Merge pull request #303 from nf-core/dev

Release PR for 1.1.3

.github/CONTRIBUTING.md

@@ -116,4 +116,3 @@ To get started:
 Devcontainer specs:
 
 - [DevContainer config](.devcontainer/devcontainer.json)
-- [Dockerfile](.devcontainer/Dockerfile)

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -42,7 +42,7 @@ body:
     attributes:
       label: System information
       description: |
-        * Nextflow version _(eg. 22.10.1)_
+        * Nextflow version _(eg. 23.04.0)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_

.github/workflows/awsfulltest.yml

@@ -14,18 +14,23 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v1
+        uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/funcscan/work-${{ github.sha }}
           parameters: |
             {
+              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/funcscan/results-${{ github.sha }}"
             }
-          profiles: test_full,aws_tower
+          profiles: test_full
+
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
+          path: |
+            tower_action_*.log
+            tower_action_*.json

.github/workflows/awstest.yml

@@ -12,18 +12,22 @@ jobs:
     steps:
       # Launch workflow using Tower CLI tool action
       - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v1
+        uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/funcscan/work-${{ github.sha }}
           parameters: |
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/funcscan/results-test-${{ github.sha }}"
             }
-          profiles: test,aws_tower
+          profiles: test
+
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
+          path: |
+            tower_action_*.log
+            tower_action_*.json

.github/workflows/ci.yml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "22.10.1"
+          - "23.04.0"
           - "latest-everything"
         parameters:
           - "--annotation_tool prodigal"
@@ -52,7 +52,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "22.10.1"
+          - "23.04.0"
           - "latest-everything"
         parameters:
           - "--annotation_tool prodigal"
@@ -72,31 +72,31 @@ jobs:
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_bgc,docker --outdir ./results ${{ matrix.parameters }}
 
-  test_deeparg:
-    name: Run pipeline with test data (DeepARG only workflow)
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/funcscan') }}"
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        NXF_VER:
-          - "22.10.1"
-          - "latest-everything"
-        parameters:
-          - "--annotation_tool bakta --annotation_bakta_db_downloadtype light"
-          - "--annotation_tool prodigal"
-          - "--annotation_tool prokka"
-          - "--annotation_tool pyrodigal"
+  # test_deeparg: #Tests switched off as long as DeepARG servers are unavaiable for database download.
+  #   name: Run pipeline with test data (DeepARG only workflow)
+  #   # Only run on push if this is the nf-core dev branch (merged PRs)
+  #   if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/funcscan') }}"
+  #   runs-on: ubuntu-latest
+  #   strategy:
+  #     matrix:
+  #       NXF_VER:
+  #         - "23.04.0"
+  #         - "latest-everything"
+  #       parameters:
+  #         - "--annotation_tool bakta --annotation_bakta_db_downloadtype light"
+  #         - "--annotation_tool prodigal"
+  #         - "--annotation_tool prokka"
+  #         - "--annotation_tool pyrodigal"
 
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
+  #   steps:
+  #     - name: Check out pipeline code
+  #       uses: actions/checkout@v2
 
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
-        with:
-          version: "${{ matrix.NXF_VER }}"
+  #     - name: Install Nextflow
+  #       uses: nf-core/setup-nextflow@v1
+  #       with:
+  #         version: "${{ matrix.NXF_VER }}"
 
-      - name: Run pipeline with test data (DeepARG workflow)
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_deeparg,docker --outdir ./results ${{ matrix.parameters }}
+  #     - name: Run pipeline with test data (DeepARG workflow)
+  #       run: |
+  #         nextflow run ${GITHUB_WORKSPACE} -profile test_deeparg,docker --outdir ./results ${{ matrix.parameters }}

.gitpod.yml

@@ -1,4 +1,9 @@
 image: nfcore/gitpod:latest
+tasks:
+  - name: Update Nextflow and setup pre-commit
+    command: |
+      pre-commit install --install-hooks
+      nextflow self-update
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack

CHANGELOG.md

@@ -3,6 +3,31 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.1.3 - [2023-08-11]
+
+### `Added`
+
+- [#290](https://github.com/nf-core/funcscan/pull/290) Merged pipeline template of nf-core/tools version 2.9, updated references. (by @jfy133)
+- [#285](https://github.com/nf-core/funcscan/pull/285) Use nf-validation for samplesheet checking and added support for `fna.gz` input FASTA files. (by @louperelo, @mirpedrol, @jfy133)
+- [#295](https://github.com/nf-core/funcscan/pull/295) Add Prokka to MultiQC output. (by @louperelo)
+
+### `Fixed`
+
+- [#296](https://github.com/nf-core/funcscan/pull/296) Fixed empty output when saving prodigal annotations. (reported by @louperelo, fix by @jasmezz)
+- [#297](https://github.com/nf-core/funcscan/pull/297) Added check for empty annotation files prior going into screening. (❤️ to @alexhbnr for requesting, added by @jfy133)
+- [#299](https://github.com/nf-core/funcscan/pull/299) Fixed pigz error with symlinks in Pyrodigal. (by @jasmezz)
+- [#300](https://github.com/nf-core/funcscan/pull/300) Fixed wrong Pyrodigal channels being submitted to antiSMASH. (reported by Till Bayer, fix by @jasmezz)
+- [#302](https://github.com/nf-core/funcscan/pull/302) Removed trouble-causing default parameters in json schema. (by @robsyme)
+
+### `Dependencies`
+
+| Tool   | Previous version | New version |
+| ------ | ---------------- | ----------- |
+| comBGC | 0.6.0            | 0.6.1       |
+| GECCO  | 0.9.2            | 0.9.8       |
+
+### `Deprecated`
+
 ## v1.1.2 - [2023-06-30]
 
