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shellcheck: Run on .nf scripts

7

I found a bug on a shell script embedded in a `script:` section of a nextflow file from one of the nf-core modules. I provided a fix on this PR:...

zeehio

ADDORREPLACEREADGROUPS and MERGEBAMALIGNMENT input/output file specificity fix.

1

When using ADDORREPLACEREADGROUPS on an HPC with scratch enabled, the globbed *.bam copys both the input and output bam from scratch to the work directory. The output needed to be...

johnoooh

update module: spaceranger

4

## PR checklist Closes #8910 by bumping the spaceranger version in the Dockerfile, also update the README. - [x] This comment contains a description of changes (with reason). - [...

camlloyd

The cram output files should be tested for those modules. This can also be done with the nft-bam plugin!

famosab

[FEATURE] Not use `export GTDBTK_DATA_PATH="\$(find -L ${db} -name 'metadata' -type d -exec dirname {} \\;)"`

3

### Is your feature request related to a problem? Please describe I'm not entirely sure why this line is used on `gtdbtk/classifywf` module: https://github.com/nf-core/modules/blob/73da03cd2508eda722a32111113e0d7da353abcd/modules/nf-core/gtdbtk/classifywf/main.nf#L36 ``` export GTDBTK_DATA_PATH="\$(find -L ${db} -name...

jolespin

### 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...

vinisalazar

new module: EMBOSS/getorf

3

### 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...

timslittle

new module: sra-human-scrubber

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...

rpetit3

New module: NCBI datasets download

4

## PR checklist Add new module ncbidatasets/download Contains tests with nf-test Closes #3420 - [x] This comment contains a description of changes (with reason). - [x] If you've fixed a...

koenbossers

### 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...

mribeirodantas