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2 changed files with 5 additions and 13 deletions
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@ -131,14 +131,6 @@ Expected (uncompressed) database files for each tool are as follows:
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- `hash.k2d`
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- `taxo.k2d`
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- `database.idx`
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- `database.kdb.counts`
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- `database50mers.kmer_distrib`
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- `database75mers.kmer_distrib`
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- `database100mers.kmer_distrib`
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- `database150mers.kmer_distrib`
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- `database200mers.kmer_distrib`
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- `database300mers.kmer_distrib`
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- `seqid2taxid.map`
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- `taxDB`
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- **Centrifuge** output of `centrifuge-build`. A directory containing:
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- `<database_name>.<number>.cf`
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@ -192,7 +184,7 @@ work # Directory containing the nextflow working files
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### Sequencing quality control
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nf-core taxprofiler offers [`falco`](https://github.com/smithlabcode/falco] as an alternative option to [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
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nf-core taxprofiler offers [`falco`][https://github.com/smithlabcode/falco] as an alternative option to [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
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### Preprocessing Steps
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@ -457,7 +449,7 @@ NXF_OPTS='-Xms1g -Xmx4g'
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## Troubleshooting and FAQs
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### I get a warning during centrifuge_kreport process with exit status 255.
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### I get a warning during centrifuge_kreport process with exit status 255
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When a sample has insufficient hits for abundance estimation, the resulting `report.txt` file will be empty.
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@ -418,18 +418,18 @@
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"help_text": "Turn on saving minimizer information in the kraken2 report thus increasing to an eight column layout.\n\nAdds `--report-minimizer-data` to the kraken2 command."
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},
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"run_krakenuniq": {
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"type": "string",
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"type": "boolean",
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"fa_icon": "fas fa-toggle-on",
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"description": "Turn on profiling with KrakenUniq. Requires database to be present CSV file passed to --databases"
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},
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"krakenuniq_save_reads": {
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"type": "string",
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"type": "boolean",
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"fa_icon": "fas fa-save",
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"description": "Turn on saving of KrakenUniq-aligned reads",
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"help_text": "Save reads that do and do not have a taxonomic classification in your output results directory in FASTQ format.\n\n> Modifies tool parameter(s):\n> - krakenuniq: `--classified-out` and `--unclassified-out`"
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},
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"krakenuniq_save_readclassifications": {
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"type": "string",
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"type": "boolean",
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"fa_icon": "fas fa-save",
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"description": "Turn on saving of KrakenUniq per-read taxonomic assignment file",
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"help_text": "Save a text file that contains a list of each read that had a taxonomic assignment, with information on specific taxonomic taxonomic assignment that that read recieved.\n\n> Modifies tool parameter(s):\n> - krakenuniq: `--output`"
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