 ### `Added`

CITATIONS.md

@@ -20,7 +20,7 @@
 
 - [AMPlify](https://doi.org/10.1186/s12864-022-08310-4)
 
-  > CLi, C., Sutherland, D., Hammond, S. A., Yang, C., Taho, F., Bergman, L., Houston, S., Warren, R. L., Wong, T., Hoang, L., Cameron, C. E., Helbing, C. C., & Birol, I. (2022). AMPlify: attentive deep learning model for discovery of novel antimicrobial peptides effective against WHO priority pathogens. BMC genomics, 23(1), 77. [DOI: 10.1186/s12864-022-08310-4](https://doi.org/10.1186/s12864-022-08310-4)
+  > Li, C., Sutherland, D., Hammond, S. A., Yang, C., Taho, F., Bergman, L., Houston, S., Warren, R. L., Wong, T., Hoang, L., Cameron, C. E., Helbing, C. C., & Birol, I. (2022). AMPlify: attentive deep learning model for discovery of novel antimicrobial peptides effective against WHO priority pathogens. BMC genomics, 23(1), 77. [DOI: 10.1186/s12864-022-08310-4](https://doi.org/10.1186/s12864-022-08310-4)
 
 - [AMRFinderPlus](https://doi.org/10.1038/s41598-021-91456-0)
 
@@ -34,6 +34,14 @@
 
   > Schwengers, O., Jelonek, L., Dieckmann, M. A., Beyvers, S., Blom, J., & Goesmann, A. (2021). Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microbial Genomics, 7(11). [DOI: 10.1099/mgen.0.000685](https://doi.org/10.1099/mgen.0.000685)
 
+- [bioawk](https://github.com/lh3/bioawk)
+
+  > Li, H. (2023). bioawk: BWK awk modified for biological data. Github. Retrieved July 12, 2023, from https://github.com/lh3/bioawk
+
+- [comBGC](https://github.com/nf-core/funcscan)
+
+  > Frangenberg, J., Fellows Yates, J. A., Ibrahim, A., Perelo, L., & Beber, M. E. (2023). nf-core/funcscan: 1.0.0 - German Rollmops - 2023-02-15. https://doi.org/10.5281/zenodo.7643100
+
 - [DeepARG](https://doi.org/10.1186/s40168-018-0401-z)
 
   > Arango-Argoty, G., Garner, E., Pruden, A., Heath, L. S., Vikesland, P., & Zhang, L. (2018). DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data. Microbiome, 6(1), 23. [DOI: 10.1186/s40168-018-0401-z](https://doi.org/10.1186/s40168-018-0401-z)
@@ -48,16 +56,16 @@
 
 - [GECCO](https://gecco.embl.de)
 
-  > Carroll, L. M. , Larralde, M., Fleck, J. S., Ponnudurai, R., Milanese, A., Cappio Barazzone, E. & Zeller, G. (2021). Accurate de novo identification of biosynthetic gene clusters with GECCO. bioRxiv [DOI: 10.1101/2021.05.03.442509](https://doi.org/10.1101/2021.05.03.442509)
-
-- [hAMRonization](https://github.com/pha4ge/hAMRonization)
-
-  > Public Health Alliance for Genomic Epidemiology (pha4ge). (2022). Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure. Github. Retrieved October 5, 2022, from [https://github.com/pha4ge/hAMRonization](https://github.com/pha4ge/hAMRonization)
+  > Carroll, L. M. , Larralde, M., Fleck, J. S., Ponnudurai, R., Milanese, A., Cappio Barazzone, E. & Zeller, G. (2021). Accurate de novo identification of biosynthetic gene clusters with GECCO. bioRxiv. [DOI: 10.1101/2021.05.03.442509](https://doi.org/10.1101/2021.05.03.442509)
 
 - [AMPcombi](https://github.com/Darcy220606/AMPcombi)
 
   > Ibrahim, A. & Perelo, L. (2023). Darcy220606/AMPcombi. [DOI: 10.5281/zenodo.7639121](https://doi.org/10.5281/zenodo.7639121).
 
