1.5.3 - 2024-11-06

Added

Changed

• #275 Update samshee module from nf-core.
• #276 Template update for nf-core/tools v3.0.2
• #284 nf-core modules and subworkflows update. nf-test version update.
• #285 Bump to version 1.5.3.

Fixed

• #277 Improved samplesheet generation to always produce all types of samplesheets, added the ability to explicitly set strandedness, and fixed output paths to correctly reflect the publishDir subdirectory structure.
• #281 Update cellranges/mkfastq module to fix missing reports and stats outputs.
• #282 Fixed downstream samplesheet paths and publishDir config.

What’s Changed

• Updated modules and subworkflows by @nschcolnicov in #259
• Fixed adapter removal by @nschcolnicov in #265
• Update diagram by @atrigila in #266
• Added miniseq bclconvert test by @nschcolnicov in #267
• Update Modules by @apeltzer in #263
• bump version by @grst in #270
• Fix release by @grst in #271
• v1.5.2 release by @grst in #269

Full Changelog: 1.5.1…1.5.2

1.5.1

Fixed

• #253 Fixed mkfastq output channels.

1.5.0 - 2024-08-12

Added

• #202 Added cellranger mkfastq subworkflow for demultiplexing 10x samples.
• #206 Add test with uncompressed data.
• #208 Added parameter for removing adapter information from samplesheets.
• #210 Add checkqc module.
• #212 Added resource setting arguments to mkfastq module to work with github CI.
• #214 Added test_pe (paired end) profile.
• #220 Added kraken2.
• #221 Added checkqc_config to pipeline schema.
• #225 Added test profile for multi-lane samples, updated handling of such samples and adapter trimming.
• #234 Added module for samplesheet validation.
• #236 Add samplesheet generation.

Changed

• #204 Update to latest bcl_demultiplex sub workflow.
• #210 Update bcl2fastq and bcl_demultiplex.
• #214 Updated method for removing adapters from samplesheet, added custom AdapterRemover function.
• #210 Update bcl2fastq and bcl_demultiplex.
• #216 List fastq reports for R1 and R2 separately in multiqc report.
• #219 Modified workflow to store samplesheet in results folder.
• #217 Update all nf-core modules and tests.
• #240 Updated samshee, stub script and error strategy

Fixed

• #224 Fix input filename collision.
• #231 Fix checkqc error message and .command.log emission.

What’s Changed

• Important! Template update for nf-core/tools v2.11 by @nf-core-bot in [#162, fixes #175 ](https://github.com/nf-core/demultiplex/pull/162, fixes #175 )
• Important! Template update for nf-core/tools v2.11.1 by @nf-core-bot in #163
• Important! Template update for nf-core/tools v2.12 by @nf-core-bot in #167
• Fix badges by @Aratz in #170
• chore: Emiller88 => edmundmiller by @edmundmiller in #173
• Pre-release v1.4.1 by @Aratz in #176
• Release candidate 1.4.1 by @Aratz in #177

Full Changelog: 1.4.0…1.4.1

What’s Changed

• Add singularity.registry = ‘quay.io’ and bump NF version to 23.04.0 by @drpatelh in #127
• Fix/ci nf tests & Remove un-necessary registry declarations by @sateeshperi in #129
• Remove_aws_ecr_public_profile by @adamrtalbot in #130
• Important! Template update for nf-core/tools v2.9 by @nf-core-bot in #132
• Make it possible to skip MultiQC by @Aratz in #140
• Important! Template update for nf-core/tools v2.10 by @nf-core-bot in #141
• Fix MultiQC report generation by @Aratz in #145
• FEAT: update bclconvert to 4.2.4 by @maxulysse in #152
• Use teams in CODEOWNERS by @Emiller88 in #148
• Fix bcl2fastq and bclconvert publishDir by @Aratz in #157
• Update all modules by @Aratz in #158
• Set publish mode for FastQs by @Emiller88 in #155
• Pre-release v1.4.0 by @Aratz in #159
• Release candidate 1.4.0 by @Aratz in #160

New Contributors

• @sateeshperi made their first contribution in #129
• @Aratz made their first contribution in #140

Full Changelog: 1.3.2…1.4.0

Neodymium Newt

This minor release is focused on updating container image locations to host as much as possible on quay.io.

What’s Changed

• Move containers for pipeline to quay.io by @drpatelh in #125
• Dev -> Master for 1.3.2 release by @drpatelh in #126

Full Changelog: 1.3.1…1.3.2

What’s Changed

• Use Nextflow.error instead of ‘exit 1’ by @adamrtalbot in #122
• Move test data from pipeline to testdatasets by @drpatelh in #123
• Dev -> Master for 1.3.1 patch release by @drpatelh in #124

Full Changelog: 1.3.0…1.3.1

[1.3.0] - 2023-05-31

Credits

Special thanks to the following for their contributions to the release:

• Matthias De Smet
• Maxime Garcia
• Adam Talbot, and doubly-so given that it’s the first contribution to nf-core/demultiplex!

Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.

What’s Changed

• CHORES: Back to business as usual by @maxulysse in #113
• Important! Template update for nf-core/tools v2.8 by @nf-core-bot in #114
• Update all modules and specify container registry using docker.registry default by @adamrtalbot in #115
• Bump fastp by @matthdsm in #117
• Re-add aws_tower config for running on Tower by @adamrtalbot in #119
• Release candidate 1.3.0 by @adamrtalbot in #118

Full Changelog: 1.2.0…1.3.0

What’s Changed

• Sgdemux dev by @sam-white04 in #91
• Update supported sequencing platforms by @nh13 in #94
• Codeowners by @Emiller88 in #95
• Fix dark image by @Emiller88 in #96
• Add fqtk as a demultiplexer by @sam-white04 in #99
• Bump bcl2fastq by @Emiller88 in #101
• FIX: update test_full with new test data for megatests by @maxulysse in #107
• FIX: Move untar to bclconvert and bcl2fastq processes by @maxulysse in #108
• prepare release: 1.2.0 by @maxulysse in #111
• Release 1.2.0 by @maxulysse in #112

New Contributors

• @sam-white04 made their first contribution in #91
• @nh13 made their first contribution in #94
• @maxulysse made their first contribution in #107

Full Changelog: 1.1.0…1.2.0

Added

• #63 Replace local bcl_demultiplex subworkflow with nf-core version (@matthdsm)
• #63 Add bases_demultiplex local subworkflow (@matthdsm)
• #63 Replace fastqc with falco for speedier QC, fixes Replace fastqc with falco #62 (@matthdsm)
• #64 Add subway map by @nvnieuwk
• #70 Make tools and trimming optional (@matthdsm)
• #71 Add nf-test (@emiller88)

Changed

• #78 Nextflow minimal version is now 22.10.1

Fixed

• #63 Fix MultiQC report inputs, fixes MultiQC report is empty (@matthdsm)
• #67 Enable institutional configs (@emiller88)
• #83 Fix skip_tools (@glichtenstein)
• #80 When NoLaneSplitting is true the process fails because of a glob. See nf-core/modules #2745. (@matthdsm)
• #79 Update link in docs to samplesheet (@glichtenstein & @emiller88)

Initial release of nf-core/demultiplex, created with the nf-core template.

Added

• #38 - Add FastP
• #39 - Add FastQC
• #51 - Add bases2fastq