Releases | Open Source Science

nf-core/methylseq 4.1.0

Highlights
- Optional BWA-MEM2 support via --use_mem2 for BWA-Meth indexing and alignment
- Nextflow requirement raised to 24.10.5
- Broad module/template updates and CI hardening
New
- Add --use_mem2 to enable the BWA-MEM2 algorithm in BWA-Meth
- BWA-Meth modules updated to honor use_mem2
- fasta_index_bismark_bwameth subworkflow updated to pass use_mem2
Improvements
- Update template to nf-core/tools v3.3.2
- General modules update
- Add GitHub Actions CI for GPU test snapshot updates
- Update AWS megatests workflow to use new CE org variables
- Add Wave to ARM megatests
Fixes
- FastQC output added twice to multiqc_ch
- Broken documentation links
- Update BWA-Meth container to fix bwa-mem2 installation
Testing
- New test covering BWA-MEM2 indexing and alignment
Requirements
- Nextflow >=24.10.5
Compatibility notes
- Default behavior unchanged unless --use_mem2 is provided.

Full Changelog: https://github.com/nf-core/methylseq/compare/4.0.0...4.1.0

- Nextflow
Published by sateeshperi 7 months ago

nf-core/methylseq v4.0.0 Release Notes

This release introduces major new features, significant refactoring, and extensive test suite improvements. Key highlights include the addition of a targeted sequencing analysis workflow, substantial refactoring of input handling and subworkflows for better modularity and robustness, and a complete overhaul of the testing framework.

Bug Fixes & Refactoring

Core Refactoring (#539):
- The FASTA index subworkflow was refactored to remove implicit parameter passing.
- Fixed workflow versions collection and improved conditional logic for FastQC and MultiQC execution.
Parabricks Fixes:
- The minimum memory for PARABRICKS_FQ2BAMMETH has been increased to 100GB as suggested by the documentation (#528).
- Fixed a parabricks/fq2bammeth failure on AWS Batch-like executors where symlinks don't exist (#536).
General:
- Reverted PR #523 which involved direct changes to subworkflows in the pipeline.
- The pipeline template has been updated to nf-core/tools v3.2.0 (#504).
- The pipeline template has been updated to nf-core/tools v3.3.1 (#504).

Pipeline Updates

Targeted Sequencing (#516, #539):
- A new --run_targeted_sequencing flag has been added to enable further analysis of targeted methylation experiments.
- A new Targeted Sequencing subworkflow has been introduced with improved parameter handling and region-specific analysis capabilities.
- The bedtools/intersect and picard/collecthsmetrics modules from nf-core/modules have been installed.
- A new --collecthsmetrics parameter has been added to allow the collection of Picard HS metrics.
Workflow & Parameter Changes:
- Bwameth:
  - Added --all_contexts and --merge_context parameters (#516).
  - Removed the --comprehensive parameter (#516).
- Bismark:
  - Decoupled --merge_non_CpG from --comprehensive in the Bismark workflow (#516).
- Trimming:
  - Added a new skip_trimming_presets flag to overwrite any preset trimming options (#506).
  - Updated --pbat trimming options to 8|8|8|8 (#506).
  - Removed --cegx and --epignome preset trimming options as the kits are discontinued (#506).
- GPU Usage:
  - Removed the --use_gpu parameter. Activating the gpu profile with --profile gpu is now the standard way to enable GPU-based pathways (#520).
- Quality Control:
  - Added --skip_fastqc and --skip_multiqc parameters to allow skipping quality control steps (#539).

Testing Updates (#539)

Test Suite Consolidation:
- Removed 19 individual test files, replacing them with comprehensive test suites.
New Test Suites:
- bismark_variants.nf.test for comprehensive Bismark testing.
- bismark_hisat_variants.nf.test for Bismark with HISAT2 aligner.
- bwameth_variants.nf.test for comprehensive Bwameth testing.
- targeted_sequencing_variants.nf.test for the new targeted sequencing workflow.
- index_downloads.nf.test for testing index download scenarios.