+- [hAMRonization](https://github.com/pha4ge/hAMRonization)
+
+  > Maguire, F., Fornika, D., Mendes, I., Phelan, J., Underwood, A., Witney, A., pvanheus, Manuele, A., Lee, T., amos, & imendes. (2023). pha4ge/hAMRonization: Zenodo Release. Zenodo. https://doi.org/10.5281/ZENODO.8131134
+
 - [HMMER](https://doi.org/10.1371/journal.pcbi.1002195.)
 
   > Eddy S. R. (2011). Accelerated Profile HMM Searches. PLoS computational biology, 7(10), e1002195. [DOI: 10.1371/journal.pcbi.1002195](https://doi.org/10.1371/journal.pcbi.1002195)
@@ -98,5 +106,8 @@
 
 - [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, G. M., Sochat, V., & Bauer, M. W. (2017). Singularity: Scientific containers for mobility of compute. PloS one, 12(5), e0177459. [DOI: 10.1371/journal.pone.0177459](https://doi.org/10.1371/journal.pone.0177459)
+
+  > 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.

README.md

@@ -1,7 +1,8 @@
 # ![nf-core/funscan](docs/images/nf-core-funcscan_logo_flat_light.png#gh-light-mode-only) ![nf-core/funscan](docs/images/nf-core-funcscan_logo_flat_dark.png#gh-dark-mode-only)
 
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/funcscan/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7643099-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7643099)
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](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/)
 [![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/)
@@ -67,11 +68,11 @@ nextflow run nf-core/funcscan \
 > provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
 > see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
 
-For more details, please refer to the [usage documentation](https://nf-co.re/funcscan/usage) and the [parameter documentation](https://nf-co.re/funcscan/parameters).
+For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/funcscan/usage) and the [parameter documentation](https://nf-co.re/funcscan/parameters).
 
 ## Pipeline output
 
-To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/funcscan/results) tab on the nf-core website pipeline page.
+To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/funcscan/results) tab on the nf-core website pipeline page.
 For more details about the output files and reports, please refer to the
 [output documentation](https://nf-co.re/funcscan/output).
 

assets/methods_description_template.yml

@@ -3,17 +3,21 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "nf-core/funcscan Methods Description"
 section_href: "https://github.com/nf-core/funcscan"
 plot_type: "html"
-## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
+## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
 ## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>
-  <p>Data was processed using nf-core/funcscan v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>).</p>
+  <p>Data was processed using nf-core/funcscan v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
   <p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
   <pre><code>${workflow.commandLine}</code></pre>
+  <p>${tool_citations}</p>
   <h4>References</h4>
   <ul>
-    <li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. <a href="https://doi.org/10.1038/nbt.3820">https://doi.org/10.1038/nbt.3820</a></li>
-    <li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. <a href="https://doi.org/10.1038/s41587-020-0439-x">https://doi.org/10.1038/s41587-020-0439-x</a></li>
+    <li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: <a href="https://doi.org/10.1038/nbt.3820">10.1038/nbt.3820</a></li>
+    <li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: <a href="https://doi.org/10.1038/s41587-020-0439-x">10.1038/s41587-020-0439-x</a></li>
+    <li>Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: <a href="https://doi.org/10.1038/s41592-018-0046-7">10.1038/s41592-018-0046-7</a></li>
+    <li>da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: <a href="https://doi.org/10.1093/bioinformatics/btx192">10.1093/bioinformatics/btx192</a></li>
+    ${tool_bibliography}
   </ul>
   <div class="alert alert-info">
     <h5>Notes:</h5>

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/funcscan" target="_blank">nf-core/funcscan</a>
+  This report has been generated by the <a href="https://github.com/nf-core/funcscan/1.1.3" target="_blank">nf-core/funcscan</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/funcscan" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/funcscan/1.1.3/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-funcscan-methods-description":
     order: -1000
@@ -15,3 +15,6 @@ export_plots: true
 custom_logo: "nf-core-funcscan_logo_flat_light.png"
 custom_logo_url: https://nf-co.re/funcscan
 custom_logo_title: "nf-core/funcscan"
+
+## Tool specific configuration
+prokka_fn_snames: True

assets/schema_input.json

@@ -10,27 +10,19 @@
             "sample": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "Sample name must be provided and cannot contain spaces"
+                "errorMessage": "Sample name must be provided and cannot contain spaces",
+                "meta": ["id"],
+                "unique": true
             },
-            "fastq_1": {
+            "fasta": {
                 "type": "string",
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
-                "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
-            },
-            "fastq_2": {
-                "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
-                "anyOf": [
-                    {
-                        "type": "string",
-                        "pattern": "^\\S+\\.f(ast)?q\\.gz$"
-                    },
-                    {
-                        "type": "string",
-                        "maxLength": 0
-                    }
-                ]
+                "format": "file-path",
+                "exists": true,
+                "pattern": "^\\S+\\.f(ast|n)?a\\.gz$",
+                "errorMessage": "Fasta file for reads must be provided, cannot contain spaces and must have extension '.fa.gz', '.fna.gz' or '.fasta.gz'",
+                "unique": true
             }
         },
-        "required": ["sample", "fastq_1"]
+        "required": ["sample", "fasta"]
     }
 }