Thomas Cokelaer

bwa mem fails to identify paired-end sequences with 'not enough pairs' message

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I faced an issue with paired data not being recognised as paired with the **bwa mem** command. The data was mapped (on mm10 genome; mouse) using bowtie2 with no problem...

Possible regression bugs from 6.8.0 to 6.9.X

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**Snakemake version**: 6.9.0 and 6.9.1 **Describe the bug** 1. Running/Executing pipelines with the --wrapper-prefix and a local git repository works in 6.8.0 but not in 6.9.0 or 6.9.1 Note this...

- [ ] class prototype - [ ] doc - [ ] test - [ ] standalone

- lazyimports.py and lazy and errors could be in utils - tools.py also ? - errors could be removed - coverage.py and bedtools should be in a submodule coverage/ -...

If we have several output files like lima_output.sample1.ccs.fastq this will lead to a sample name called lima_output version of sequana 0.11.0

Please, let us know if you would like to join the project. You can contribute in various ways: - improving the documentation in https://github.com/sequana/sequana - add new Python functions /...

Request from a user. Could be nice indeed to have this feature - [x] pdb to FAA in 0.6.2

Join the team (post here to be added to the bioconvert team)

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Everybody is welcome to contribute a converter or a method in a converter. Simply reply to this issue and you will be added to the bioconvert team. Edit: After you...