Lint fixes

.github/workflows/awsfulltest.yml

@@ -24,9 +24,6 @@ jobs:
 
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

CHANGELOG.md

@@ -5,6 +5,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v1.3.0dev - [date]
 
+### `Fixed`
+
+- [PR #44](https://github.com/nf-core/denovotranscript/pull/44) - Resolved linting warnings. Completed `toolCitationText` and `toolBibliographyText` for reporting (by @vagkaratzas)
+
 ### `Changed`
 
 - [PR #43](https://github.com/nf-core/denovotranscript/pull/43) - Default branch changed from `master` to `main` (by @vagkaratzas)

CITATIONS.md

@@ -28,6 +28,8 @@
 
 - [gawk](https://www.gnu.org/software/gawk/)
 
+  > Robbins AD. Gawk: Effective AWK Programming. Boston: Free Software Foundation. 2004;3.
+
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

assets/methods_description_template.yml

@@ -3,7 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "nf-core/denovotranscript Methods Description"
 section_href: "https://github.com/nf-core/denovotranscript"
 plot_type: "html"
-## 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>

nextflow.config

@@ -209,7 +209,6 @@ profiles {
 includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
 
 // Load nf-core/denovotranscript custom profiles from different institutions.
-// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
 includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/denovotranscript.config" : "/dev/null"
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile

ro-crate-metadata.json

@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-05-23T09:44:35+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-denovotranscript_logo_dark.png\">\n    <img alt=\"nf-core/denovotranscript\" src=\"docs/images/nf-core-denovotranscript_logo_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/denovotranscript/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/denovotranscript/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/denovotranscript/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/denovotranscript/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/denovotranscript/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/denovotranscript)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23denovotranscript-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/denovotranscript)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/denovotranscript** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/denovotranscript \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/denovotranscript/usage) and the [parameter documentation](https://nf-co.re/denovotranscript/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/denovotranscript/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/denovotranscript/output).\n\n## Credits\n\nnf-core/denovotranscript was originally written by Avani Bhojwani and Timothy Little.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#denovotranscript` channel](https://nfcore.slack.com/channels/denovotranscript) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/denovotranscript for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "datePublished": "2025-05-26T15:51:56+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-denovotranscript_logo_dark.png\">\n    <img alt=\"nf-core/denovotranscript\" src=\"docs/images/nf-core-denovotranscript_logo_light.png\">\n  </picture>\n</h1>\n[![GitHub Actions CI Status](https://github.com/nf-core/denovotranscript/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/denovotranscript/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/denovotranscript/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/denovotranscript/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/denovotranscript/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.13324371-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.13324371)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/denovotranscript)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23denovotranscript-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/denovotranscript)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/denovotranscript** is a bioinformatics pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq. It takes a samplesheet and FASTQ files as input, perfoms quality control (QC), trimming, assembly, redundancy reduction, pseudoalignment, and quantification. It outputs a transcriptome assembly FASTA file, a transcript abundance TSV file, and a MultiQC report with assembly quality and read QC metrics.\n\n![nf-core/transfuse metro map](docs/images/denovotranscript_metro_map.drawio.svg)\n\n1. Read QC of raw reads ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Adapter and quality trimming ([`fastp`](https://github.com/OpenGene/fastp))\n3. Read QC of trimmed reads ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n4. Remove rRNA or mitochondrial DNA (optional) ([`SortMeRNA`](https://hpc.nih.gov/apps/sortmeRNA.html))\n5. Transcriptome assembly using any combination of the following:\n\n   - [`Trinity`](https://github.com/trinityrnaseq/trinityrnaseq/wiki) with normalised reads (default=True)\n   - [`Trinity`](https://github.com/trinityrnaseq/trinityrnaseq/wiki) with non-normalised reads\n   - [`rnaSPAdes`](https://ablab.github.io/spades/rna.html) medium filtered transcripts outputted (default=True)\n   - [`rnaSPAdes`](https://ablab.github.io/spades/rna.html) soft filtered transcripts outputted\n   - [`rnaSPAdes`](https://ablab.github.io/spades/rna.html) hard filtered transcripts outputted\n\n6. Redundancy reduction with [`Evidential Gene tr2aacds`](http://arthropods.eugenes.org/EvidentialGene/). A transcript to gene mapping is produced from Evidential Gene's outputs using [`gawk`](https://www.gnu.org/software/gawk/).\n7. Assembly completeness QC ([`BUSCO`](https://busco.ezlab.org/))\n8. Other assembly quality metrics ([`rnaQUAST`](https://github.com/ablab/rnaquast))\n9. Transcriptome quality assessment with [`TransRate`](https://hibberdlab.com/transrate/), including the use of reads for assembly evaluation. This step is not performed if profile is set to `conda` or `mamba`.\n10. Pseudo-alignment and quantification ([`Salmon`](https://combine-lab.github.io/salmon/))\n11. HTML report for raw reads, trimmed reads, BUSCO, and Salmon ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/denovotranscript \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/denovotranscript/usage) and the [parameter documentation](https://nf-co.re/denovotranscript/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/denovotranscript/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/denovotranscript/output).\n\n## Credits\n\nnf-core/denovotranscript was written by Avani Bhojwani ([@avani-bhojwani](https://github.com/avani-bhojwani/)) and Timothy Little ([@timslittle](https://github.com/timslittle/)).\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#denovotranscript` channel](https://nfcore.slack.com/channels/denovotranscript) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/denovotranscript for your analysis, please cite it using the following doi: [10.5281/zenodo.13324371](https://doi.org/10.5281/zenodo.13324371)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -102,7 +102,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#b5d8f586-3a26-429d-b9bb-686a7236d515"
+                    "@id": "#923120d2-708a-4979-92b5-502723f6fcbb"
                 }
             ],
             "name": "nf-core/denovotranscript"
@@ -130,7 +130,7 @@
                 "ComputationalWorkflow"
             ],
             "dateCreated": "",
-            "dateModified": "2025-05-23T10:44:35Z",
+            "dateModified": "2025-05-26T16:51:56Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -172,11 +172,11 @@
             "version": "!>=24.04.2"
         },
         {
-            "@id": "#b5d8f586-3a26-429d-b9bb-686a7236d515",
+            "@id": "#923120d2-708a-4979-92b5-502723f6fcbb",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#67881ca6-82d7-42ea-adf8-1155f43b711a"
+                    "@id": "#0bbfa8d5-16ce-4b19-b05c-579a4c9bbebd"
                 }
             ],
             "mainEntity": {
@@ -185,7 +185,7 @@
             "name": "Test suite for nf-core/denovotranscript"
         },
         {
-            "@id": "#67881ca6-82d7-42ea-adf8-1155f43b711a",
+            "@id": "#0bbfa8d5-16ce-4b19-b05c-579a4c9bbebd",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/denovotranscript",
             "resource": "repos/nf-core/denovotranscript/actions/workflows/ci.yml",