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fix(bcl_demultiplex): Extract InterOp files from input channel

4

Extract InterOp files directly from the input channel rather than emitting them from BCLCONVERT/BCL2FASTQ process outputs. This avoids passing files through a process unchanged, allowing downstream consumers to access InterOp...

robsyme

## 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,...

SkyLexS

### Have you checked the docs? - [x] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - [x] [nf-core modules documentation](https://nf-co.re/docs/contributing/modules) ### Description of the bug The memory conversion method in the FASTQC module generates...

ahwanpandey

Add fq2bam fq align dd bwamem

14

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

eduard-watchmaker

### Is there an existing module for this? - [x] I have searched for the existing module ### Is there an open PR for this? - [x] I have searched...

georgiakes

## 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,...

chaochaowong

### Is there an existing module for this? - [x] I have searched for the existing module ### Is there an open PR for this? - [x] I have searched...

jpcartailler

update module: HISAT2/ALIGN

3

# Why the update There is an issue with how hisat2 handles tmp memory. In an HPC environment, when many jobs are running in the same cpu it is easy...

RaqManzano

update module: METAPHLAN/METAPHLAN_METAPHALAN add flag to run with `-t rel_ab_w_read_stats`

2

### Is there an existing module for this? - [x] I have searched for the existing module ### Is there an open PR for this? - [x] I have searched...

nickp60

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

Copilot