Anders Sune Pedersen

Adding md5-sums to the test-yml-files

2

#695 Adding checks for md5-sums in CI-tests - where possible. For text-based output-files with changing md5-sums, I've tried adding some tests of certain strings in the output-files. The binary-output-files with...

Output from ascat not stable

4

### Description of the bug When running the following test, which is also also part of the CI-test `tests/test_tools_manually.yml`, ```nextflow run main.nf -profile test,tools_somatic_ascat``` @SusiJo found that the content (not...

### Description of feature Do we want to pass a target-bed-file to the module `BCFTOOLS_STATS` in `subworkflows/nf-core/vcf_qc.nf`? By supplying a target-bed-file to `BCFTOOLS_STATS`, we (supposedly) get some nice depth-plot. With...

Add md5-sums to CI-tests

1

### Description of feature Add md5-sums to CI-tests. Okayed by @maxulysse

Definition of relatedness as implemented in somalier

1

This might be more of a request for clarification than an actual issue or problem with the code. I noticed that the definition of relatedness seem to have changed with...

Add some info on the gitHub-authorization required by the nf-core tool

1

### Description of feature When running `nf-core modules update -a` in Sarek, I kept getting the message ``` ... │ 88 │ │ raise LookupError( │ │ ❱ 89 │...

DRAFT: Concatenating vcfs

1

This is a DRAFT PR for #738. Still lots more to be done and things that needs to be discussed. So far I am just concatenating the germline-vcfs from haplotypecaller...

Removing stub option from nf-cmd in the test of pipeline-download

1

This download test can't run with the option `-stub`. The test cmd works fine (locall) without that option, and it should also run okay on GitHub. https://nfcore.slack.com/archives/CE5LG7WMB/p1710342898081509?thread_ts=1710341749.045159&cid=CE5LG7WMB https://nfcore.slack.com/archives/CE5LG7WMB/p1710344889022759?thread_ts=1710341749.045159&cid=CE5LG7WMB ## PR...

### Description of the bug Need to update the following modules: - [x] [bwa/index](https://github.com/nf-core/modules/pull/4987) - [x] [bwa/mem](https://github.com/nf-core/modules/pull/4988) - [x] [cat/cat](https://github.com/nf-core/modules/pull/4990) - [x] cat/fastq (Already updated in modules, but needs to...

Figure out if Sarek-dev works with Spark

2

### Description of the bug Spark may have stopped working after docker.userEmulation was removed in https://github.com/nf-core/sarek/pull/1405. ### Command used and terminal output _No response_ ### Relevant files _No response_ ###...