# nf-core/methylseq

## [v2.5.0](https://github.com/nf-core/methylseq/releases/tag/2.5.0) - 2023-10-18

### Pipeline Updates

- 🔄 Updated template to nf-core/tools v2.9
- 🔄 Updated template to nf-core/tools v2.10
- 🔧 Updated nf-core modules for FastQC, samtools sort, samtools flagstat
  - ❌ Removes problematic `-m` memory assignment for samtools sort [#81](https://github.com/nf-core/methylseq/issues/81)
- 🧾 Use `fromSamplesheet` from nf-validation [#341](https://github.com/nf-core/methylseq/pull/341)
- 🚀 Update Maintainers and add CODEOWNERS [#345](https://github.com/nf-core/methylseq/pull/345)
- ⚙️ Update schema to utilize exists and add more patterns [#342](https://github.com/nf-core/methylseq/pull/342)
- 📁 Support pipeline-specific configs [#343](https://github.com/nf-core/methylseq/pull/343)

### Bug fixes & refactoring

- 🛠️ Added publishing of coverage (`*cov.gz`) files for NOMe-seq filtered reads for `coverage2cytosine`
- 🛠️ Wrong display values for "zymo" and "em_seq" presets on help page [#335](https://github.com/nf-core/methylseq/pull/335)
- 📚 Use new Citation tools functions [#336](https://github.com/nf-core/methylseq/issues/336)

## [v2.4.0](https://github.com/nf-core/methylseq/releases/tag/2.4.0) - 2023-06-02

### Pipeline Updates

- Updated template to nf-core/tools v2.8
- Add `--bamqc_regions_file` parameter for targeted methylation sequencing data #302
- ✨ Add NF-TEST tests and snapshots for the pipeline test profile #310

### Bug fixes & refactoring

- 🛠️ update index file channels to explicit value channels #310
- 🐛 fix `params.test_data_base` in test and test_full configs #310
- 🤖 GitHub Actions CI - pull_request to `dev` tests with NXF_VER `latest-everything` #310
- 🤖 GitHub Actions CI - pull_request to `master` tests with NXF_VER `22.10.1` & `latest-everything` #310
- 🤖 GitHub Actions CI - `fail-fast` set to false #310
- 🐛 get to the bottom of index tests #278
- ✨ Support for Bismark methylation extraction `ignore` and `ignore_3prime` parameters when `ignore_r1` or `ignore_3prime_r1` are greater than 0. #322
- 🛠️ rename `ignore` -> `ignore_r1` and `ignore_3prime` -> `ignore_3prime_r1` params #322
- 🐛 fix `ignore_3prime_r2` param #299
- 🐛 removed unused directory #297

## [v2.3.0](https://github.com/nf-core/methylseq/releases/tag/2.3.0) - 2022-12-16

### Pipeline Updates

- ⚙️ Dramatically increase the default process time config requests for Bismark and bwa meth alignment
- ✨ Add a `tower.yml` file to enable Reports in Nextflow Tower
- 🤖 GitHub Actions CI - download the test data prior to running tests

### Bug fixes & refactoring

- 🧹 Refactor genome indices preparation into a separate workflow
- 🧹 Refactor subworkflow logic out of alignment subworkflows, for later sharing
- 🐛 Fix a bug with using a local genome reference FASTA file
- 🐛 Fix a bunch of problems in the CI tests using nf-test ([#279](https://github.com/nf-core/methylseq/pull/279))

## [v2.2.0](https://github.com/nf-core/methylseq/releases/tag/2.2.0) - 2022-11-29

### Pipeline Updates

- ✨ Updated the `bismark2summary` step so that it no longer stages the aligned BAM files into the working directory ([#268](https://github.com/nf-core/methylseq/pull/268))
  - Should be much faster / cheaper for running on the cloud.
- ✨ Added ability to merge FastQ files based on shared IDs in sample sheet ([#272](https://github.com/nf-core/methylseq/pull/272))

### Bug fixes & refactoring

- 🐛 Fixed typo in parameter handling for input reference indices ([#263](https://github.com/nf-core/methylseq/issues/263))
- 🧹 Removed orphaned `--bismark_align_cpu_per_multicore` and `--bismark_align_cpu_per_multicore` parameters.
  - Multi-core usage for Bismark alignment is now automatically set. If you would like to overwrite this, you can do so by setting `ext.args` for the process in a custom config.
- 🧹 Removed duplicate option `--coverage2cytosine` ([#273](https://github.com/nf-core/methylseq/issues/273))
  - Use the existing option `--cytosine_report` to launch the new `COVERAGE2CYTOSINE` process.
  - Removed option `--cytosine_report genome_index` from the Bismark methylation extractor.

