From 795706e07669f1b61d63121df8f9fd1163413a3c Mon Sep 17 00:00:00 2001 From: tm4zza Date: Mon, 3 Feb 2025 19:52:12 +0000 Subject: [PATCH 1/3] bump version to 1.1.0dev and update CHANGELOG.md for new release --- .nf-core.yml | 4 ++-- CHANGELOG.md | 8 +++++--- README.md | 5 ++--- assets/multiqc_config.yml | 7 ++++--- nextflow.config | 2 +- ro-crate-metadata.json | 41 ++++++++++++++++++++++++++------------- 6 files changed, 41 insertions(+), 26 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 210f9a2..1ec2108 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -10,5 +10,5 @@ template: org: nf-core outdir: . skip_features: - - igenomes - version: 1.0.0 + - igenomes + version: 1.1.0dev diff --git a/CHANGELOG.md b/CHANGELOG.md index a23c9e9..f19fb23 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,9 +3,7 @@ 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). -## v[1.0.0](https://github.com/nf-core/fastqrepair/releases/tag/1.0.0) - Catanzaro YellowRed [04/02/2025] - -Initial release of nf-core/fastqrepair, created with the [nf-core](https://nf-co.re/) template. +## v[1.1.0](https://github.com/nf-core/fastqrepair/releases/tag/1.1.0) - Trento YellowBlue [XX/YY/202Z] +## v[1.0.0](https://github.com/nf-core/fastqrepair/releases/tag/1.0.0) - Catanzaro YellowRed [04/02/2025] + +Initial release of nf-core/fastqrepair, created with the [nf-core](https://nf-co.re/) template. + ### `Fixed` - [PR #2](https://github.com/nf-core/fastqrepair/pull/2) - First release diff --git a/README.md b/README.md index 77e0f39..4a2ae81 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ [![GitHub Actions CI Status](https://github.com/nf-core/fastqrepair/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/fastqrepair/actions/workflows/ci.yml) -[![GitHub Actions Linting Status](https://github.com/nf-core/fastqrepair/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/fastqrepair/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/fastqrepair/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![GitHub Actions Linting Status](https://github.com/nf-core/fastqrepair/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/fastqrepair/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/fastqrepair/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.14796348-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.14796348) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/) @@ -87,8 +87,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations - - +If you use nf-core/fastqrepair for your analysis, please cite it using the following doi: [10.5281/zenodo.14796348](https://doi.org/10.5281/zenodo.14796348) An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index ed42af5..ce0e3c4 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,8 @@ report_comment: > - This report has been generated by the nf-core/fastqrepair - analysis pipeline. For information about how to interpret these results, please see the - documentation. + This report has been generated by the nf-core/fastqrepair analysis pipeline. For information about + how to interpret these results, please see the documentation. report_section_order: "nf-core-fastqrepair-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 3807503..6cb683b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -243,7 +243,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'main' nextflowVersion = '!>=24.04.2' - version = '1.0.0' + version = '1.1.0dev' doi = '' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index a96cad1..d98d2b9 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,9 +21,9 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "Stable", - "datePublished": "2025-01-27T14:46:50+00:00", - "description": "

\n \n \n \"nf-core/fastqrepair\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/fastqrepair/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/fastqrepair/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/fastqrepair/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/fastqrepair/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/fastqrepair/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/fastqrepair)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23fastqrepair-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/fastqrepair)[![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/fastqrepair** is a bioinformatics pipeline that ...\n\n\n\n\n1. 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\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/fastqrepair \\\n -profile \\\n --input samplesheet.csv \\\n --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/fastqrepair/usage) and the [parameter documentation](https://nf-co.re/fastqrepair/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/fastqrepair/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/fastqrepair/output).\n\n## Credits\n\nnf-core/fastqrepair was originally written by Tommaso Mazza.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\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 `#fastqrepair` channel](https://nfcore.slack.com/channels/fastqrepair) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\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", + "creativeWorkStatus": "InProgress", + "datePublished": "2025-02-03T19:43:01+00:00", + "description": "

