Merge pull request #40 from biocorecrg/v2.0

Update of ExOrthist to DSL2 version and more

.github/workflows/test.yml

@@ -1,17 +1,30 @@
-on:
-  push:
-  workflow_dispatch:
+name: NF-test
 
-name: test-ExOrthist
+on: [push, pull_request, workflow_dispatch]
 
 jobs:
   test:
     runs-on: ubuntu-latest
+
     steps:
-    - name: Check out the repo
-      uses: actions/checkout@v3
-    - name: Install Nextflow
-      uses: nf-core/[email protected]
-      with:
-        version: 20.04.1
-    - run: nextflow run ${GITHUB_WORKSPACE} -with-docker
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up JDK 11
+        uses: actions/setup-java@v2
+        with:
+          java-version: '11'
+          distribution: 'adopt'
+
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "24.10.0"
+
+      - name: Install nf-test
+        run: |
+          wget -qO- https://get.nf-test.com | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Run Tests
+        run: nf-test test --ci

.gitignore

@@ -5,5 +5,6 @@ work
 trace*
 *report*
 logs/*
-*output*
+output*/*
 .nextflow*
+.nf-test*

CITATION.cff

@@ -0,0 +1,62 @@
+# YAML 1.2
+---
+authors:
+  -
+    family-names: Cozzuto
+    given-names: Luca
+    orcid: "https://orcid.org/0000-0003-3194-8892"
+  -
+    family-names: Mantica
+    given-names: Federica
+    orcid: "https://orcid.org/0000-0001-9794-9770"
+  -
+    family-names: Hermoso-Pulido
+    given-names: Antonio
+    orcid: "https://orcid.org/0000-0003-2016-6465"
+cff-version: "1.2.0"
+keywords:
+  - exon
+  - orthology
+  - evolution
+  - containerization
+  - pipeline
+  - reproducibility
+license: MIT
+message: "If you use this software, please cite it using these metadata."
+repository-code: "https://github.com/biocorecrg/ExOrthist"
+title: "ExOrthist: a tool to infer exon orthologies at any evolutionary distance"
+preferred-citation:
+  type: article
+  authors:
+    - family-names: Márquez
+      given-names: Yamile
+      orcid: "https://orcid.org/0000-0003-1686-5992"
+    - family-names: Mantica
+      given-names: Federica
+      orcid: "https://orcid.org/0000-0001-9794-9770"
+    - family-names: Cozzuto
+      given-names: Luca
+      orcid: "https://orcid.org/0000-0003-3194-8892"
+    - family-names: Burguera
+      given-names: Demian
+      orcid: "https://orcid.org/0000-0001-8627-1634"
+    - family-names: "Hermoso-Pulido"
+      given-names: Antonio
+      orcid: "https://orcid.org/0000-0003-2016-6465"
+    - family-names: Ponomarenko
+      given-names: Julia
+      orcid: "https://orcid.org/0000-0002-1477-9444"
+    - family-names: W. Roy
+      given-names: Scott
+    - family-names: Irimia
+      given-names: Manuel
+      orcid: "https://orcid.org/0000-0002-2179-2567"
+  doi: "10.1186/s13059-021-02441-9"
+  journal: "Genome Biology"
+  title: "ExOrthist: a tool to infer exon orthologies at any evolutionary distance"
+  abstract: "Several bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes. However, no corresponding tool allows the detection of exon homology relationships. Here, we present ExOrthist, a fully reproducible Nextflow-based software enabling inference of exon homologs and orthogroups, visualization of evolution of exon-intron structures, and assessment of conservation of alternative splicing patterns. ExOrthist evaluates exon sequence conservation and considers the surrounding exon-intron context to derive genome-wide multi-species exon homologies at any evolutionary distance. We demonstrate its use in different evolutionary scenarios: whole genome duplication in frogs and convergence of Nova-regulated splicing networks (https://github.com/biocorecrg/ExOrthist)."
+  year: 2021
+  volume: 22
+  number: 1
+  issn: 1474-760X
+...

CITATIONS.md

@@ -0,0 +1,29 @@
+# nf-core/demo: Citations
+
+## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
+
+> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.
+
+## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)
+
+> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
+
+## Pipeline tools
+
+- [Mafft](https://pubmed.ncbi.nlm.nih.gov/23329690/)
+
+  > Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013 Apr;30(4):772-80. doi: 10.1093/molbev/mst010. Epub 2013 Jan 16. PMID: 23329690; PMCID: PMC3603318.
+
+## Software packaging/containerisation tools
+
+- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
+
+  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.
+
+- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
+
+  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
+
+- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
+
+  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.