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Removed metatdenovo typo #59

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danilodileo merged 1 commit into from
Jun 13, 2024
Merged

Removed metatdenovo typo #59

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6 changes: 3 additions & 3 deletions docs/usage.md
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Expand Up @@ -21,7 +21,7 @@ Note that the pipeline can map to any collection of genomes, including single ge
A typical command for running the workflow is:

```bash
nextflow run nf-core/metatdenovo -profile docker --outdir results/ --input samples.csv --genomeinfo localgenomes.csv
nextflow run nf-core/magmap -profile docker --outdir results/ --input samples.csv --genomeinfo localgenomes.csv
```

### Samplesheet input
Expand Down Expand Up @@ -122,15 +122,15 @@ Specify a fasta file, gzipped or not, with the --sequence_filter sequences.fasta
For further documentation, see the [BBduk official website](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/).

```bash
nextflow run nf-core/metatdenovo -profile docker --outdir results/ --input samples.csv --genomeinfo localgenomes.csv --sequence_filter path/to/file
nextflow run nf-core/magmap -profile docker --outdir results/ --input samples.csv --genomeinfo localgenomes.csv --sequence_filter path/to/file
```

### Sourmash (optional)

with [Sourmash](https://sourmash.readthedocs.io/en/latest/index.html) you can filter the genomes to be used by magmap in the mapping step. This function is optional but can speed up the process and let you get a better genomes /reads mapping ratio since you are removing all the genomes that are not passing the threshold (that you can select).

```bash
nextflow run nf-core/metatdenovo -profile docker --outdir results/ --input samples.csv --genomeinfo localgenomes.csv --sourmash true
nextflow run nf-core/magmap -profile docker --outdir results/ --input samples.csv --genomeinfo localgenomes.csv --sourmash true
```

### ORF caller option
Expand Down