Merge pull request #41 from qbic-pipelines/d4straub-ampliseq-readme

Update ampliseq.md

Author: d4straub

docs/markdown/pipelines/ampliseq.md

@@ -1,35 +1,32 @@
 # 16S amplicon sequencing
 
-This is how to perform 16S amplicon analyses.
+This is how to perform 16S amplicon analyses. A video explanation of the biology, the bioinformatics problem and the analysis pipeline can be found for version 2.1.0 in the [nf-core bytesize talk 25](https://nf-co.re/events/2021/bytesize-25-nf-core-ampliseq).
 
 ## Ampliseq pipeline
 
 To perform 16S amplicon sequencing analyses we employ the [nf-core/ampliseq](https://github.com/nf-core/ampliseq) pipeline.
 
 ### Quick start
 
-* Latest stable release `-r 2.1.0`
+* Latest stable release `-r 2.1.1`
 
 A typical command would look like this
 
 ```bash
-nextflow run nf-core/ampliseq -profile cfc -r 2.1.0 \
+nextflow run nf-core/ampliseq -profile cfc -r 2.1.1 \
 --input “data” \
 --FW_primer "GTGYCAGCMGCCGCGGTAA" \
 --RV_primer "GGACTACNVGGGTWTCTAAT" \
 --metadata "metadata.tsv" \
---trunc_qmin 35 \
---classifier_removeHash
+--trunc_qmin 35
 ```
 
-See [here](https://nf-co.re/ampliseq/1.2.0/parameters#manifest) the info on how to create the `metadata.tsv` file.
+Sequencing data can be analysed with the pipeline using a folder containing `.fastq.gz` files with [direct fastq input](https://nf-co.re/ampliseq/2.1.1/usage#direct-fastq-input) or [samplesheet input](https://nf-co.re/ampliseq/2.1.1/usage#samplesheet-input), also see [here](https://nf-co.re/ampliseq/2.1.1/parameters#input).
 
-If data are distributed on multiple sequencing runs, please use `--multipleSequencingRuns` and note the different requirements for metadata file and folder structure in the [pipeline documentation](https://nf-co.re/ampliseq/1.2.0/parameters#multiplesequencingruns)
-
-### Known bugs
+See [here](https://nf-co.re/ampliseq/2.1.1/parameters#metadata) the info on how to create the `metadata.tsv` file.
 
-* All versions include a known bug that is why the `--classifier_removeHash` param should be used.
+If data are distributed on multiple sequencing runs, please use `--multipleSequencingRuns` and note the different requirements for metadata file and folder structure in the [pipeline documentation](https://nf-co.re/ampliseq/1.2.0/parameters#multiplesequencingruns)
 
 ## Reporting
 
-There are no details about reporting yet.
+There are no details about reporting yet. Please refer to the [output documentation](https://nf-co.re/ampliseq/2.1.1/output).