Releases: nf-core/methylseq
Releases · nf-core/methylseq
Endless Tofu
What's Changed
- post-release version bump by @sateeshperi in #450
- Fix/fasta gunzip & bismark align cache by @sateeshperi in #457
- Feat/fastq align dedup bismark by @sateeshperi in #465
- Fasta index bismark bwameth by @sateeshperi in #468
- Conf modules configs by @sateeshperi in #469
run_preseq
param + skippreseq/lcextrap
by default by @sateeshperi in #470run_qualimap
param and skip qualimap/bamqc by default by @sateeshperi in #471- Removed ambiguity in the multilane sample information by @bounlu in #452
- Disable gunzip publish by @sateeshperi in #474
- CI: add gpu tag test job by @sateeshperi in #478
- Fasta align dedup bwameth by @sateeshperi in #475
- Checking if shards > 0 are present before firing tests by @GallVp in #484
- Updated metro maps. by @ewels in #479
- Test replicates by @sateeshperi in #486
- Doc updates by @sateeshperi in #489
- Template update for nf-core/tools v3.1.0 by @sateeshperi in #490
- Important! Template update for nf-core/tools v3.1.0 by @nf-core-bot in #488
- 2.8.0 bump-version by @sateeshperi in #491
- Cytosine report test by @sateeshperi in #493
- First attempt at fact-checking chatGPT by @FelixKrueger in #495
- add bs-seq-primer doc by @sateeshperi in #494
- bump ver to 3.0.0 semver by @sateeshperi in #496
- Dev -> Master 3.0.0 by @sateeshperi in #492
New Contributors
Full Changelog: 2.7.1...v3.0.0
Shattners Bassoon
What's Changed
- post-release version bump by @sateeshperi in #446
- Patch release 2.7.1 by @sateeshperi in #448
- Dev -> Master 2.7.1 by @sateeshperi in #449
Full Changelog: 2.7.0...2.7.1
Chubby Unicorn
What's Changed
- post-release dev bump version and snapshots by @sateeshperi in #371
- add missing comma to awstestfull yml by @sateeshperi in #375
- Important! Template update for nf-core/tools v2.12 by @nf-core-bot in #377
- Fix/samplename join by @sateeshperi in #381
- Important! Template update for nf-core/tools v2.13 by @nf-core-bot in #380
- Important! Template update for nf-core/tools v2.13.1 by @nf-core-bot in #384
- remove duplicate section from usage.md by @fbnrst in #386
- Important! Template update for nf-core/tools v2.14.1 by @nf-core-bot in #399
- Fix/sample merge by @sateeshperi in #401
- test(#392): Add boilerplate for tests by @edmundmiller in #393
- fix usage of Fasta references for bwameth / samtools faidx by @maxulysse in #403
- Bump preseq by @ewels in #390
- Add length_trim parameter to nextflow.config file by @geethavenk in #416
- Add missing type field to entry in nextflow_schema.json by @scoughlan2 in #417
- Feat/workflow updates by @sateeshperi in #414
- Fix/readme 391 by @sateeshperi in #418
- bump-version and update CHANGELOG by @sateeshperi in #419
- update date for 2.7.0 release by @sateeshperi in #421
- Template update for nf-core/tools v3.0.2 by @sateeshperi in #426
- Important! Template update for nf-core/tools v3.0.2 by @nf-core-bot in #427
- update bismark+bwameth modules; sub-wf; wf by @sateeshperi in #428
- udpate tests to use nft-bam for bam files by @sateeshperi in #429
- update SAMTOOLS_FAIDX fasta input after reorg by @sateeshperi in #430
- apply code review suggestions and activate igenomes bwameth index use by @sateeshperi in #431
- @sateeshperi fix bismark, bwameth align modules * other module updates + update snaps by @sateeshperi in #432
- update CI and Changelog by @sateeshperi in #433
- update spacing in nextflow.config to test nf-test trigger by @sateeshperi in #434
- rm conda from CI tests until the file lock resolution by @sateeshperi in #435
- Adding Metromap (with Sections) by @Shaun-Regenbaum in #438
- rm resourceLimits for test_full profile by @sateeshperi in #439
- update changelog and readme by @sateeshperi in #442
- Update metromap.svg by @ewels in #443
- add hisat2 bismark index to igenomes by @sateeshperi in #444
- apply suggestions from nextflow vscode formatter + update date in cha… by @sateeshperi in #445
- Dev -> Master 2.7.0 by @sateeshperi in #420
New Contributors
- @fbnrst made their first contribution in #386
- @geethavenk made their first contribution in #416
- @scoughlan2 made their first contribution in #417
- @Shaun-Regenbaum made their first contribution in #438
Full Changelog: 2.6.0...2.7.0
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 ignore_r1 and ignore_3prime_r1 variable expansion #359 @noecochetel
- 🐛 No groups #362 @edmundmiller
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
- ❌ Removes problematic
- 🧾 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 forcoverage2cytosine
@FelixKrueger - 🛠️ Wrong display values for "zymo" and "em_seq" presets on help page #335 @wassimsalam01
- 📚 Use new Citation tools functions #336 @emiller88
Full Changelog: 2.4.0...2.5.0
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 - pull_reqest to
dev
tests with NXF_VERlatest-everything
#310 - 🤖 GitHub Actions CI - pull_reqest to
master
tests with NXF_VER22.10.1
&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
andignore_3prime
parameters whenignore_r1
orignore_3prime_r1
are greater than 0. #322 - 🛠️ rename
ignore
->ignore_r1
andignore_3prime
->ignore_3prime_r1
params #322 - 🐛 removed unused directory #297
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)
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.
- Multi-core usage for Bismark alignment is now automatically set. If you would like to overwrite this, you can do so by setting
- 🧹 Removed duplicate option
--coverage2cytosine
(#273)- Use the existing option
--cytosine_report
to launch the newCOVERAGE2CYTOSINE
process. - Removed option
--cytosine_report genome_index
from the Bismark methylation extractor.
- Use the existing option
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
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 | fastq_1 | fastq_2 | 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!