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This commit is contained in:
James Fellows Yates 2022-11-03 14:05:43 +01:00
parent aecf308840
commit 6459d8920f
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:
- `hash.k2d`
- `taxo.k2d`
- `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`
- **Centrifuge** output of `centrifuge-build`. A directory containing:
- `<database_name>.<number>.cf`
@ -192,7 +184,7 @@ work # Directory containing the nextflow working files
### 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
@ -457,7 +449,7 @@ NXF_OPTS='-Xms1g -Xmx4g'
## 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.

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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."
},
"run_krakenuniq": {
"type": "string",
"type": "boolean",
"fa_icon": "fas fa-toggle-on",
"description": "Turn on profiling with KrakenUniq. Requires database to be present CSV file passed to --databases"
},
"krakenuniq_save_reads": {
"type": "string",
"type": "boolean",
"fa_icon": "fas fa-save",
"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`"
},
"krakenuniq_save_readclassifications": {
"type": "string",
"type": "boolean",
"fa_icon": "fas fa-save",
"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`"