All tools should have some form of MultiQC modules

[nf-core]

All tools should have some form of MultiQC modules

[jfy133]

Yup exactly, this is why they are not yet ticked :)

[jfy133]

Solutio nfor centrifuge/kraken problem:

[sofstam]

Centrifuge and porechop are not supported by multiqc at the moment.

[jfy133]

Ok BBDuk not displayed as our particular command isn't supported by MQC (as in the requested search patterns not found)

https://github.com/ewels/MultiQC/blob/master/multiqc/utils/search_patterns.yaml

[jfy133]

Note issue: #38 (comment)

[jfy133]

Current issues:

• [2022-05-10 10:11:54,296] multiqc.modules.malt.malt [DEBUG ] Duplicate sample name found! Overwriting: 2612_ERR5766180.unmapped (I guess based on name stored in log, need to infer from directory name - so need to stage in MQC report work dir directory?)?
• [2022-05-10 10:11:54,285] multiqc.modules.base_module [DEBUG ] bowtie2 - Skipping './2612_ERR5766176_B.bowtie2.log' as it didn't match the path_filters for 'Bowtie 2 / HiSAT2' (dafuq?)

[jfy133]

Fix for centrifuge/kraken in!

[jfy133]

Just waiting for the final modules for MQC then we can merge

[sofstam]

I think we have forgotten minimap2 for long-reads.

[jfy133]

All modueles created for now (even if not merged into MultiQC itself)