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update version in usage docs
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d4straub committed Nov 10, 2023
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Expand Up @@ -36,7 +36,7 @@ The typical command for running the pipeline is as follows:

```bash
nextflow run nf-core/ampliseq \
-r 2.7.0 \
-r 2.7.1 \
-profile singularity \
--input "samplesheet.tsv" \
--FW_primer GTGYCAGCMGCCGCGGTAA \
Expand All @@ -45,7 +45,7 @@ nextflow run nf-core/ampliseq \
--outdir "./results"
```

In this example, `--input` is the [Samplesheet input](#samplesheet-input), other options are [Direct FASTQ input](#direct-fastq-input) and [ASV/OTU fasta input](#asvotu-fasta-input). For more details on metadata, see [Metadata](#metadata). For [Reproducibility](#reproducibility), specify the version to run using `-r` (= release, e.g. 2.7.0, please use the most recent release). See the [nf-core/ampliseq website documentation](https://nf-co.re/ampliseq/parameters) for more information about pipeline specific parameters.
In this example, `--input` is the [Samplesheet input](#samplesheet-input), other options are [Direct FASTQ input](#direct-fastq-input) and [ASV/OTU fasta input](#asvotu-fasta-input). For more details on metadata, see [Metadata](#metadata). For [Reproducibility](#reproducibility), specify the version to run using `-r` (= release, e.g. 2.7.1, please use the most recent release). See the [nf-core/ampliseq website documentation](https://nf-co.re/ampliseq/parameters) for more information about pipeline specific parameters.

It is possible to not provide primer sequences (`--FW_primer` & `--RV_primer`) and skip primer trimming using `--skip_cutadapt`, but this is only for data that indeed does not contain any PCR primers in their sequences. Also, metadata (`--metadata`) isnt required, but aids downstream analysis.

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