post release bump version

.nf-core.yml

@@ -16,4 +16,4 @@ template:
   name: methylseq
   org: nf-core
   outdir: .
-  version: 3.0.0
+  version: 3.1.0dev

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

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/methylseq/releases/tag/3.0.0"
+  This report has been generated by the <a href="https://github.com/nf-core/methylseq/tree/dev"
   target="_blank">nf-core/methylseq</a> analysis pipeline. For information about how
-  to interpret these results, please see the <a href="https://nf-co.re/methylseq/3.0.0/docs/output"
+  to interpret these results, please see the <a href="https://nf-co.re/methylseq/dev/docs/output"
   target="_blank">documentation</a>.
 report_section_order:
   "nf-core-methylseq-methods-description":

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'
 }
 

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": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-methylseq_logo_dark.png\">\n    <img alt=\"nf-core/methylseq\" src=\"docs/images/nf-core-methylseq_logo_light.png\">\n  </picture>\n</h1>\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 <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>\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",

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"
                 }
             },
             [

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"
                 }
             },
             [

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"
                 }
             },
             [

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"
                 }
             },
             [

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"
                 }
             },
             [

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"
                 }
             },
             [

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"
                 }
             },
             [

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"
                 }
             },
             [

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"
                 }
             },
             [

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"
                 }
             },
             [

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"
                 }
             },
             [

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"
                 }
             },
             [

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"
                 }
             },
             [

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"
                 }
             },
             [

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"
                 }
             },
             [

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"
                 }
             },
             [

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"
                 }
             },
             [

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"
                 }
             },
             [

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"
                 }
             },
             [

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"
                 }
             },
             [

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"
                 }
             },
             [

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"
                 }
             },
             [

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"
                 }
             },
             [