diff --git a/.nf-core.yml b/.nf-core.yml index 66892cca..6d63961e 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -16,4 +16,4 @@ template: name: methylseq org: nf-core outdir: . - version: 3.0.0 + version: 3.1.0dev diff --git a/CHANGELOG.md b/CHANGELOG.md index 0058b0c2..526c890e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,16 @@ 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). +## [v3.1.0](https://github.com/nf-core/methylseq/releases/tag/3.1.0) - [] + +### Bug fixes & refactoring + +- + +### Pipeline Updates + +- + ## [v3.0.0](https://github.com/nf-core/methylseq/releases/tag/3.0.0) - [2024-12-16] ### Bug fixes & refactoring diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index a702a0b7..0639e2fa 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/methylseq analysis pipeline. For information about how - to interpret these results, please see the documentation. report_section_order: "nf-core-methylseq-methods-description": diff --git a/nextflow.config b/nextflow.config index 275b2202..42b4ed51 100644 --- a/nextflow.config +++ b/nextflow.config @@ -361,7 +361,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=24.10.2' - version = '3.0.0' + version = '3.1.0dev' doi = '10.5281/zenodo.1343417' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 788e0b89..278d75c8 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -4,8 +4,8 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "Stable", - "datePublished": "2024-12-16T12:03:17+00:00", + "creativeWorkStatus": "InProgress", + "datePublished": "2024-12-17T03:21:12+00:00", "description": "

\n \n \n \"nf-core/methylseq\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/methylseq/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/methylseq/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/methylseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/methylseq/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/methylseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1343417-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1343417)\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%A524.10.2-23aa62.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/methylseq)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23methylseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/methylseq)[![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/methylseq** is a bioinformatics analysis pipeline used for Methylation (Bisulfite) sequencing data. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.\n\n![nf-core/methylseq metro map](docs/images/3.0.0_metromap.png)\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), 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.\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/methylseq/results).\n\n> Read more about **Bisulfite Sequencing & Three-Base Aligners** used in this pipeline [here](./docs/bs-seq-primer.md)\n\n## Pipeline Summary\n\nThe pipeline allows you to choose between running either [Bismark](https://github.com/FelixKrueger/Bismark) or [bwa-meth](https://github.com/brentp/bwa-meth) / [MethylDackel](https://github.com/dpryan79/methyldackel).\n\nChoose between workflows by using `--aligner bismark` (default, uses bowtie2 for alignment), `--aligner bismark_hisat` or `--aligner bwameth`. For higher performance, the pipeline can leverage the [Parabricks implementation of bwa-meth (fq2bammeth)](https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam_meth.html), which implements the baseline tool `bwa-meth` in a performant method using fq2bam (BWA-MEM + GATK) as a backend for processing on GPU. To use this option, include the `--use_gpu` flag along with `--aligner bwameth`.\n\n| Step | Bismark workflow | bwa-meth workflow |\n| -------------------------------------------- | ------------------------ | --------------------- |\n| Generate Reference Genome Index _(optional)_ | Bismark | bwa-meth |\n| Merge re-sequenced FastQ files | cat | cat |\n| Raw data QC | FastQC | FastQC |\n| Adapter sequence trimming | Trim Galore! | Trim Galore! |\n| Align Reads | Bismark (bowtie2/hisat2) | bwa-meth |\n| Deduplicate Alignments | Bismark | Picard MarkDuplicates |\n| Extract methylation calls | Bismark | MethylDackel |\n| Sample report | Bismark | - |\n| Summary Report | Bismark | - |\n| Alignment QC | Qualimap _(optional)_ | Qualimap _(optional)_ |\n| Sample complexity | Preseq _(optional)_ | Preseq _(optional)_ |\n| Project Report | 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\nsample,fastq_1,fastq_2,genome\nSRR389222_sub1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz,,\nSRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz,,\nSRR389222_sub3,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz,,\nEcoli_10K_methylated,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz,\n```\n\n> Each row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using default parameters as:\n\n```bash\nnextflow run nf-core/methylseq --input samplesheet.csv --outdir --genome GRCh37 -profile \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/methylseq/usage) and the [parameter documentation](https://nf-co.re/methylseq/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/methylseq/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/methylseq/output).