What's Changed

post release bump version by @sateeshperi in https://github.com/nf-core/methylseq/pull/497
Update test command in usage.md by @fbnrst in https://github.com/nf-core/methylseq/pull/502
Important! Template update for nf-core/tools v3.2.0 by @nf-core-bot in https://github.com/nf-core/methylseq/pull/504
Update snapshot 3.2.0 template by @sateeshperi in https://github.com/nf-core/methylseq/pull/505
create separate test_gpu profile by @sateeshperi in https://github.com/nf-core/methylseq/pull/517
update ci runners to runson by @sateeshperi in https://github.com/nf-core/methylseq/pull/522
Fix faix notprovided error by @lpantano in https://github.com/nf-core/methylseq/pull/523
Added CUDA test for runsOn by @GallVp in https://github.com/nf-core/methylseq/pull/534
Removed parameter use_gpu by @GallVp in https://github.com/nf-core/methylseq/pull/533
Bumped PARABRICKS_FQ2BAMMETH memory to 100.GB by @GallVp in https://github.com/nf-core/methylseq/pull/535
Revert fix faix error by @sateeshperi in https://github.com/nf-core/methylseq/pull/530
Updated parabricks/fq2bammeth by @GallVp in https://github.com/nf-core/methylseq/pull/537
skip trimming presets by @sateeshperi in https://github.com/nf-core/methylseq/pull/518
Important! Template update for nf-core/tools v3.2.1 by @nf-core-bot in https://github.com/nf-core/methylseq/pull/525
Targeted analysis by @dcarrillox in https://github.com/nf-core/methylseq/pull/516
Important! Template update for nf-core/tools v3.3.1 by @nf-core-bot in https://github.com/nf-core/methylseq/pull/538
refactor-workflow-tests by @sateeshperi in https://github.com/nf-core/methylseq/pull/539
bump-version 4.0.0 by @sateeshperi in https://github.com/nf-core/methylseq/pull/540
update metro map 4.0.0 by @sateeshperi in https://github.com/nf-core/methylseq/pull/542
apply suggestions from code review by @sateeshperi in https://github.com/nf-core/methylseq/pull/543
Dev -> Main v4.0.0 by @sateeshperi in https://github.com/nf-core/methylseq/pull/541

New Contributors

@lpantano made their first contribution in https://github.com/nf-core/methylseq/pull/523
@dcarrillox made their first contribution in https://github.com/nf-core/methylseq/pull/516

Full Changelog: https://github.com/nf-core/methylseq/compare/3.0.0...4.0.0

- Nextflow
Published by sateeshperi 8 months ago

methylseq - Endless Tofu

What's Changed

post-release version bump by @sateeshperi in https://github.com/nf-core/methylseq/pull/450
Fix/fasta gunzip & bismark align cache by @sateeshperi in https://github.com/nf-core/methylseq/pull/457
Feat/fastq align dedup bismark by @sateeshperi in https://github.com/nf-core/methylseq/pull/465
Fasta index bismark bwameth by @sateeshperi in https://github.com/nf-core/methylseq/pull/468
Conf modules configs by @sateeshperi in https://github.com/nf-core/methylseq/pull/469
run_preseq param + skip preseq/lcextrap by default by @sateeshperi in https://github.com/nf-core/methylseq/pull/470
run_qualimap param and skip qualimap/bamqc by default by @sateeshperi in https://github.com/nf-core/methylseq/pull/471
Removed ambiguity in the multilane sample information by @bounlu in https://github.com/nf-core/methylseq/pull/452
Disable gunzip publish by @sateeshperi in https://github.com/nf-core/methylseq/pull/474
CI: add gpu tag test job by @sateeshperi in https://github.com/nf-core/methylseq/pull/478
Fasta align dedup bwameth by @sateeshperi in https://github.com/nf-core/methylseq/pull/475
Checking if shards > 0 are present before firing tests by @GallVp in https://github.com/nf-core/methylseq/pull/484
Updated metro maps. by @ewels in https://github.com/nf-core/methylseq/pull/479
Test replicates by @sateeshperi in https://github.com/nf-core/methylseq/pull/486
Doc updates by @sateeshperi in https://github.com/nf-core/methylseq/pull/489
Template update for nf-core/tools v3.1.0 by @sateeshperi in https://github.com/nf-core/methylseq/pull/490
Important! Template update for nf-core/tools v3.1.0 by @nf-core-bot in https://github.com/nf-core/methylseq/pull/488
2.8.0 bump-version by @sateeshperi in https://github.com/nf-core/methylseq/pull/491
Cytosine report test by @sateeshperi in https://github.com/nf-core/methylseq/pull/493
First attempt at fact-checking chatGPT by @FelixKrueger in https://github.com/nf-core/methylseq/pull/495
add bs-seq-primer doc by @sateeshperi in https://github.com/nf-core/methylseq/pull/494
bump ver to 3.0.0 semver by @sateeshperi in https://github.com/nf-core/methylseq/pull/496
Dev -> Master 3.0.0 by @sateeshperi in https://github.com/nf-core/methylseq/pull/492

