Skip to content

Commit

Permalink
update docs
Browse files Browse the repository at this point in the history
  • Loading branch information
Danilo Di Leo committed Jun 12, 2024
1 parent ad0c958 commit 1275035
Showing 1 changed file with 7 additions and 1 deletion.
8 changes: 7 additions & 1 deletion docs/usage.md
Original file line number Diff line number Diff line change
Expand Up @@ -73,14 +73,20 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p

### Genomes input

Magmap needs two mandatory input to run. One, the samplesheet, was explained above while the second, genome input needs to be specified with the option `--genomeinfo`. The file is a `.csv` file and it requires three columns: accnos, genomes_fna, genome_gff. it looks as follow:
Magmap needs two mandatory input to run. One, the samplesheet, was explained above while the second, genome input needs to be specified with the option `--genomeinfo`. The file is a `.csv` file and it requires three columns: accno, genome_fna, genome_gff. it looks as follow:

```csv title="genomes.csv"
GCA_002688505.1,https://github.com/nf-core/test-datasets/raw/magmap/testdata/GCA_002688505.1_ASM268850v1_genomic.fna.gz,https://github.com/nf-core/test-datasets/raw/magmap/testdata/GCA_002688505.1_ASM268850v1_genomic.gff.gz
```

N.B.: you don't need to provide gff, Prokka can handle if you only provide fasta files but we reccomend when adding gff that the file is generated by using prokka in order to don't get any conflict with other generated gffs.

```csv title="samplesheet.csv"
accno,genome_fna,genome_gff
GCA_002688505,./genomes/GCA_002688505.fna,./genomes/GCA_002688505.gff
GCA_002688515,./genomes/GCA_002688515.fna,./genomes/GCA_002688515.gff
```

### Other inputs (optional)

Magmap can handle several types of input that can be used for different purpose.
Expand Down

0 comments on commit 1275035

Please sign in to comment.