Merge pull request nf-core#367 from nf-core/subway_map

ADD Subway map

CHANGELOG.md

@@ -20,6 +20,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 
 ### Enhancements & fixes
 
+- [[#297](https://github.com/nf-core/viralrecon/issues/297)] - Add tube map for pipeline
 - [[#316](https://github.com/nf-core/viralrecon/issues/316)] - Variant calling isn't run when using `--skip_asciigenome` with metagenomic data
 - [[#317](https://github.com/nf-core/viralrecon/issues/317)] - `ivar_variants_to_vcf`: Ignore lines without annotation in ivar tsv file
 - [[#320](https://github.com/nf-core/viralrecon/issues/320)] - Pipeline fails at email step: Failed to invoke `workflow.onComplete` event handler

README.md

@@ -31,6 +31,8 @@ A number of improvements were made to the pipeline recently, mainly with regard
 
 ### Illumina
 
+![nf-core/viralrecon Illumina metro map](docs/images/nf-core-viralrecon_metro_map_illumina.png)
+
 1. Merge re-sequenced FastQ files ([`cat`](http://www.linfo.org/cat.html))
 2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
 3. Adapter trimming ([`fastp`](https://github.com/OpenGene/fastp))
@@ -61,6 +63,8 @@ A number of improvements were made to the pipeline recently, mainly with regard
 
 ### Nanopore
 
+![nf-core/viralrecon Nanopore metro map](docs/images/nf-core-viralrecon_metro_map_nanopore.png)
+
 1. Sequencing QC ([`pycoQC`](https://github.com/a-slide/pycoQC))
 2. Aggregate pre-demultiplexed reads from MinKNOW/Guppy ([`artic guppyplex`](https://artic.readthedocs.io/en/latest/commands/))
 3. Read QC ([`NanoPlot`](https://github.com/wdecoster/NanoPlot))