New Contributors

@bounlu made their first contribution in https://github.com/nf-core/methylseq/pull/452
@GallVp made their first contribution in https://github.com/nf-core/methylseq/pull/484

Full Changelog: https://github.com/nf-core/methylseq/compare/2.7.1...v3.0.0

- Nextflow
Published by sateeshperi about 1 year ago

methylseq - Shattners Bassoon

What's Changed

post-release version bump by @sateeshperi in https://github.com/nf-core/methylseq/pull/446
Patch release 2.7.1 by @sateeshperi in https://github.com/nf-core/methylseq/pull/448
Dev -> Master 2.7.1 by @sateeshperi in https://github.com/nf-core/methylseq/pull/449

Full Changelog: https://github.com/nf-core/methylseq/compare/2.7.0...2.7.1

- Nextflow
Published by sateeshperi over 1 year ago

methylseq - Chubby Unicorn

What's Changed

post-release dev bump version and snapshots by @sateeshperi in https://github.com/nf-core/methylseq/pull/371
add missing comma to awstestfull yml by @sateeshperi in https://github.com/nf-core/methylseq/pull/375
Important! Template update for nf-core/tools v2.12 by @nf-core-bot in https://github.com/nf-core/methylseq/pull/377
Fix/samplename join by @sateeshperi in https://github.com/nf-core/methylseq/pull/381
Important! Template update for nf-core/tools v2.13 by @nf-core-bot in https://github.com/nf-core/methylseq/pull/380
Important! Template update for nf-core/tools v2.13.1 by @nf-core-bot in https://github.com/nf-core/methylseq/pull/384
remove duplicate section from usage.md by @fbnrst in https://github.com/nf-core/methylseq/pull/386
Important! Template update for nf-core/tools v2.14.1 by @nf-core-bot in https://github.com/nf-core/methylseq/pull/399
Fix/sample merge by @sateeshperi in https://github.com/nf-core/methylseq/pull/401
test(#392): Add boilerplate for tests by @edmundmiller in https://github.com/nf-core/methylseq/pull/393
fix usage of Fasta references for bwameth / samtools faidx by @maxulysse in https://github.com/nf-core/methylseq/pull/403
Bump preseq by @ewels in https://github.com/nf-core/methylseq/pull/390
Add length_trim parameter to nextflow.config file by @geethavenk in https://github.com/nf-core/methylseq/pull/416
Add missing type field to entry in nextflow_schema.json by @scoughlan2 in https://github.com/nf-core/methylseq/pull/417
Feat/workflow updates by @sateeshperi in https://github.com/nf-core/methylseq/pull/414
Fix/readme 391 by @sateeshperi in https://github.com/nf-core/methylseq/pull/418
bump-version and update CHANGELOG by @sateeshperi in https://github.com/nf-core/methylseq/pull/419
update date for 2.7.0 release by @sateeshperi in https://github.com/nf-core/methylseq/pull/421
Template update for nf-core/tools v3.0.2 by @sateeshperi in https://github.com/nf-core/methylseq/pull/426
Important! Template update for nf-core/tools v3.0.2 by @nf-core-bot in https://github.com/nf-core/methylseq/pull/427
update bismark+bwameth modules; sub-wf; wf by @sateeshperi in https://github.com/nf-core/methylseq/pull/428
udpate tests to use nft-bam for bam files by @sateeshperi in https://github.com/nf-core/methylseq/pull/429
update SAMTOOLS_FAIDX fasta input after reorg by @sateeshperi in https://github.com/nf-core/methylseq/pull/430
apply code review suggestions and activate igenomes bwameth index use by @sateeshperi in https://github.com/nf-core/methylseq/pull/431
@sateeshperi fix bismark, bwameth align modules * other module updates + update snaps by @sateeshperi in https://github.com/nf-core/methylseq/pull/432
update CI and Changelog by @sateeshperi in https://github.com/nf-core/methylseq/pull/433
update spacing in nextflow.config to test nf-test trigger by @sateeshperi in https://github.com/nf-core/methylseq/pull/434
rm conda from CI tests until the file lock resolution by @sateeshperi in https://github.com/nf-core/methylseq/pull/435
Adding Metromap (with Sections) by @Shaun-Regenbaum in https://github.com/nf-core/methylseq/pull/438
rm resourceLimits for test_full profile by @sateeshperi in https://github.com/nf-core/methylseq/pull/439
update changelog and readme by @sateeshperi in https://github.com/nf-core/methylseq/pull/442
Update metromap.svg by @ewels in https://github.com/nf-core/methylseq/pull/443
add hisat2 bismark index to igenomes by @sateeshperi in https://github.com/nf-core/methylseq/pull/444
apply suggestions from nextflow vscode formatter + update date in cha… by @sateeshperi in https://github.com/nf-core/methylseq/pull/445
Dev -> Master 2.7.0 by @sateeshperi in https://github.com/nf-core/methylseq/pull/420

