Alexander Peltzer

Deduplication Parallelization

1

We could think about splitting BAMs as DeDup/MarkDup takes quite some time normally and use a `file.size>2GB` (or similar operator) to speed up things significantly. A subsequent merge would be...

Consider competitive mapping for contaminant removal

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See here : https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-07229-y

Weird occassional error when running nf-core pipelines with bi profile

1

Examples are always like this: ``` Launching `nf-core/scrnaseq` [focused_einstein] - revision: ef3f49479f [dev] NOTE: Your local project version looks outdated - a different revision is available in the remote repository...

Check that nextflow config -show-profiles doesn't fail

2

As suggested by @piotr-faba-ardigen , we should check this in the CI stuff.

Checkqc recipe / Illumina-interop not working ?

1

Dear all, we've been trying to use the checkqc container on quay.io that was created from the checkqc recipe and receive an error about interop not being installed properly: ```...

### Description of feature https://github.com/nf-core/modules/pull/2291 outlines how we will restructure to use `params.container_registry` for docker containers in the future, e.g. to allow using container mirrors from ECR or potentially other...

Test GHA self-hosted runners for events

3

### Description of feature We should have some way of setting up custom runners for events such as hackathons to speed up CI on such days. This is fairly easy,...

Linting message not 100% correct

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### Description of the bug Lint error says I have to update Samtools:  However, the conda handle has two different recipes listed:  ### Command used and terminal output...

Lint linter config for Python < 3.6 and issue warning if Actions are using Python 3.6 and older

4

### Description of the bug ``` Run nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md ``` ```python Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.6.15/x64/bin/nf-core", line 5, in from nf_core.__main__ import...

Do not require schema path (fix #1838)

1

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