Adding Kraken2 metagenomics classifier #355
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jfy133
requested changes
Feb 20, 2020
README.md
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| @@ -67,6 +67,7 @@ Additional functionality contained by the pipeline currently includes: | |||
| #### Metagenomic Screening | |||
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| * Taxonomic binner with alignment (`MALT`) | |||
| * Taxonomic binner without alignment (`Kraken2`) | |||
| * aDNA characteristic screening of taxonomically binned data (`MaltExtract`) | |||
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| * aDNA characteristic screening of taxonomically binned data (`MaltExtract`) | |
| * aDNA characteristic screening of taxonomically binned data from MALT (`MaltExtract`) |
bin/kraken_parse.py
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| ''' | ||
| INPUT: | ||
| infile (str): path to kraken report file | ||
| countlim (int): lower count threshold to report hit |
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| countlim (int): lower count threshold to report hit | |
| countlim (int): lowest count threshold to report hit |
bin/merge_kraken_res.py
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| '-o', | ||
| dest="output", | ||
| default=None, | ||
| help="Output file. Default = sources.csv") |
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What does 'sources' mean here? Or is this a leftover from CoproID? Maybe should be changed to same on line 58?
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From kraken-nf actually ;)
Changed to use the name given by the CLI. (default="kraken_count_table.csv")
docs/usage.md
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| respectively. Ensure your database matches the mode. Check the [MALT manual](http://ab.inf.uni-tuebingen.de/data/software/malt/download/manual.pdf) for more details. Default: 'BlastN' | ||
| respectively. Ensure your database matches the mode. Check the [MALT manual](http://ab.inf.uni-tuebingen.de/data/software/malt/download/manual.pdf) for more details. Default: 'BlastN' | ||
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| Only when `--metagenomic_tool malt` |
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| Only when `--metagenomic_tool malt` | |
| Only when `--metagenomic_tool malt` is also supplied |
While I thought this would've been implicit with the paramtere name, better to be explicit ;). The complete sentence can be applied to all below as well.
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Changed every occurence to your suggestion
nextflow.config
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| database = '' | ||
| percent_identity = 85 | ||
| malt_mode = 'BlastN' | ||
| malt_alignment_mode = 'SemiGlobal' | ||
| malt_top_percent = 1 | ||
| malt_min_support_mode = 'percent' | ||
| malt_min_support_percent = 0.01 | ||
| malt_min_support_reads = 1 | ||
| metagenomic_min_support_reads = 1 |
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Duplicate here with line 168? Any reason why?
jfy133
approved these changes
Feb 21, 2020
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Adding Kraken2 metagenomics classifier
main.nfbinPR checklist
nextflow run . -profile test,docker).nf-core lint .).docsis updatedCHANGELOG.mdis updatedREADME.mdis updatedLearn more about contributing: https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md