Workflow common modifications

sanjaynagi / AmpSeeker

A snakemake workflow for amplicon sequencing

https://sanjaynagi.github.io/AmpSeeker/

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Workflow common modifications #11

Closed ChabbyTMD closed 1 year ago

ChabbyTMD commented 1 year ago

In this PR;

Main workflow tidied up to follow Snakemake best practices.
Added activation control in configuration file.
Modified BgZipTabixMerge to have its output match the input in common.smk.
Added .gitignore to not track specific files and directories.
Added conditional logic and defined unified input function for rule all in common.smk.

ChabbyTMD commented 1 year ago

Hi Sanjay,

Is it possible the CI checks are failing because there isn't any .fastq.gz data the pipeline needs to execute?

Please advise.

ChabbyTMD commented 1 year ago

Hi Sanjay,

Is it possible the CI checks are failing because there isn't any .fastq.gz data the pipeline needs to execute?

Please advise.

Well, this is a facepalm moment 😅. Turns out I had forgotten to update the .test/ config file, that's why the CI checks were failing. It didn't have the up-to-date config options.

ChabbyTMD commented 1 year ago

Surely I was warned 😅 I guess it happens to the best of us.