## [v2.1.0](https://github.com/nf-core/methylseq/releases/tag/2.1.0) - 2022-11-10

### Pipeline Updates

- ✨ Added option to run the Bismark `coverage2cytosine` script using the `--coverage2cytosine` and `--nomeseq` parameters.
- 🐛 Fixed bad bug where trimming presets were not being applied ([#261](https://github.com/nf-core/methylseq/pull/261))

### Software Updates

- Update Bismark v0.23.0 to v0.24.0

## [v2.0.0](https://github.com/nf-core/methylseq/releases/tag/2.0.0) - 2022-11-09

### Pipeline Updates

Major pipeline rewrite to use DSL2 with shared [nf-core/modules](https://github.com/nf-core/modules).

> **Warning**: Breaking change! ⚠️

The pipeline now requires a sample sheet to be passed to the pipeline with `--input`:

| sample | fastq_1 | fastq_2 | genome |
| ------ | ------- | ------- | ------ |

See an example [here](https://github.com/nf-core/test-datasets/blob/methylseq/samplesheet.csv)

> **Note**: The `genome` column is not yet used but will give the ability to map to multiple genomes in a single run in a future release. See [#181](https://github.com/nf-core/methylseq/issues/181).

Supplying the reference geneome with `--genome` as before works as usual.

### Software Updates

Major updates in commands and software versions for nearly every tool.

Please treat this new version with a little more care than usual and let us know if you find any problems!

## [v1.6.1](https://github.com/nf-core/methylseq/releases/tag/1.6.1) - 2021-05-08

### Pipeline Updates

- Added new config profile to run minimal test paired-end dataset, with `-profile test_paired`. Added to the CI tests.

### Bug fixes

- Fixed silent bug in Bismark alignment command that had no effect on the output ([#210](https://github.com/nf-core/methylseq/issues/210))

### Software updates

- Picard `2.25.1` > `2.25.4`
- MultiQC `1.10` > `1.10.1`

## [v1.6](https://github.com/nf-core/methylseq/releases/tag/1.6) - 2021-03-26

**:warning: Breaking change!**

In line with a standardisation change across all of nf-core, we have changed the main parameter name for supplying files to the pipeline.
In this release, please use `--input` instead of `--reads`.
The parameter still works in the same way as before.

### Pipeline Updates

- Increased resources for `fastqc` process ([#143](https://github.com/nf-core/methylseq/issues/143))
- Raised Nextflow version requirement to `20.07.1`
- Updated template to nf-core/tools 1.13.3
- Renamed `--reads` to `--input`
- Added new `--maxins` and `--minins` parameters to pass on to Bismark
- New `--em_seq` preset
  - Sets `bismark_maxins = 1000`, `clip_r1 = 8`, `clip_r2 = 8`, `three_prime_clip_r1 = 8`, `three_prime_clip_r2 = 8`
- New `--publish_dir_mode` parameter to customise results folder behaviour
- Fix bug on AWS for `bismark_hisat` known splice file ([#177](https://github.com/nf-core/methylseq/issues/177))
- Moved parameter documentation into new `nextflow_schema.json` file
  - This improves web documentation and enables `nf-core launch` functionality. See <https://nf-co.re/launch?pipeline=methylseq>
- Added a `-profile test_full` config for running the pipeline with a full-size test dataset
  - See [the config file](https://github.com/nf-core/methylseq/blob/dev/conf/test_full.config) for details
  - This will be used for automated release tests on AWS, results browsable on the website

### Software updates

- Python base `3.7.3` > `3.8.8`
- markdown `3.1.1` > `3.3.4`
- pymdown-extensions `6.0` > `8.1.1`
- pygments `2.6.1` > `2.8.1`
- pigz `2.3.4` > `2.6`
- samtools `1.9` > `1.11`
- TrimGalore! `0.6.5` > `0.6.6`
- Bowtie2 `2.3.5` > `2.4.2`
- Hisat2 `2.2.0` > `2.2.1`
- Bismark `0.22.3` > `0.23.0`
- Picard `2.22.2` > `2.25.1`
- MethylDackel `0.5.0` > `0.5.2`
- MultiQC `1.8` > `1.10`

