Maxime U Garcia

FEAT: Uncouple uncompress and prepare genome

1

WIP

linting modules/subworkflows - add failure when no snapshots for versions

3

### Description of the bug the versions of tools is highly reproducible on docker/singularity, but it's often a lottery in conda. I'd like a linting test that ensure we snapshot...

template: update comments in .editorconfig file

1

I don't think we need to ignore README as we ignore python and markdown just after. + Adding comments about ignoring markdown ## PR checklist - [ ] This comment...

Social preview image autogerated by github, and social media posts needs to be consistent over pipelines

2

### Description of the bug cf https://nfcore.slack.com/archives/C043UU89KKQ/p1709055343026059 GiHub use the release notes to generate the social preview image. Classic example https://twitter.com/nf_core/status/1760983113294078288 has no pipeline name and the tweet had a...

Template: fix more pipeline name placeholder errors

2

## PR checklist - [ ] This comment contains a description of changes (with reason) - [ ] `CHANGELOG.md` is updated - [ ] If you've fixed a bug or...

Update devcontainer.json

2

it's a jsonc file ## PR checklist - [ ] This comment contains a description of changes (with reason) - [ ] `CHANGELOG.md` is updated - [ ] If you've...

nf-core subworkflows lint issue with no emit statements

2

### Description of the bug cf discussion in https://nfcore.slack.com/archives/CE6PELWR4/p1705575911588159 When a subworkflow has no emit statement, the linting is failing: ``` ╭─ [✗] 1 Subworkflow Test Failed ──────────────────────────────────────────────╮ │ ╷...

Add nf-prov

5

## PR checklist - [ ] This comment contains a description of changes (with reason) - [ ] `CHANGELOG.md` is updated - [ ] If you've fixed a bug or...

### Description of the bug @lindenb reported a bug with `/LAB-DATA/BiRD/shares/ITX/ITX_GLICID/commun/PF/NTS-333_NGS_Rimbert_ATAC-Seq/fastq/P1_S1_B1_S1` as a sample id, that created files in this position, because this id was used as prefix... I do...

check out extensions for input files

1

### Description of the bug with `-r 1.11.0` No extension fails as expected ``` ERROR ~ ERROR: Validation of pipeline parameters failed! -- Check '.nextflow.log' file for details The following...