Erik Danielsson

Add Nextclade module

4

Added new `Nextclade` module. Some of the columns in the `Nextclade` table should probably removed. Will close #1455. - [x] This comment contains a description of changes (with reason) -...

Should close #1719. - [x] This comment contains a description of changes (with reason) - [x] `CHANGELOG.md` has been updated

Tried to rewrite GitHub actions to run only the changed module if a single module is changed by the PR. The logic for this is shown in this boolean: ```Python...

Made path filters without complete paths work correctly by prefixing analysis directories when filtering. Should close #1308. - [x] This comment contains a description of changes (with reason) - [x]...

Make file search parallel

3

Made MultiQC file search run in parallel. One can specify the number of processes that MultiQC can start with the `--cpu` flag. If not specified, it defaults to `1` and...

Speed up `nf-core modules` pytests

2

### Description of feature The pytests for the `nf-core modules` commands are very slow. I believe this partly due to that every test pulls several remote git repositories in the...

### Description of the bug The link created by `nf-core modules info` is broken since the move from the github api. The link is set on https://github.com/nf-core/tools/blob/dev/nf_core/modules/info.py#L164-L168, but the `self.remote_location`...

### Description of feature When the `modules.json` is removed in a pipeline containing patched modules, and then recreated using a `nf-core modules` command, the `create` method is unable to determine...

### Description of feature Tthe recently implemented modules lint tests for patch files have very low coverage. I'd suggest we do it in a similar fashion to how the the...

### Description of feature The `--base-path` option in the `nf-core modules` command was added without considering all the cases it could be used. For example, in the current implementation we...