\n \n \n \"nf-core/fastqrepair\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/fastqrepair/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/fastqrepair/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/fastqrepair/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/fastqrepair/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/fastqrepair/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/fastqrepair)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23fastqrepair-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/fastqrepair)[![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/fastqrepair** is a bioinformatics pipeline that can be used to recover corrupted `FASTQ.gz` files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered. It takes a `samplesheet` with FASTQ/FASTQ.gz files as input (both single-end and paired-end) and produces clean FASTQ files and QC reports.\n\n![pipeline_diagram](docs/images/fastqrepair-flow-diagram-v1.0.png)\n\n1. Recover reads from corrupted fastq.gz file ([`gzrt`](https://github.com/arenn/gzrt))\n2. Make recovered reads well-formed ([`wipertools`](https://github.com/mazzalab/fastqwiper))\n3. Re-pair reads ([`bbmap/repair.sh`](https://sourceforge.net/projects/bbmap/))\n4. Check QC of recovered reads ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n5. Aggregate and report QC ([`MultiQC`](https://github.com/MultiQC/MultiQC))\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 title=\"samplesheet.csv\"\nsample,fastq_1,fastq_2\nmysampleA,sample_R1.fastq.gz,sample_R2.fastq.gz\nmysampleB,sample_R3.fq,sample_R4.fq\nmysampleC,sample_R5.fq.gz\n```\n\nEach row represents a FASTQ file (single-end) or a pair of FASTQ files (paired-end).\n\n> [!WARNING]\n> Rows with different file extensions (e.g., `mysampleA,sample_R1.fastq.gz,sample_R2.fastq`) are not allowed.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/fastqrepair \\\n -profile \\\n --input samplesheet.csv \\\n --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/fastqrepair/usage) and the [parameter documentation](https://nf-co.re/fastqrepair/parameters).\n\n## Pipeline output\n\nThis pipeline produces clean and well-formed FASTQ files together with short textual reports of the cleaning actions.\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/fastqrepair/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/fastqrepair/output).\n\n## Credits\n\n`nf-core/fastqrepair` was designed and written by [Tommaso Mazza](https://github.com/mazzalab).\n\n\n\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 `#fastqrepair` channel](https://nfcore.slack.com/channels/fastqrepair) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\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" @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#634a2825-3e33-4286-8cfb-628125724925" + "@id": "#9b2f3ac6-ea91-4257-b44c-e327c98b221d" } ], "name": "nf-core/fastqrepair" @@ -121,9 +121,13 @@ }, { "@id": "main.nf", - "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], + "@type": [ + "File", + "SoftwareSourceCode", + "ComputationalWorkflow" + ], "dateCreated": "", - "dateModified": "2025-01-27T14:46:50Z", + "dateModified": "2025-02-03T19:43:01Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -139,16 +143,25 @@ "unpaired-reads", "well-formed" ], - "license": ["MIT"], - "name": ["nf-core/fastqrepair"], + "license": [ + "MIT" + ], + "name": [ + "nf-core/fastqrepair" + ], "programmingLanguage": { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" }, "sdPublisher": { "@id": "https://nf-co.re/" }, - "url": ["https://github.com/nf-core/fastqrepair", "https://nf-co.re/fastqrepair/1.0.0/"], - "version": ["1.0.0"] + "url": [ + "https://github.com/nf-core/fastqrepair", + "https://nf-co.re/fastqrepair/dev/" + ], + "version": [ + "1.1.0dev" + ] }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", @@ -163,11 +176,11 @@ "version": "!>=24.04.2" }, { - "@id": "#634a2825-3e33-4286-8cfb-628125724925", + "@id": "#9b2f3ac6-ea91-4257-b44c-e327c98b221d", "@type": "TestSuite", "instance": [ { - "@id": "#3d1b71a6-acbd-420b-a915-8dfc6840f2fc" + "@id": "#060cccf9-d2ae-4790-a11c-ec498a820d7a" } ], "mainEntity": { @@ -176,7 +189,7 @@ "name": "Test suite for nf-core/fastqrepair" }, { - "@id": "#3d1b71a6-acbd-420b-a915-8dfc6840f2fc", + "@id": "#060cccf9-d2ae-4790-a11c-ec498a820d7a", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/fastqrepair", "resource": "repos/nf-core/fastqrepair/actions/workflows/ci.yml", @@ -305,4 +318,4 @@ "url": "https://nf-co.re/" } ] -} +} \ No newline at end of file From aa7d04a9cb4523e08b95b99dab71d26f02debf23 Mon Sep 17 00:00:00 2001 From: tm4zza Date: Mon, 3 Feb 2025 19:56:25 +0000 Subject: [PATCH 2/3] Fix line ending in .nf-core.yml --- .nf-core.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.nf-core.yml b/.nf-core.yml index 1ec2108..1feb395 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -10,5 +10,5 @@ template: org: nf-core outdir: . skip_features: - - igenomes + - igenomes version: 1.1.0dev From 89dc47ee473599f8aa878bdf1cea625f67024232 Mon Sep 17 00:00:00 2001 From: tm4zza Date: Mon, 3 Feb 2025 20:02:21 +0000 Subject: [PATCH 3/3] Add newline at end of ro-crate-metadata.json --- ro-crate-metadata.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index d98d2b9..3d4f894 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -318,4 +318,4 @@ "url": "https://nf-co.re/" } ] -} \ No newline at end of file +}