Input samples given only via samplesheet (#40)

* changed how tags are used

Now they show information about the sample, not the task

* updating changelog

* label was wrongly remove

* starting to reimplement pipeline using only samplesheet

* updating docs, now must update quickstart

* fixing docs index

* small fix

* updating docs section levels

* already adding changelog

* organizing tags

* changing versions

* Update nextflow_schema.json

* updating example YAML info

* updating info about fast5 tags

* quickstart updated

* adding test dataset

* fixing test dataset

* fixing test dataset path

* fixing flye and unicycler docker image

* cleaning file

* correct species

* adding manifest

* making yaml parsing more concise

* fixing output parameter usage

* fixing samplesheet copy to output

* fixing samplesheet basename

* update zenodo json

* updating version information

* add resfinder manual information

* update quickstart information

* little update

.gitignore

@@ -2,5 +2,6 @@
 .Rhistory
 .RData
 .Ruserdata
+TESTE
 docs/_html
-teste
+teste

.zenodo.json

@@ -1,8 +1,8 @@
 {
-    "description": "<p>The pipeline</p>\n\n<p>bacannot, is a customisable, easy to use, pipeline that uses state-of-the-art software for comprehensively annotating prokaryotic genomes having only Docker and Nextflow as dependencies. It is able to annotate and detect virulence and resistance genes, plasmids, genomic islands, prophages, ICEs, KO, and more.</p>\n\n<p>Release notes</p>\n\n<p>This is a super small fix:</p>", 
+    "description": "<p>The pipeline</p>\n\n<p>bacannot, is a customisable, easy to use, pipeline that uses state-of-the-art software for comprehensively annotating prokaryotic genomes having only Docker and Nextflow as dependencies. It is able to annotate and detect virulence and resistance genes, plasmids, secondary metabolites, genomic islands, prophages, ICEs, KO, and more.</p>", 
     "license": "other-open", 
-    "title": "fmalmeida/bacannot: fmalmeida/bacannot v2.4.2", 
-    "version": "v2.4.2", 
+    "title": "fmalmeida/bacannot: A generic but comprehensive bacterial annotation pipeline", 
+    "version": "v3.0", 
     "upload_type": "software",
     "creators": [
         {

README.md

@@ -1,6 +1,11 @@
 <img src="images/lOGO_3.png" width="300px">
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3627669.svg)](https://doi.org/10.5281/zenodo.3627669) [![GitHub release (latest by date including pre-releases)](https://img.shields.io/github/v/release/fmalmeida/bacannot?include_prereleases&label=Latest%20release)](https://github.com/fmalmeida/bacannot/releases) [![Documentation](https://img.shields.io/badge/Documentation-readthedocs-brightgreen)](https://bacannot.readthedocs.io/en/latest/?badge=latest) [![Dockerhub](https://img.shields.io/badge/Docker-fmalmeida/bacannot-informational)](https://hub.docker.com/r/fmalmeida/bacannot) [![Nextflow version](https://img.shields.io/badge/Nextflow%20>=-v20.07-important)](https://www.nextflow.io/docs/latest/getstarted.html) [![License](https://img.shields.io/badge/License-GPL%203-black)](https://github.com/fmalmeida/bacannot/blob/master/LICENSE)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3627669.svg)](https://doi.org/10.5281/zenodo.3627669)
+[![GitHub release (latest by date including pre-releases)](https://img.shields.io/github/v/release/fmalmeida/bacannot?include_prereleases&label=Latest%20release)](https://github.com/fmalmeida/bacannot/releases)
+[![Documentation](https://img.shields.io/badge/Documentation-readthedocs-brightgreen)](https://bacannot.readthedocs.io/en/latest/?badge=latest)
+[![Dockerhub](https://img.shields.io/badge/Docker-fmalmeida/bacannot-informational)](https://hub.docker.com/r/fmalmeida/bacannot)
+[![Nextflow version](https://img.shields.io/badge/Nextflow%20>=-v20.07-important)](https://www.nextflow.io/docs/latest/getstarted.html)
+[![License](https://img.shields.io/badge/License-GPL%203-black)](https://github.com/fmalmeida/bacannot/blob/master/LICENSE)
 
 <p align="center">
 
@@ -78,20 +83,19 @@ These images have been kept separate to not create massive Docker image and to a
 
     * Required
 
-          docker pull fmalmeida/bacannot:v2.4         # Main image for core annotations
-          docker pull fmalmeida/bacannot:v2.4_renv    # R packages for reports
+          docker pull fmalmeida/bacannot:v3.0         # Main image for core annotations
+          docker pull fmalmeida/bacannot:v3.0_renv    # R packages for reports
           docker pull fmalmeida/bacannot:jbrowse      # JBrowse software
 
     * Optional
 
           docker pull fmalmeida/bacannot:kofamscan    # If user wants KO annotation
           docker pull fmalmeida/bacannot:antismash    # If user wants antismash annotation
           docker pull fmalmeida/bacannot:server       # If user wants to open the shiny parser
-          docker pull fmalmeida/mpgap:v2.3            # If using raw reads as input
 
 🔥 Nextflow can also automatically handle images download on the fly when executed. However, some servers may hang the download due to the image size (view below).
 
-❗ If the download of `fmalmeida/bacannot:v2.4` image keeps hanging due to its size, download `fmalmeida/bacannot:main_tools` first. It is the core of the versioned tag and it will help on the download by creating some cache.
+❗ If the download of `fmalmeida/bacannot:v3.0` image keeps hanging due to its size, download `fmalmeida/bacannot:main_tools` first. It is the core of the versioned tag and it will help on the download by creating some cache.
 
 2. Install Nextflow (version 20.07 or higher):
 
@@ -105,33 +109,19 @@ These images have been kept separate to not create massive Docker image and to a
 
 ### Maintaining databases up-to-date
 
-By default, github actions have been set to build the docker image containing the databases (`fmalmeida/bacannot:v2.4`) in the first day of every month. Therefore, to use the most up-to-date databases users must run `docker pull fmalmeida/bacannot:v2.4` before running the pipeline.
+To use the most up-to-date databases users must run `docker pull fmalmeida/bacannot:v3.0` before running the pipeline. We try to keep this image updated every three months if they pass execution tests after built.
 
-Additionally, a custom script is provided to allow users to update the database image any time.
+A custom script is provided to allow users to update the database image any time, if desired.
 
 ```bash
 bash <(wget -O - -o /dev/null https://github.com/fmalmeida/bacannot/raw/master/bin/update_database_image.sh)
 ```
 
-> This command line will trigger a custom script that downloads the databases and build the fmalmeida/bacannot:v2.4 docker image.
+> This command line will trigger a custom script that downloads the databases and build the main docker image.
 
 ## Quickstart
 
-For a rapid and simple quickstart we will use as input the _Escherichia coli_ reference genome.
-
-```bash
-
-  # Download the ecoli ref genome
-  wget -O ecoli_ref.fna.gz https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/008/865/GCF_000008865.2_ASM886v2/GCF_000008865.2_ASM886v2_genomic.fna.gz
-  gzip -d ecoli_ref.fna.gz
-
-  # Run the pipeline using the Escherichia coli resfinder database
-  nextflow run fmalmeida/bacannot \
-  --prefix ecoli \
-  --genome ecoli_ref.fna \
-  --outdir _ANNOTATION \
-  --threads 4 \
-  --resfinder_species "Escherichia coli"
+<a href="https://bacannot.readthedocs.io/en/latest/quickstart.html"><strong>Please refer to the quickstart page »</strong></a>
 ```
 
 ### Overview of outputs