This Nextflow DSL2 pipeline calls variants on long read alignment. It is run after sanger-tol/readmapping in the Sanger ToL production suite but with options to run on unaligned reads.
We're coming up with a guideline for versioning scripts, starting with the automate_io subworkflow. This PR updates a couple of scripts and modules accordingly
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.
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.
Can you then 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 !
PS: this PR has extra changes in tol_input.sh so that it is (almost) exactly the same as in the other pipelines
Hi @DLBPointon
We're coming up with a guideline for versioning scripts, starting with the automate_io subworkflow. This PR updates a couple of scripts and modules accordingly
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. 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.
Can you then 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 !
PS: this PR has extra changes in tol_input.sh so that it is (almost) exactly the same as in the other pipelines