\n\n## Credits\n\nnf-core/methylseq was originally written by Phil Ewels ([@ewels](https://github.com/ewels)), and Sateesh Peri ([@sateeshperi](https://github.com/sateeshperi)) is its active maintainer.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- Felix Krueger ([@FelixKrueger](https://github.com/FelixKrueger))\n- Edmund Miller ([@EMiller88](https://github.com/emiller88))\n- Rickard Hammar\u00e9n ([@Hammarn](https://github.com/Hammarn/))\n- Alexander Peltzer ([@apeltzer](https://github.com/apeltzer/))\n- Patrick H\u00fcther ([@phue](https://github.com/phue/))\n- Maxime U Garcia ([@maxulysse](https://github.com/maxulysse/))\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 `#methylseq` channel](https://nfcore.slack.com/channels/methylseq) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/methylseq for your analysis, please cite it using the following doi: [10.5281/zenodo.1343417](https://doi.org/10.5281/zenodo.1343417)\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": [ { @@ -101,7 +101,7 @@ "@id": "main.nf", "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], "dateCreated": "", - "dateModified": "2024-12-16T12:03:17Z", + "dateModified": "2024-12-17T03:21:12Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -123,8 +123,8 @@ "sdPublisher": { "@id": "https://nf-co.re/" }, - "url": ["https://github.com/nf-core/methylseq", "https://nf-co.re/methylseq/3.0.0/"], - "version": ["3.0.0"] + "url": ["https://github.com/nf-core/methylseq", "https://nf-co.re/methylseq/dev/"], + "version": ["3.1.0dev"] }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", diff --git a/tests/bismark_cat_fastq_skip_trimming_skip_deduplication.nf.test.snap b/tests/bismark_cat_fastq_skip_trimming_skip_deduplication.nf.test.snap index fc01cbc3..5a5fb292 100644 --- a/tests/bismark_cat_fastq_skip_trimming_skip_deduplication.nf.test.snap +++ b/tests/bismark_cat_fastq_skip_trimming_skip_deduplication.nf.test.snap @@ -19,7 +19,7 @@ "gunzip": 1.1 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [ diff --git a/tests/bismark_cytosine_report.nf.test.snap b/tests/bismark_cytosine_report.nf.test.snap index 810644a4..4a991394 100644 --- a/tests/bismark_cytosine_report.nf.test.snap +++ b/tests/bismark_cytosine_report.nf.test.snap @@ -21,7 +21,7 @@ "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [ diff --git a/tests/bismark_emseq_clip_r1.nf.test.snap b/tests/bismark_emseq_clip_r1.nf.test.snap index 9a5aacac..f1f824ae 100644 --- a/tests/bismark_emseq_clip_r1.nf.test.snap +++ b/tests/bismark_emseq_clip_r1.nf.test.snap @@ -21,7 +21,7 @@ "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [ diff --git a/tests/bismark_hisat.nf.test.snap b/tests/bismark_hisat.nf.test.snap index 16c77cd1..cf14e78e 100644 --- a/tests/bismark_hisat.nf.test.snap +++ b/tests/bismark_hisat.nf.test.snap @@ -31,7 +31,7 @@ "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [ diff --git a/tests/bismark_hisat_rrbs.nf.test.snap b/tests/bismark_hisat_rrbs.nf.test.snap index 6a58914c..8be6b161 100644 --- a/tests/bismark_hisat_rrbs.nf.test.snap +++ b/tests/bismark_hisat_rrbs.nf.test.snap @@ -21,7 +21,7 @@ "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [ diff --git a/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap b/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap index cf46b88c..4a4a1d29 100644 --- a/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap +++ b/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap @@ -21,7 +21,7 @@ "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [ diff --git a/tests/bismark_nomeseq.nf.test.snap b/tests/bismark_nomeseq.nf.test.snap index bb7ed499..1c48227a 100644 --- a/tests/bismark_nomeseq.nf.test.snap +++ b/tests/bismark_nomeseq.nf.test.snap @@ -21,7 +21,7 @@ "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [ diff --git a/tests/bismark_rrbs.nf.test.snap b/tests/bismark_rrbs.nf.test.snap index 5caa643b..d0589cce 100644 --- a/tests/bismark_rrbs.nf.test.snap +++ b/tests/bismark_rrbs.nf.test.snap @@ -21,7 +21,7 @@ "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [ diff --git a/tests/bismark_run_preseq.nf.test.snap b/tests/bismark_run_preseq.nf.test.snap index ed543141..ae714d5d 100644 --- a/tests/bismark_run_preseq.nf.test.snap +++ b/tests/bismark_run_preseq.nf.test.snap @@ -21,7 +21,7 @@ "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [ diff --git a/tests/bismark_run_qualimap.nf.test.snap b/tests/bismark_run_qualimap.nf.test.snap index e50cf433..5b904b7e 100644 --- a/tests/bismark_run_qualimap.nf.test.snap +++ b/tests/bismark_run_qualimap.nf.test.snap @@ -24,7 +24,7 @@ "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [ diff --git a/tests/bismark_save_reference_save_align_intermeds.nf.test.snap b/tests/bismark_save_reference_save_align_intermeds.nf.test.snap index c61a623f..0a1e4652 100644 --- a/tests/bismark_save_reference_save_align_intermeds.nf.test.snap +++ b/tests/bismark_save_reference_save_align_intermeds.nf.test.snap @@ -21,7 +21,7 @@ "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [ diff --git a/tests/bismark_skip_deduplication.nf.test.snap b/tests/bismark_skip_deduplication.nf.test.snap index 13e694bd..639da1b5 100644 --- a/tests/bismark_skip_deduplication.nf.test.snap +++ b/tests/bismark_skip_deduplication.nf.test.snap @@ -21,7 +21,7 @@ "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [ diff --git a/tests/bismark_skip_multiqc.nf.test.snap b/tests/bismark_skip_multiqc.nf.test.snap index 9a099e70..5b64f472 100644 --- a/tests/bismark_skip_multiqc.nf.test.snap +++ b/tests/bismark_skip_multiqc.nf.test.snap @@ -21,7 +21,7 @@ "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [ diff --git a/tests/bismark_skip_trimming.nf.test.snap b/tests/bismark_skip_trimming.nf.test.snap index 46e38ad9..474da6bb 100644 --- a/tests/bismark_skip_trimming.nf.test.snap +++ b/tests/bismark_skip_trimming.nf.test.snap @@ -16,7 +16,7 @@ "gunzip": 1.1 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [ diff --git a/tests/bwameth.nf.test.snap b/tests/bwameth.nf.test.snap index 9b16a241..00282e40 100644 --- a/tests/bwameth.nf.test.snap +++ b/tests/bwameth.nf.test.snap @@ -21,7 +21,7 @@ "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [ diff --git a/tests/bwameth_cat_fastq_skip_trimming_skip_deduplication.nf.test.snap b/tests/bwameth_cat_fastq_skip_trimming_skip_deduplication.nf.test.snap index c4994328..a48f6b39 100644 --- a/tests/bwameth_cat_fastq_skip_trimming_skip_deduplication.nf.test.snap +++ b/tests/bwameth_cat_fastq_skip_trimming_skip_deduplication.nf.test.snap @@ -19,7 +19,7 @@ "gunzip": 1.1 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [ diff --git a/tests/bwameth_rrbs.nf.test.snap b/tests/bwameth_rrbs.nf.test.snap index 1bf48be2..9de6d98f 100644 --- a/tests/bwameth_rrbs.nf.test.snap +++ b/tests/bwameth_rrbs.nf.test.snap @@ -21,7 +21,7 @@ "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [ diff --git a/tests/bwameth_run_qualimap.nf.test.snap b/tests/bwameth_run_qualimap.nf.test.snap index c5aa4055..38a4e1c7 100644 --- a/tests/bwameth_run_qualimap.nf.test.snap +++ b/tests/bwameth_run_qualimap.nf.test.snap @@ -24,7 +24,7 @@ "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [ diff --git a/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap b/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap index f7d7f4c5..59d9dc09 100644 --- a/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap +++ b/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap @@ -21,7 +21,7 @@ "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [ diff --git a/tests/bwameth_skip_deduplication.nf.test.snap b/tests/bwameth_skip_deduplication.nf.test.snap index abdf69c6..5e1bfff9 100644 --- a/tests/bwameth_skip_deduplication.nf.test.snap +++ b/tests/bwameth_skip_deduplication.nf.test.snap @@ -21,7 +21,7 @@ "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [ diff --git a/tests/bwameth_skip_trimming.nf.test.snap b/tests/bwameth_skip_trimming.nf.test.snap index 68e34400..18749010 100644 --- a/tests/bwameth_skip_trimming.nf.test.snap +++ b/tests/bwameth_skip_trimming.nf.test.snap @@ -16,7 +16,7 @@ "gunzip": 1.1 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [ diff --git a/tests/bwameth_use_gpu.nf.test.snap b/tests/bwameth_use_gpu.nf.test.snap index 176d3108..9284b2f3 100644 --- a/tests/bwameth_use_gpu.nf.test.snap +++ b/tests/bwameth_use_gpu.nf.test.snap @@ -21,7 +21,7 @@ "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [ diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 2f84d4c0..8d05f2b5 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -31,7 +31,7 @@ "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v3.0.0" + "nf-core/methylseq": "v3.1.0dev" } }, [