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Co-authored-by: Till E. <[email protected]>
nf-core · Oct 19, 2023 · 3278e5b · 3278e5b
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diff --git a/README.md b/README.md
@@ -16,7 +16,7 @@
 
 ## Introduction
 
-**nfcore/ampliseq** is a bioinformatics analysis pipeline used for amplicon sequencing, supporting denoising of any amplicon and taxonomic assignment. Phylogenetic placement is also possible. Supported is paired-end Illumina or single-end Illumina, PacBio and IonTorrent data. Default is the analysis of 16S rRNA gene amplicons sequenced paired-end with Illumina.
+**nfcore/ampliseq** is a bioinformatics analysis pipeline used for amplicon sequencing, supporting denoising of any amplicon and supports a variety of taxonomic databases for taxonomic assignment including 16S, ITS, CO1 and 18S. Phylogenetic placement is also possible. Supported is paired-end Illumina or single-end Illumina, PacBio and IonTorrent data. Default is the analysis of 16S rRNA gene amplicons sequenced paired-end with Illumina.
 
 A video about relevance, usage and output of the pipeline (version 2.1.0; 26th Oct. 2021) can also be found in [YouTube](https://youtu.be/a0VOEeAvETs) and [billibilli](https://www.bilibili.com/video/BV1B44y1e7MM), the slides are deposited at [figshare](https://doi.org/10.6084/m9.figshare.16871008.v1).
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -819,7 +819,7 @@ process {
         ]
     }
 
-    withName: 'PHYLOSEQ' {
+    withName: PHYLOSEQ {
         publishDir = [
             path: { "${params.outdir}/phyloseq" },
             mode: params.publish_dir_mode,
@@ -835,7 +835,7 @@ process {
         ]
     }
 
-    withName: 'MULTIQC' {
+    withName: MULTIQC {
         ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
         publishDir = [
             path: { "${params.outdir}/multiqc" },

diff --git a/docs/usage.md b/docs/usage.md
@@ -36,7 +36,7 @@ The typical command for running the pipeline is as follows:
 
 ```bash
 nextflow run nf-core/ampliseq \
-    -r 2.6.1 \
+    -r 2.7.0 \
     -profile singularity \
     --input "samplesheet.tsv" \
     --FW_primer GTGYCAGCMGCCGCGGTAA \
@@ -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. 2.6.1, 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.
+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.
 
 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.