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feat: BUSCO auto lineage mode, tempdir, updated version (#526)
* Added tempdir to store all outputs that are copied as requested, options to specify dataset_dir, and new example * Fixed linting * Added full_table and missing_busco to output * Fixed typo * Added lineage checks * Update bio/busco/environment.yaml Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
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@@ -3,5 +3,4 @@ channels: | |
- bioconda | ||
- nodefaults | ||
dependencies: | ||
- busco==5.1.2 | ||
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- busco =5.4 |
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name: busco | ||
description: | | ||
Assess assembly and annotation completeness with BUSCO | ||
url: https://busco.ezlab.org/ | ||
authors: | ||
- Tessa Pierce | ||
- Filipe G. Vieira | ||
input: | ||
- assembly fasta | ||
output: | ||
- annotation quality files | ||
notes: | | ||
* The `mode` parameter sets the assessment mode (mandatory), and only allows for arguments: "genome", "transcriptome", and "proteins". | ||
* The `lineage` parameter sets the lineage dataset ot use (optional). In `auto-lineage` mode, `output` or `dataset` folders need to be retrieved as a whole, since it is not possible to infer the output file names (they depend on the best lineage match). | ||
* The `extra` param allows for additional program arguments. |
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rule run_busco: | ||
input: | ||
"transcripts.fasta" | ||
"protein.fasta", | ||
output: | ||
directory("txome_busco") | ||
short_json="txome_busco/short_summary.json", | ||
short_txt="txome_busco/short_summary.txt", | ||
full_table="txome_busco/full_table.tsv", | ||
miss_list="txome_busco/busco_missing.tsv", | ||
dataset_dir=directory("resources/busco_downloads"), | ||
log: | ||
"logs/quality/transcriptome_busco.log" | ||
threads: 8 | ||
"logs/proteins_busco.log", | ||
params: | ||
mode="transcriptome", | ||
mode="proteins", | ||
lineage="stramenopiles_odb10", | ||
downloads_path="resources/busco_downloads", | ||
# optional parameters | ||
extra="" | ||
extra="", | ||
threads: 8 | ||
wrapper: | ||
"master/bio/busco" | ||
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rule run_busco_euk: | ||
input: | ||
"protein.fasta", | ||
output: | ||
out_dir=directory("txome_busco/euk"), | ||
dataset_dir=directory("resources/busco_downloads"), | ||
log: | ||
"logs/proteins_busco_euk.log", | ||
params: | ||
mode="proteins", | ||
# optional parameters | ||
extra="--auto-lineage-euk", | ||
threads: 8 | ||
wrapper: | ||
"master/bio/busco" | ||
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rule run_busco_prok: | ||
input: | ||
"protein.fasta", | ||
output: | ||
out_dir=directory("txome_busco/prok"), | ||
dataset_dir=directory("resources/busco_downloads"), | ||
log: | ||
"logs/proteins_busco_prok.log", | ||
params: | ||
mode="proteins", | ||
# optional parameters | ||
extra="--auto-lineage-prok", | ||
threads: 8 | ||
wrapper: | ||
"master/bio/busco" |
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