Make the website a delight to use

README.md

@@ -14,7 +14,7 @@
 __Paula Ruiz-Rodriguez<sup>1</sup>__ 
 __and Mireia Coscolla<sup>1</sup>__
 <br>
-<sub> 1. I<sup>2</sup>SysBio, University of Valencia-CSIC, FISABIO Joint Research Unit Infection and Public Health, Valencia, Spain </sub>  
+<sub> 1. I<sup>2</sup>SysBio, University of Valencia-CSIC, FISABIO Joint Research Unit Infection and Public Health, Paterna, Spain </sub>  
 
 <picture>
   <source media="(prefers-color-scheme: dark)" srcset="docs/assets/readme/hero-dark.gif">
@@ -87,14 +87,14 @@ lines are what travels between them. On the website the map is
 
 1. **Database setup** ([eggNOG](https://github.com/eggnogdb/)): builds the eggNOG database if it is not already there.
 2. **MTBC lineage typing** ([pathotypr](https://github.com/PathoGenOmics-Lab/pathotypr)): assigns lineages from phylogenetic markers and renames the genomes accordingly. Turned off with `--skip_typing`.
-3. **Genome annotation** ([Bakta](https://github.com/oschwengers/bakta)): CDS, tRNAs and other features, the baseline that AMAP corrects.
+3. **Genome annotation** ([Bakta](https://github.com/oschwengers/bakta)): CDS, rRNAs and other features (tRNAs are skipped), the baseline that AMAP corrects.
 4. **Protein alignment** ([miniprot](https://github.com/lh3/miniprot)): the reference proteome aligned onto each genome.
 5. **CDS case classification**: every CDS sorted by how it relates to the reference (novel, perfect match, imperfect match, conflicting coordinates, or a reference gene the annotator missed).
 6. **Annotation correction**: conflicts resolved, coordinates adjusted and every gene translated into a corrected gene set.
 7. **Functional annotation** ([eggNOG-mapper](https://github.com/eggnogdb/eggnog-mapper)): COG, KEGG, GO, EC, PFAM and CAZy assignments, and the corrected GFF3 and GenBank.
 8. **Gene duplication analysis**: duplication families per genome, plus homologous communities across genomes with network metrics.
 9. **Pangenome analysis** ([pangene](https://github.com/lh3/pangene)): gene content compared across the whole set.
-10. **Report**: a single self-contained HTML file covering all of the above.
+10. **Reports**: `amap_report.html` in every run, and `final_report.html` after eggNOG, each one self-contained HTML file.
 
 Mycobrowser's functional categories describe tuberculosis genes, so they are
 skipped on their own when a custom reference is not a *Mycobacterium*; lineage
@@ -106,17 +106,20 @@ You need [Nextflow](https://www.nextflow.io/) 24.04 or newer and a container
 engine. Nothing else: every tool lives in the AMAP image, and there is no need
 to clone this repository.
 
+Nextflow needs Java 17 or newer, and Conda brings both:
+
 ```bash
-conda create -n nextflow-env
+conda create -n nextflow-env -c conda-forge -c bioconda nextflow
 conda activate nextflow-env
-conda install -c bioconda nextflow
 ```
 
-Check the installation. This annotates the reference genome bundled in the
-container, so you need no data of your own:
+Check the installation. The test profile annotates the H37Rv genome bundled in
+the image, so you need no data of your own, and `--skip_functional_annotation`
+leaves out eggNOG, so you need no database either:
 
 ```bash
-nextflow run PathoGenOmics-Lab/AMAP -profile docker,test
+nextflow run PathoGenOmics-Lab/AMAP -profile docker,test \
+    --skip_functional_annotation --outdir amap-test
 ```
 
 Write a tab-separated sample sheet:
@@ -152,14 +155,16 @@ for the full set of profiles and options.
 
 ## Results
 
-Everything lands under `--outdir`, `results/` by default. The three to open
-first:
+Everything lands under `--outdir`, `results/` by default. Lineage typing puts
+the lineage in front of each sample's name, so `CDC1551` becomes `L4_CDC1551`,
+and `--skip_typing` leaves the sample ID alone. The ones to open first:
 
 | What | Where |
 | :--- | :--- |
-| The full interactive report | `results/final_report.html` |
-| Corrected annotation, per sample | `results/AMAP/{sampleId}/*-AMAP.gff3` |
-| Proteins for downstream tools | `results/AMAP/{sampleId}/*-AMAP.clean.faa` |
+| Each genome and gene, question by question, in every run | `results/amap_report.html` |
+| The full report, after a run with eggNOG | `results/final_report.html` |
+| Corrected annotation, per sample, after eggNOG | `results/AMAP/{lineage}_{sampleId}/*-AMAP.gff3` |
+| Proteins for downstream tools, after eggNOG | `results/AMAP/{lineage}_{sampleId}/*-AMAP.clean.faa` |
 
 Alongside them, `results/pipeline_info/` holds `software_versions.yml` and
 `params.yml`, which are what belongs in a methods section. Every directory is
@@ -194,7 +199,7 @@ See
   author = {Ruiz-Rodriguez, Paula and Coscolla, Mireia},
   doi = {10.5281/zenodo.8024446},
   license = {GPL-3.0},
-  month = apr,
+  month = jul,
   title = {{AMAP}},
   url = {https://github.com/PathoGenOmics-Lab/AMAP},
   version = {1.0.1},

bin/report/header.html

@@ -11,3 +11,10 @@
 <img id="logo-right-fixed"
      src="PGO.png"
      alt="PathoGenOmics Lab">
+
+<!-- The tab's icon, the website's, inlined like the logos: without one the
+     browser asks the server for /favicon.ico, which is not there. This
+     file goes in the body, and browsers read icons only from the head, so
+     the script moves it there. -->
+<link id="amap-icon" rel="icon" type="image/png" href="data:image/png;base64,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">
+<script>document.head.appendChild(document.getElementById("amap-icon"));</script>