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James Fellows Yates 2022-11-03 14:05:43 +01:00
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12
docs/usage.md
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@ -131,14 +131,6 @@ Expected (uncompressed) database files for each tool are as follows:
- `hash.k2d` - `hash.k2d`
- `taxo.k2d` - `taxo.k2d`
- `database.idx` - `database.idx`
- `database.kdb.counts`
- `database50mers.kmer_distrib`
- `database75mers.kmer_distrib`
- `database100mers.kmer_distrib`
- `database150mers.kmer_distrib`
- `database200mers.kmer_distrib`
- `database300mers.kmer_distrib`
- `seqid2taxid.map`
- `taxDB` - `taxDB`
- **Centrifuge** output of `centrifuge-build`. A directory containing: - **Centrifuge** output of `centrifuge-build`. A directory containing:
- `<database_name>.<number>.cf` - `<database_name>.<number>.cf`
@ -192,7 +184,7 @@ work # Directory containing the nextflow working files
### Sequencing quality control ### Sequencing quality control
nf-core taxprofiler offers [`falco`](https://github.com/smithlabcode/falco] as an alternative option to [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). nf-core taxprofiler offers [`falco`][https://github.com/smithlabcode/falco] as an alternative option to [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
### Preprocessing Steps ### Preprocessing Steps
@ -457,7 +449,7 @@ NXF_OPTS='-Xms1g -Xmx4g'
## Troubleshooting and FAQs ## Troubleshooting and FAQs
### I get a warning during centrifuge_kreport process with exit status 255. ### I get a warning during centrifuge_kreport process with exit status 255
When a sample has insufficient hits for abundance estimation, the resulting `report.txt` file will be empty. When a sample has insufficient hits for abundance estimation, the resulting `report.txt` file will be empty.

6
nextflow_schema.json
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@ -418,18 +418,18 @@
"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." "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."
}, },
"run_krakenuniq": { "run_krakenuniq": {
"type": "string", "type": "boolean",
"fa_icon": "fas fa-toggle-on", "fa_icon": "fas fa-toggle-on",
"description": "Turn on profiling with KrakenUniq. Requires database to be present CSV file passed to --databases" "description": "Turn on profiling with KrakenUniq. Requires database to be present CSV file passed to --databases"
}, },
"krakenuniq_save_reads": { "krakenuniq_save_reads": {
"type": "string", "type": "boolean",
"fa_icon": "fas fa-save", "fa_icon": "fas fa-save",
"description": "Turn on saving of KrakenUniq-aligned reads", "description": "Turn on saving of KrakenUniq-aligned reads",
"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`" "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`"
}, },
"krakenuniq_save_readclassifications": { "krakenuniq_save_readclassifications": {
"type": "string", "type": "boolean",
"fa_icon": "fas fa-save", "fa_icon": "fas fa-save",
"description": "Turn on saving of KrakenUniq per-read taxonomic assignment file", "description": "Turn on saving of KrakenUniq per-read taxonomic assignment file",
"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`" "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`"