Kyle Hazen

bamtobed adds an additional entry that does not exists in the BAM file. This seems to occur when the last read is unpaired and the previous read is paired in...

fastq_screen does not yield non-zero exit code when aligner returns non-zero exit code

1

fastq_screen does not yield non-zero exit code when aligner returns non-zero exit code. This seems like a problem since the expected output files are all made, but the reported values...

Cannot import compute environment from file when Labels are included

2

As the title says when I am trying to make a compute environment via `tw compute-envs import -n test1 test-no-label.json` everything is ok `New AWS-BATCH compute environment 'test1' added at...

fix(labels-import): pass the type info to the mapper

1

https://github.com/seqeralabs/tower-cli/issues/394 Fixes the issue when creating a compute environemnt from a json file with the labels field

Escape angle brackets in output.md

1

Some of the directory descriptions contain an angle bracket < which must be escaped in markdown. I have added the escape character. ## PR checklist - [X ] This comment...

new File breaks cloud execution in bcl_demultiplex

8

### 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 This bug relates to the bcl_demultiplex sub workflow. `new...

Handle empty files

11

This PR fixes #5612 This PR also handles empty FASTQ files by including a empty fastq emit channel

This is required to run the docker self hosted tests in the CI workflow because docker is rootless on the self hosted runner