Prod release v0.2.0

[priyanka-surana]

This is a bit long and messy. I am running a full test here: /lustre/scratch123/tol/teams/tolit/users/ps22/pipelines/blobtoolkit. Will update once it completes, but please start reviewing if you can. Would be great to get it merged this week. Thanks :)

[priyanka-surana]

@gq1 Can you please take a look at the tests for this pipeline? Thanks.

[gq1]

@gq1 Can you please take a look at the tests for this pipeline? Thanks.

Can you run the test locally?

Not much help from the log, run out of disk space?

2023-12-20T14:34:17.7624742Z   touch: cannot touch '.command.trace': Permission denied
2023-12-20T14:34:17.7625306Z 
2023-12-20T14:34:17.7625598Z Work dir:
2023-12-20T14:34:17.7626480Z   /home/runner/work/blobtoolkit/blobtoolkit/work/d9/ce32b60e9dba5d624bc89e3bcf10c8

[muffato]

I looked at /lustre/scratch123/tol/teams/tolit/users/ps22/pipelines/blobtoolkit/results/GCA_927399515.1 and browsed the data on the BTK viewer.

These seem fine:

• GC%
• Read coverage
• Lengths
• Gaps (Ns)
• "position" and "proportion" files
• Summary files GCA*.summary.json (incl. the BUSCO score), identifiers.json, meta.json

These seem weird:

• ${lineage}_odb10_count*.json only have 0s for the related eukaryote lineages (fungi and below) and non-0s for bacteria/archaea ! Maybe there's some filtering happening.
• I also don't know / understand what's supposed to be in the buscogenes* and buscoregions* JSON files, so can't really tell whether the counts are correct

[muffato]

Approving this PR on principle, pending sorting out the BUSCO JSON files and the if statement

[muffato]

I know you're on it, but for the record: please check that the if is working as expected

[priyanka-surana]

I tried branching and filtering but with no better results so leaving as is for now. This might be a fix for the next version.

[github-actions]

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[priyanka-surana]

I looked at /lustre/scratch123/tol/teams/tolit/users/ps22/pipelines/blobtoolkit/results/GCA_927399515.1 and browsed the data on the BTK viewer.

These seem fine:

• GC%
• Read coverage
• Lengths
• Gaps (Ns)
• "position" and "proportion" files
• Summary files GCA*.summary.json (incl. the BUSCO score), identifiers.json, meta.json

These seem weird:

• ${lineage}_odb10_count*.json only have 0s for the related eukaryote lineages (fungi and below) and non-0s for bacteria/archaea ! Maybe there's some filtering happening.
• I also don't know / understand what's supposed to be in the buscogenes* and buscoregions* JSON files, so can't really tell whether the counts are correct

This is fixed.