Support draft assemblies #97
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Python linting (
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I've added some code to achieve the goal of As far as I understand the requirements, this is the last bit that was missing to complete support for draft assemblies. I'll mark this pull-request as ready. |
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@eeaunin . I've rebased this branch. It now includes the fixes I've made for blast |
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Release 0.5
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I had a closer look at how
So the exclusion of taxids is supposed to be optional and configurable by the user. https://github.com/blobtoolkit/pipeline/blob/master/v1/example.yaml However, I couldn't find a setting for the same thing in the Snakemake pipeline v2 code. Maybe the authors just forgot to include it? In my runs with the Snakemake pipeline negative taxids were not used but there are suppressed error messages buried in the run logs relating to that. In a run with a Plasmodium yoelii yoelii assembly there is this error in the logs ( So it ran into the error but then just quietly continued running. It is unclear to me what caused this error, as the taxid used there (352914) is at strain level. In another run it has skipped using the taxid filter due to another error: So the filtering doesn't work if the supplied database is V4 instead of V5 but this also doesn't crash the Snakemake pipeline and just produces an error message in the logs. I guess it would be okay if the |
The filter in SEQTK_SUBSEQ is not sufficient because some BLOBTOOLKIT_CHUNK further excludes masked regions
Skip blastn if there are no chunks
…y-classifications/
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…NA taxon_ids NCBI is still the first database we query
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@eeaunin . I've added a I've rebased the branch onto the latest stable release 0.5.1 |
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That's good then! I think it's fine to merge the |
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On this branch, there is no input Yaml file. The only mandatory parameters are:
--taxon)--fasta)--input) to list the read files--accessionis optional and is used to pull assembly information from ENA into the blobDir's meta.json.I haven't restructured the pipeline much. All the blobtools command at the end still require a yaml file. My solution is to add a script at the beginning of the pipeline that generates the minimal yaml file required (as per #77 (comment)). It still allows clearly getting some parameters in the input-check sub-workflow and making the busco sub-workflow more focused on running buco + blastp.
Busco lineages are inferred from the taxonomy directly here. Like in the genome-note pipeline, I've moved away from using GoaT as GoaT is just a proxy to the NCBI taxonomy. This way, I can keep control of both the version of Busco and the list of lineages in the same place.
I've also introduced the
--busco_lineagesparameter to allow precisely selecting the lineages that are used, rather than the taxonomy-based defaults.Still a draft for now as I want to review
/nfs/team135/yy5/btk_config/taxonomiser_v2.pyand maybe incorporate some elements of it.PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).