:arrow_up: upgrade pipeline modules

cnr-ibba / nf-resequencing-mem

Nextflow resequencing pipeline with bwa-mem and freebayes

MIT License

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:arrow_up: upgrade pipeline modules #4

Closed bunop closed 2 years ago

bunop commented 3 years ago

Try to update modules to latest version:

$ nf-core modules lint

Should return 0 warnings

Upgrade modules:

[x] picard/markduplicates
[x] bwa/mem
[x] samtools/flagstat
[ ] ~~samtools/sort~~
[x] bwa/index
[x] bwa/mem
[x] fastqc
[x] multiqc
[x] picard/markduplicates
[x] samtools/flagstat
[x] trimgalore

bunop commented 2 years ago

Some modules require an update in conda package, while others require to emit software versions as recommended by guidelines. Those modules are managed by the community so we can wait for their updates