New Contributors

@fbnrst made their first contribution in https://github.com/nf-core/methylseq/pull/386
@geethavenk made their first contribution in https://github.com/nf-core/methylseq/pull/416
@scoughlan2 made their first contribution in https://github.com/nf-core/methylseq/pull/417
@Shaun-Regenbaum made their first contribution in https://github.com/nf-core/methylseq/pull/438

Full Changelog: https://github.com/nf-core/methylseq/compare/2.6.0...2.7.0

- Nextflow
Published by sateeshperi over 1 year ago

methylseq - Huggy mollusc

Pipeline Updates

🔄 Updated template to nf-core/tools v2.11.1 #368 @sateeshperi @edmundmiller

Bug fixes & refactoring

🛠 Copy methylKit-compatible files to publishDir #357 @ltosti-tagomics
🐛 fix ignorer1 and ignore3prime_r1 variable expansion #359 @noecochetel
🐛 No groups #362 @edmundmiller

- Nextflow
Published by sateeshperi about 2 years ago

methylseq - Crema Catalana

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 @ewels
- ❌ Removes problematic -m memory assignment for samtools sort #81
🧾 Use fromSamplesheet from nf-validation #341 @Emiller88
🚀 Update Maintainers and add CODEOWNERS #345 @Emiller88
⚙️ Update schema to utilize exists and add more patterns #342 @Emiller88
📁 Support pipeline-specific configs #343 @maxulysse

Bug fixes & refactoring

🛠️ Added publishing of coverage (*cov.gz) files for NOMe-seq filtered reads for coverage2cytosine @FelixKrueger
🛠️ Wrong display values for "zymo" and "em_seq" presets on help page #335 @wassimsalam01
📚 Use new Citation tools functions #336 @Emiller88

Full Changelog: https://github.com/nf-core/methylseq/compare/2.4.0...2.5.0

- Nextflow
Published by Emiller88 over 2 years ago

methylseq - 2.4.0 [Gillespie Gaia]

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 - pullreqest to dev tests with NXFVER latest-everything #310
🤖 GitHub Actions CI - pullreqest to master tests with NXFVER 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
🐛 removed unused directory #297

- Nextflow
Published by sateeshperi over 2 years ago

methylseq - 2.3.0 [Pyrite Alligator]

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)

- Nextflow
Published by ewels about 3 years ago

methylseq - 2.2.0 [Quartzite Lemur]

Pipeline Updates

✨ Updated the bismark2summary step so that it no longer stages the aligned BAM files into the working directory (#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)

Bug fixes & refactoring

🐛 Fixed typo in parameter handling for input reference indices (#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)
- Use the existing option --cytosine_report to launch the new COVERAGE2CYTOSINE process.
- Removed option --cytosine_report genome_index from the Bismark methylation extractor.

