From 5699258e4d6b4ccbec9a3d9bfa691d5faef142ae Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Tue, 26 Sep 2023 13:12:09 -0400 Subject: [PATCH] Release v2.6.1 (#23) * avoid running on empty lines * update docker image to named all possible tool versions and update to v2.6 * fix missing meta * allow illumina or bgiseq * fixed fasterq-dump * update changelog * 21 add citation information (#22) * Create CITATION.cff * Update CITATION.cff * Update CITATION.cff * Update CITATION.cff * update docs to have citations * update citation console message * update changelog * update version information * small fix on pacbio download from sra --- .zenodo.json | 2 +- CHANGELOG.md | 7 +++++++ CITATION.cff | 22 ++++++++++++++++++++++ README.md | 11 +++++++++-- docs/index.rst | 11 +++++++++++ lib/WorkflowMain.groovy | 2 +- modules/get_fastq.nf | 14 +++++++++++++- nextflow.config | 2 +- 8 files changed, 65 insertions(+), 6 deletions(-) create mode 100644 CITATION.cff diff --git a/.zenodo.json b/.zenodo.json index c3f8a7c..73b8387 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -2,7 +2,7 @@ "description": "

The pipeline

\n\n

ngs-preprocess is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. It is an easy to use pipeline that uses state-of-the-art software for quality check and pre-processing ngs reads of Illumina, Pacbio and Oxford Nanopore Technologies.

", "license": "other-open", "title": "fmalmeida/ngs-preprocess: A pipeline for preprocessing short and long sequencing reads", - "version": "v2.6", + "version": "v2.6.1", "upload_type": "software", "creators": [ { diff --git a/CHANGELOG.md b/CHANGELOG.md index a475d2f..e5d5f3d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,13 @@ The tracking for changes started in v2.2 +## v2.6.1 -- [2023-Oct-26] + +* [[#21](https://github.com/fmalmeida/ngs-preprocess/issues/21)] - Added/updated citation information +* Small fix on pacbio download from sra + +> Nothing has changed in terms of how tools are called and used, thus the docker image still the same. In fact, patch/fix releases (x.x.x) will always use the docker from breaking/features release (x.x) + ## v2.6 -- [2023-Apr-16] Small bug fixes on SRA_FETCH download modules. Updated pipeline to understand Illumina / BGIseq sequences for short reads. Updated Docker image with named versions of tools whenever possible. diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..9e356ed --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,22 @@ +cff-version: 1.2.0 +message: "If you use this software, please cite it as below." +preferred-citation: + authors: + - family-names: "Almeida" + given-names: "Felipe Marques de" + orcid: "https://orcid.org/0000-0002-6855-3379" + - family-names: "Campos" + given-names: "Tatiana Amabile de" + orcid: "https://orcid.org/0000-0002-0582-2324" + - family-names: "Pappas Jr" + given-names: "Georgios Joannis" + orcid: "https://orcid.org/0000-0002-1100-976X" + title: "Scalable and versatile container-based pipelines for de novo genome assembly and bacterial annotation." + doi: 10.12688/f1000research.139488.1 + date-released: 2023-09-25 + journal: "F1000Research" + volume: 12 + year: 2023 + number: 1205 + type: "article" + diff --git a/README.md b/README.md index 1688ce2..a7bd8ff 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ -[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3451405.svg)](https://doi.org/10.5281/zenodo.3451405) +[![F1000 Paper](https://img.shields.io/badge/Citation%20F1000-10.12688/f1000research.139488.1-orange)](https://doi.org/10.12688/f1000research.139488.1) [![Releases](https://img.shields.io/github/v/release/fmalmeida/ngs-preprocess)](https://github.com/fmalmeida/ngs-preprocess/releases) [![Documentation](https://img.shields.io/badge/Documentation-readthedocs-brightgreen)](https://ngs-preprocess.readthedocs.io/en/latest/?badge=latest) [![Dockerhub](https://img.shields.io/badge/Docker-fmalmeida/ngs--preprocess-informational)](https://hub.docker.com/r/fmalmeida/ngs-preprocess) @@ -10,6 +10,7 @@ [![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/ngs-preprocess/blob/master/LICENSE) +[![Zenodo Archive](https://img.shields.io/badge/Zenodo-Archive-blue)](https://doi.org/10.5281/zenodo.3451405)