Update to BUSCO 4.0.6 #81
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And importantly it solves #77. |
| assemblersample=\$(echo \"$assemblersampleunique\" | sed 's/[][]//g') | ||
| IFS=', ' read -r -a assemblersamples <<< \"\$assemblersample\" | ||
| # replace dots in bin names within summary file names with underscores | ||
| # (currently, v4.1.2, generate_plot.py does not allow further dots) |
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true (just also holds for newer version), will adjust
| file("${bin}_buscos.faa") optional true | ||
| file("${bin}_buscos.fna") optional true |
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when we are already thinking about making the result folder smaller in size, why not gzip these too? These files might be not large, however there might be many bins. This is optional obviously.
| file("${assembly}_buscos.faa") | ||
| file("${assembly}_buscos.fna") | ||
| set val(assembler), val(sample), file("short_summary.specific.${db}.${bin}.txt") into (ch_busco_multiqc, ch_busco_to_summary, ch_busco_plot) | ||
| file("${bin}_busco.log") |
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At least this filename changed, probably the output.md needs an update too?
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The summary output and also the plots etc. are yet listed, I will add them. For "${assembly}_buscos.faa" just the variable name changed, not that actual file name.
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I meant _busco_log.txt -> _busco.log, and yes, thats nit-picky.
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Hm, test_hybrid failed when busco found no relevant genes (Prodigal found no genes matching ref database) and therefore and also: |
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yeah, will have a look |
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I can not reproduce the |
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Will close this, since there remains the issue with BUSCO (https://gitlab.com/ezlab/busco/-/issues/305). Will create a new PR with a newer BUSCO version when this is fixed. |
Here is an update to BUSCO 4.0.6 (v4.1.2 is in conflict with the MAG python version 3.6.7). It contains only the basic functionality so far, without the automatic lineage selection and without automatic DB download which is provided since BUSCO 4 (which would require extra error handling among among others with the current BUSCO version).
I renamed the variable ${assembly} to ${bin} within the busco processes.
Additionally I changed the
busco_plotprocess and the channel logic, so that the process now runs on eachassembler-samplecombination (instead of calling the busco scriptgenerate_plot.pyfor each combination within the process). This also fixes the grouping of BUSCO summaries for the plot, which was wrong in case one sample name was the prefix of another one.For the final busco summary for all bins I created an extra process.
Since current versions of the BUSCO
generate_plot.py(v4.0.6-4.1.2) can not handle additional dots within the summary file names, I unfortunately had to replace also dots with underscores in the bin names, which will also appear as such in the BUSCO plots.PR checklist
nextflow run . -profile test,docker).nf-core lint .).docsis updatedCHANGELOG.mdis updatedREADME.mdis updatedLearn more about contributing: https://github.com/nf-core/mag/tree/master/.github/CONTRIBUTING.md