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add dedicated output channel for trimmomatic stderr log (needed for multiqc)

4

## Description & Reason The Trimmomatic module does not appear to capture the standard error log (`2>`) that is required for parsing by MultiQC as an output. Although there is...

jpalmer37

add UPP

1

Adds a module for running MSA using UPP to nf-core. As there are some issues with the conda package for SEPP/UPP, this is drafted for now. - [X] This comment...

lrauschning

SPADES changed flag for single-read in illumina reads

2

## PR checklist Changed flag for single-read illumina reads to --s, since -s is used in spades for singletons from a pair-end library (see Input data in https://github.com/ablab/spades/blob/spades_3.15.5/README.md) - [x]...

aidaanva

New module: checkqc

8

Adding new module checkQC. Related to issue: https://github.com/nf-core/modules/issues/4011 Depends on https://github.com/nf-core/test-datasets/pull/1024 for tests to work. Note: The CheckQC version used in the module is not the latest. I was forced...

matrulda

## PR checklist Closes #XXX - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should...

rolivella

new list of proteomics modules

13

### DDA | Process name | Link to quantms local module | Call | Tool|Test data | Test data (chunked)| |-----|-----|-----|-----|-----|-----| | cdecoy_pr | NA | [create_decoy](https://github.com/proteomicsunitcrg/atlas/blob/43aad5531b492b2cf21320615179e57523cc793a/subworkflows/search_engine/search_engine.nf#L56) | [decoy.pl](https://github.com/proteomicsunitcrg/atlas/blob/43aad5531b492b2cf21320615179e57523cc793a/tools/mascot/decoy.pl) |[sp_human_2024_02.fasta_decoy.fasta](https://www.dropbox.com/scl/fi/ssnblxp5rn9ihllz6g6j0/sp_human_2024_02.fasta_decoy.fasta?rlkey=x35hixsaciks4tfx4rzna9pxr&st=jmgdlcz7&dl=0)...

rolivella

Fix documentation link

2

This PR corrects a link found in two of the bwa modules meta.yml file. They did incorrectly point to a samtools website. ## PR checklist - [x] This comment contains...

pbiology

Newmodule verkko 3

1

This new module was created for Verkko It only includes the option to use PacBio reads. To be able to use ONT (nano-ore) reads, we have to wait for the...

scorreard

Add skani round 2

3

## PR checklist Re-opens #5502 - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should...

CarsonJM

New module: tiledbvcf

7

## PR checklist Closes #XXX - [x] This comment contains a description of changes (with reason). - [x] If you've fixed a bug or added code that should be tested,...

atrigila