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
fmalmeida · Sep 26, 2023 · 5699258 · 5699258
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diff --git a/.zenodo.json b/.zenodo.json
@@ -2,7 +2,7 @@
     "description": "<p>The pipeline</p>\n\n<p>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.</p>", 
     "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
@@ -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
@@ -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
@@ -1,6 +1,6 @@
 <img src="images/lOGO_3.png" width="300px">
 
-[![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)
 
 <p align="center">
   <!-- <a href="https://github.com/othneildrew/Best-README-Template">
@@ -201,7 +202,13 @@ It will result in the following:
 
 # Citation
 
-To cite this tool please refer to our [Zenodo tag](https://doi.org/10.5281/zenodo.3451405).
+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.3451405).
 
 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).
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -70,6 +70,17 @@ It wraps up the following tools:
   config
   examples
 
+Citation
+********
+
+In order to cite this pipeline, please refer to:
+
+.. code-block:: bash
+
+      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.3451405>`_.
+
 Support Contact
 ***************
 

diff --git a/lib/WorkflowMain.groovy b/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.3451405\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" +

diff --git a/modules/get_fastq.nf b/modules/get_fastq.nf
@@ -20,6 +20,18 @@ process GET_FASTQ {
     --threads $task.cpus \\
     --outdir ./${sra_ids}_data \\
     --progress \\
-    $sra_ids
+    $sra_ids &> fasterq-dump.err || true
+  
+  # is pacbio?
+  if [ \$(grep -ic "is PACBIO, please use fastq-dump instead" fasterq-dump.err) -eq 1 ]
+  then
+      fastq-dump \\
+        --split-files \\
+        --outdir ./${sra_ids}_data \\
+        $sra_ids
+  else
+    echo "fasterq-dump error was:"
+    cat fasterq-dump.err
+  fi
   """
 }
diff --git a/nextflow.config b/nextflow.config
@@ -93,5 +93,5 @@ manifest {
   homePage        = "https://github.com/fmalmeida/ngs-preprocess"
   mainScript      = "main.nf"
   nextflowVersion = ">=21.10.0"
-  version         = "2.6"
+  version         = "2.6.1"
 }