- Nextflow
Published by ewels about 3 years ago

methylseq - 2.1.0 [Granite Iguana]

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)

Software Updates

Update Bismark v0.23.0 to v0.24.0

- Nextflow
Published by ewels over 3 years ago

methylseq - 2.0.0 [Obsidian Gecko]

Pipeline Updates

Major pipeline rewrite to use DSL2 with shared nf-core/modules.

Warning: Breaking change! ⚠️

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

| sample | fastq1 | fastq2 | genome | | ------ | ------- | ------- | ------ |

See an example here

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.

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!

- Nextflow
Published by ewels over 3 years ago

methylseq - 1.6.1 [Nauseous Serpent]

Minor release to fix a bug in the command for the Bismark alignment. This change should have no effect on the pipeline output, though single-end alignments with Bismark should now be 2x faster. See issue #210 for full investigation.

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)

Software updates

Picard 2.25.1 > 2.25.4
MultiQC 1.10 > 1.10.1

- Nextflow
Published by ewels almost 5 years ago

methylseq - 1.6 [Queasy Serpent]

: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)
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)
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 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

- Nextflow
Published by ewels almost 5 years ago

methylseq - 1.5 [ Belated Dodo ]

New features

Added multicore support for TrimGalore!
Improved the multicore support for Bismark methXtract for more parallelisation (#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)

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)
Removed awsbatch config profile because it is now served by 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

- Nextflow
Published by ewels almost 6 years ago

methylseq - 1.4 [Mercury Rattlesnake]

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
Added support for running bismark with HISAT2 as an aligner option #85
Added support for centralized configuration profiles 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)
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)

- Nextflow
Published by phue over 6 years ago

methylseq - 1.3

A fairly quick release on the heels of 1.2 to fix a nasty bug introduced that prevented the pipeline from running on more than one file. Whilst we're here we added in a new tool: preseq.

New features

Added 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
- Introduced in previous release. TrimGalore onwards would only process one sample.

- Nextflow
Published by ewels about 7 years ago

methylseq - 1.2

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)

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)
Fixed bug in MultiQC process that skipped results from some tools
Supply available memory as argument to Picard MarkDuplicates

- Nextflow
Published by ewels about 7 years ago

methylseq - 1.1

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
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

- Nextflow
Published by ewels over 7 years ago

methylseq - 1.0

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 to 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

For earlier releases and development notes, please see the (now archived) fork at SciLifeLab/NGI-MethylSeq.

- Nextflow
Published by ewels almost 8 years ago

Recent Releases of methylseq

methylseq - Burrows Stardust

nf-core/methylseq 4.1.0

methylseq - Wallace Chrysalis

nf-core/methylseq v4.0.0 Release Notes

Bug Fixes & Refactoring

Pipeline Updates

Testing Updates (#539)

What's Changed

New Contributors

methylseq - Endless Tofu

What's Changed

New Contributors

methylseq - Shattners Bassoon

What's Changed

methylseq - Chubby Unicorn

What's Changed

New Contributors

methylseq - Huggy mollusc

methylseq - Crema Catalana

Pipeline Updates

Bug fixes & refactoring

methylseq - 2.4.0 [Gillespie Gaia]

Pipeline Updates

Bug fixes & refactoring

methylseq - 2.3.0 [Pyrite Alligator]

Pipeline Updates

Bug fixes & refactoring

methylseq - 2.2.0 [Quartzite Lemur]

Pipeline Updates

Bug fixes & refactoring

methylseq - 2.1.0 [Granite Iguana]

Pipeline Updates

Software Updates

methylseq - 2.0.0 [Obsidian Gecko]

Pipeline Updates

Software Updates

methylseq - 1.6.1 [Nauseous Serpent]

Pipeline Updates

Bug fixes

Software updates

methylseq - 1.6 [Queasy Serpent]

Pipeline Updates

Software updates

methylseq - 1.5 [ Belated Dodo ]

New features

Software updates

Pipeline Updates

Bug fixes

methylseq - 1.4 [Mercury Rattlesnake]

New features

Software updates

Pipeline updates

Bug fixes

methylseq - 1.3

New features

Bug fixes

methylseq - 1.2

New features

Software updates

Bug fixes

methylseq - 1.1

methylseq - 1.0