## [v1.5](https://github.com/nf-core/methylseq/releases/tag/1.5) - 2020-04-09

### New features

- Added multicore support for `TrimGalore!`
- Improved the multicore support for Bismark methXtract for more parallelisation ([#121](https://github.com/nf-core/methylseq/issues/121))
- Added `--cytosine_report` option to tell Bismark to give reports for all cytosines in the genome.
- Added options `--bismark_align_cpu_per_multicore` and `--bismark_align_cpu_per_multicore` to customise how Bismark align `--multicore` is decided ([#124](https://github.com/nf-core/methylseq/issues/124))
  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).

### Software updates

- _New_: pigz `2.3.4`
- Python base `2.7` > `3.7.3`
- FastQC `0.11.8` > `0.11.9`
- TrimGalore! `0.6.4` > `0.6.5`
- HiSAT2 `2.1.0` > `2.2.0`
- Bismark `0.22.2` > `0.22.3`
- Qualimap `2.2.2c` > `2.2.2d`
- Picard `2.21.3` > `2.22.2`
- MethylDackel `0.4.0` > `0.5.0`
- MultiQC `1.7` > `1.8`

### Pipeline Updates

- Fixed bug where the iGenomes config was loaded after the references were set ([#121](https://github.com/nf-core/methylseq/issues/121))
- Removed awsbatch config profile because it is now served by [nf-core/configs](https://github.com/nf-core/configs)
- Tidied up the summary log messages when starting the pipeline
  - Fewer messages saying what you're _not_ doing, sanitised the order of some logs and removed a few things
- Slightly refactored the code for trimming parameters
- Updated template to tools 1.9

### Bug fixes

- Fixed error where MethylDackel would consume the Nextflow channels and not work with more than one sample [#140](https://github.com/nf-core/methylseq/issues/140)

## [v1.4](https://github.com/nf-core/methylseq/releases/tag/1.4) - 2019-11-19

### New features

- Changed all parameter names to `snake_case`
- Added `--local_alignment` option to run Bismark with the `--local` flag to allow soft-clipping of reads.
- Added support for bismark's [SLAM-seq mode](https://github.com/FelixKrueger/Bismark/blob/master/CHANGELOG.md#slam-seq-mode)
- Added support for running bismark with HISAT2 as an aligner option [#85](https://github.com/nf-core/methylseq/issues/85)
- Added support for centralized configuration profiles [nf-core/configs](https://github.com/nf-core/configs)
- Add `--meth_cutoff` parameter to change default for `bismark_methylation_extractor`
  - eg. use `--meth_cutoff 5` on the command line or `params.meth_cutoff = 5` to require 5 overlapping reads to call a methylation site.
- Added `--methyl_kit` option to run MethylDackel with the `--methylKit` flag, producing output suitable for the methylKit R package.

### Software updates

- _new dependency_: hisat2 `2.1.0`
- _new dependency_: r-markdown `1.1`
- TrimGalore! `0.5.0` > `0.6.4`
- Bismark `0.20.0` > `0.22.2`
- Bowtie2 `2.3.4.3` > `2.3.5`
- Picard `2.18.21` > `2.21.3`
- Qualimap `2.2.2b` > `2.2.2c`
- MethylDackel `0.3.0` > `0.4.0`

### Pipeline updates

- Keep memory in GB for samtools, to avoid problems with unit conversion ([#99](https://github.com/nf-core/methylseq/issues/99))
- Changed `params.container` for `process.container`
- Synchronised with version 1.7 of the nf-core/tools template

### Bug fixes

- Fixed a bug that caused conda dependencies to be resolved very slowly
- Allowed some spare memory in the samtools sort steps, avoiding crashes for some users ([#81](https://github.com/nf-core/methylseq/issues/81))

## [v1.3](https://github.com/nf-core/methylseq/releases/tag/1.3) - 2019-02-01

### New features

- Added [preseq](http://smithlabresearch.org/software/preseq/) analysis to calculate sample complexity.
  - This new step can help decide sufficient sequencing depth has been reached.

