search

sanger-tol / genomeassembly

Implementation of ToL genome assembly workflows
https://pipelines.tol.sanger.ac.uk/genomeassembly
MIT License
17 stars 2 forks source link

Version check_samplesheet.py #5

Closed muffato closed 1 year ago

muffato commented 2 years ago

Hi @ksenia-krasheninnikova

We're coming up with a guideline for versioning scripts, starting with the automate_io subworkflow. I know you're not using it any more, so this PR is more about keeping you up-to-date.

For Python scripts, support for --version can be added with a one-liner like this. Then, the .nf shoud call that rather printing the Python version, cf https://github.com/sanger-tol/nf-core-pipeline/blob/main/subworkflows/automate_input/modules/local/samplesheet_check.nf#L24

For shell scripts, you can add a one-liner in your shell script to check that the number of arguments is correct, and print a short usage message + version otherwise. See https://github.com/sanger-tol/nf-core-pipeline/blob/main/subworkflows/automate_input/bin/tol_input.sh#L5 and https://github.com/sanger-tol/nf-core-pipeline/blob/main/subworkflows/automate_input/modules/local/input_tol.nf#L27

Can you consider doing the same for your own scripts ? They're all essentially very easy to add, and then the scripts are versioned and it's clear which version of the script was used.

Thanks !

muffato commented 1 year ago

Closing this PR as this script is not used any more and could be deleted (cf #6)