Saving code that was wrongly merged to master instead of dev (#56)

* 31 new directory called final output (#48)

* add illumina docker test (#44)

* Update github actions for testing profiles (#46)

* add illumina docker test

* add other workflows as template

* update sreads singularity test action

* update lreads test actions

* add hybrid test actions

* remove unnecessary comments

* 30 change to unicycler v050 (#45)

* update version information

* remove old spades binary for new unicycler version

* update dockerfile to use new conda recipe

* add testing profiles

* working conda installation

* update multiqc report

* fixed docker image

* increase asked cpus

* Update nextflow_schema.json

* decrease expected genome size

* fix long reads assemblers installation

* split long reads samplesheets

* flye require 10.GB RAM

* update workflows

* easimon do not work in macos

* update java

* small update for tests

* canu needs 4 cpus

* update genome size value

* split samplesheet in ont & pacbio

* split proflies in ont & pacbio (hybrid)

* delete unused files

* new docker image has new python version

* docker image fixed

* skip flye tht requires much memory

* fixed pacbio execution

* revert to ubuntu

* canu also is too much for git actions

* remove unnecessary files

* modify pilon polish script to run on number of desired rounds

* fix output namings

* fix outputs

* pacbio profile working

* update pilon info in docs

* update changelog

* upload yml with version of installed tools

* update docs

* use quast to save resulting assemblies

* include citation information (#51)

* Update README.md

* update config

README.md

@@ -1,15 +1,16 @@
 <img src="assets/lOGO_3.png" width="300px">
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3997375.svg)](https://doi.org/10.5281/zenodo.3445485)
-[![Releases](https://img.shields.io/github/v/release/fmalmeida/mpgap)](https://github.com/fmalmeida/mpgap/releases)
+[![F1000 Paper](https://img.shields.io/badge/Citation%20F1000-10.12688/f1000research.139488.1-orange)](https://doi.org/10.12688/f1000research.139488.1)
+[![GitHub release (latest by date including pre-releases)](https://img.shields.io/github/v/release/fmalmeida/mpgap?include_prereleases&label=Latest%20release)](https://github.com/fmalmeida/mpgap/releases)
 [![Documentation](https://img.shields.io/badge/Documentation-readthedocs-brightgreen)](https://mpgap.readthedocs.io/en/latest/?badge=latest)
-[![Dockerhub](https://img.shields.io/badge/Docker-fmalmeida/mpgap-informational)](https://hub.docker.com/r/fmalmeida/mpgap)
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.04.0-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
-[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
-[![Follow on Twitter](http://img.shields.io/badge/twitter-%40fmarquesalmeida-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/fmarquesalmeida)
 [![License](https://img.shields.io/badge/License-GPL%203-black)](https://github.com/fmalmeida/mpgap/blob/master/LICENSE)
+[![Follow on Twitter](http://img.shields.io/badge/twitter-%40fmarquesalmeida-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/fmarquesalmeida)
+[![Zenodo Archive](https://img.shields.io/badge/Zenodo-Archive-blue)](https://doi.org/10.5281/zenodo.3445485)
+
+[![Open in Gitpod](https://gitpod.io/button/open-in-gitpod.svg)](https://gitpod.io/github.com/fmalmeida/mpgap)
 
 <p align="center">
 
@@ -290,7 +291,11 @@ It will result in the following:
 
 ## Citation
 
-To cite this tool please refer to our [Zenodo tag](https://doi.org/10.5281/zenodo.3445485).
+In order to cite this pipeline, please refer to:
+
+> Almeida FMd, Campos TAd and Pappas Jr GJ. Scalable and versatile container-based pipelines for de novo genome assembly and bacterial annotation. [version 1; peer review: awaiting peer review]. F1000Research 2023, 12:1205 (https://doi.org/10.12688/f1000research.139488.1)
+
+Additionally, archived versions of the pipeline are also found in [Zenodo](https://doi.org/10.5281/zenodo.3445485).
 
 This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [GPLv3](https://github.com/fmalmeida/ngs-preprocess/blob/master/LICENSE).
 

docs/index.rst

@@ -45,6 +45,15 @@ It wraps up the following tools:
    manual
    config
 
+Citation
+--------
+
+In order to cite this pipeline, please refer to:
+
+> Almeida FMd, Campos TAd and Pappas Jr GJ. Scalable and versatile container-based pipelines for de novo genome assembly and bacterial annotation. [version 1; peer review: awaiting peer review]. F1000Research 2023, 12:1205 (https://doi.org/10.12688/f1000research.139488.1)
+
+Additionally, archived versions of the pipeline are also found in `Zenodo <https://doi.org/10.5281/zenodo.3445485>`_.
+
 Support Contact
 ---------------
 Whenever a doubt arise feel free to contact me at [email protected]

lib/WorkflowMain.groovy

@@ -10,7 +10,7 @@ class WorkflowMain {
     public static String citation(workflow) {
         return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
             "* The pipeline\n" +
-            "  https://doi.org/10.5281/zenodo.3445485\n\n" +
+            "  https://doi.org/10.12688/f1000research.139488.1\n\n" +
             "* The nf-core framework\n" +
             "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
             "* Software dependencies\n" +

markdown/CHANGELOG.md

@@ -6,6 +6,7 @@ The tracking for changes started in v2.
 
 * Update unicyler to v0.5.0
 * Adjust Pilon polishing module to select how many rounds of poloshing to run. Default is 4.
+* Add a directory called `final_assemblies` in the main output directory holding all the assemblies generated in the pipeline execution.
 
 ## v3.1.4 -- [2022-Sep-03]