### Bug fixes

- Fixed new bug that meant pipeline only worked with one sample at a time [#66](https://github.com/nf-core/methylseq/issues/66)
  - Introduced in previous release. TrimGalore onwards would only process one sample.

## [v1.2](https://github.com/nf-core/methylseq/releases/tag/1.2) - 2019-01-02

### New features

- Trim 9bp from both ends of both reads for PBAT mode.
- Save `where_are_my_files.txt` to results directory to inform the user about missing intermediate files [#42](https://github.com/nf-core/methylseq/issues/42)

### Software updates

- Fastqc `0.11.7` > `0.11.8`
- Bowtie2 `2.3.4.2` > `2.3.4.3`
- Bismark `0.19.1` > `0.20.0`
- Qualimap `2.2.2a` > `2.2.2b`
- Picard `2.18.11` > `2.18.21`
- MultiQC `1.6` > `1.7`

### Bug fixes

- Fixed error when running the pipeline with `--unmapped`
  - Previously, could result in error `Error ~ No such variable: bismark_unmapped`
- Fixed error where single-sample reports could mix up log files [#48](https://github.com/nf-core/methylseq/issues/48)
- Fixed bug in MultiQC process that skipped results from some tools
- Supply available memory as argument to Picard MarkDuplicates

## [v1.1](https://github.com/nf-core/methylseq/releases/tag/1.1) - 2018-08-09

- Tests simplified - now work by simply using the `test` config profile
  - eg: `nextflow run nf-core/methylseq -profile test,docker`
  - Removed previous `run_test.sh` script and data
- New `Singularity` build script for direct compatibility with [singularity-hub](https://singularity-hub.org/)
- Minor improvements to the docs
- A number of boilerplate nf-core code updates
- Updated `process$name` nextflow syntax to avoid warnings in new versions of nextflow
- Updated software tools
  - `trim-galore` `v0.4.5` update to `0.5.0`
  - `samtools` `v1.8` update to `1.9`
  - `bowtie2` `v2.3.4.1` update to `2.3.4.2`
  - `multiqc` `v1.5` update to `1.6`
  - `picard` `v2.18.2` update to `2.18.11`
  - `bwameth` `v0.2.0` update to `0.2.2`

## [v1.0](https://github.com/nf-core/methylseq/releases/tag/1.0) - 2018-04-17

Version 1.0 marks the first release of this pipeline under the nf-core flag. It also marks a significant step up in the maturity of the workflow, with everything now in a single script and both aligner workflows fully supported.

- Renamed and moved [SciLifeLab/NGI-MethylSeq](https://github.com/SciLifeLab/NGI-MethylSeq/) to [nf-core/methylseq](https://github.com/nf-core/methylseq/)
- Merged bwa-meth and bismark pipeline scripts, now chosen with `--aligner` flag
- Refactored multi-core parameters for Bismark alignment and methylation extraction
- Rewrote most of the documentation
- Changed the Docker container to use Bioconda installations

---

Previous to these releases, this pipeline was called [SciLifeLab/NGI-MethylSeq](https://github.com/SciLifeLab/NGI-MethylSeq):

## v0.4dev

- Fixed MultiQC channel bug
- Integrated config for QBiC Tuebingen
- Numerous small container bugfixes
- Refactored how the config is loaded
- Fix for resource limit function, improved resource request defaults
- Fix for iGenomes base path in configs

## [v0.3.1](https://github.com/SciLifeLab/NGI-MethylSeq/releases/tag/0.3.1) - 2017-09-05

- Include base profile name and documentation about Singularity.
- Testing automated docker hub image tagging for releases.

## [v0.3](https://github.com/SciLifeLab/NGI-MethylSeq/releases/tag/0.3) - 2017-09-01

- Fix `--rrbs` mode ([#24](https://github.com/SciLifeLab/NGI-MethylSeq/issues/24))
- Fixed fairly major bug where only a single sample would run past alignment
- Merged test scripts and rewrote to use command line flags / new travis script.
- Refactored software version collection code to be more resilient and cleaner / easier to maintain.
- Dropped support for environment modules and added support for use of Singularity on UPPMAX

## [v0.2](https://github.com/SciLifeLab/NGI-MethylSeq/releases/tag/0.2) - 2017-07-17

First (semi-) stable release of the new NGI-MethylSeq pipeline, as we head towards deployment in production.
