Matthieu Muffato

MultiQC timeouts after 1 hour on GitHub CI

1

### Description of the bug Since around the batch of module upgrades triggered by the Anaconda licensing issues (#154, #155, #156), the MultiQC has been taking much longer to run,...

Merquryfk bug

5

### Description of the bug Taking `/lustre/scratch122/tol/data/5/a/3/5/2/0/Ypsolopha_sequella` (`/lustre/scratch124/tol/projects/darwin/data/insects/Ypsolopha_sequella`) as an example, and using the database `genomic_data/ilYpsSequ2/pacbio/kmer/k31/ilYpsSequ2.k31.ktab` - completeness of `assembly/release/ilYpsSequ2.1/insdc/GCA_934047225.1.fasta.gz`: ``` Assembly Region Found Total % Covered ilYpsSequ2.1.GCA_934047225.1 all 659008770...

Implement nf-test

1

We want tests at the pipeline level to check that the outputs are all correct.

Update pipeline template

1

Update to the latest nf-core pipeline template

Support modules with `exec:` blocks

1

With the current version, linting a module that has an `exec:` block yields the following error ``` ╭─ [✗] 1 Module Test Failed ───────────────────────────────────────────────────╮ │ ╷ ╷ │ │ Module...

Moved all singularity-related download functions into a new file

1

Closes #3019 Supersedes #3163 Ongoing work part of the "Workflows to go" hackathon project. I've started moving all singularity functions into a new file. Overview of the moves from `nf_core/pipelines/download.py`...

### Description of the bug This is just a display issue. Internally, the install/uninstall work correctly. See this example sub-workflow that uses 3 nf-core samtools modules ### Command used and...

Can't install modules when `version_naming` is set

3

**Describe the bug** Sorry I couldn't chime in during #679, I got sick. I'm now trying to test the feature but can't make it work. The problem I'm facing is...