/blob/5cc30494a6b8e7e53be64d308b582190ca7d2585/nextflow_schema.json#L674-L679

implement sharding of tests

1

Adapted from https://github.com/nf-core/sarek/pull/1668 by @edmundmiller | @maxulysse ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug...

Restore the set -C when the concerned modules are fixed

1

TODO: restore the -C when the concerned modules are fixed _Originally posted by @maxulysse in https://github.com/nf-core/rnaseq/pull/1401#discussion_r1795036538_

Stubs all the way down

1

Implement stubs all the way down, properly

Updating picard to 3.2.0 fails pipeline level tests

3

New error coming out of Picard: > `A field field parsed out of a read name was expected to contain an integer and did not. Read name: SRR6357072.6014972. Cause: String...