nf-core/demultiplex

#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.

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What’s Changed

Updated modules and subworkflows by @nschcolnicov in https://github.com/nf-core/demultiplex/pull/259
Fixed adapter removal by @nschcolnicov in https://github.com/nf-core/demultiplex/pull/265
Update diagram by @atrigila in https://github.com/nf-core/demultiplex/pull/266
Added miniseq bclconvert test by @nschcolnicov in https://github.com/nf-core/demultiplex/pull/267
Update Modules by @apeltzer in https://github.com/nf-core/demultiplex/pull/263
bump version by @grst in https://github.com/nf-core/demultiplex/pull/270
Fix release by @grst in https://github.com/nf-core/demultiplex/pull/271
v1.5.2 release by @grst in https://github.com/nf-core/demultiplex/pull/269

Full Changelog: https://github.com/nf-core/demultiplex/compare/1.5.1…1.5.2

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1.5.1

`Fixed`

#253 Fixed mkfastq output channels.

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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.

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What’s Changed

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

Full Changelog: https://github.com/nf-core/demultiplex/compare/1.4.0…1.4.1

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What’s Changed

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

New Contributors

@sateeshperi made their first contribution in https://github.com/nf-core/demultiplex/pull/129
@Aratz made their first contribution in https://github.com/nf-core/demultiplex/pull/140

Full Changelog: https://github.com/nf-core/demultiplex/compare/1.3.2…1.4.0

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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 https://github.com/nf-core/demultiplex/pull/125
Dev -> Master for 1.3.2 release by @drpatelh in https://github.com/nf-core/demultiplex/pull/126

Full Changelog: https://github.com/nf-core/demultiplex/compare/1.3.1…1.3.2

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What’s Changed

Use Nextflow.error instead of ‘exit 1’ by @adamrtalbot in https://github.com/nf-core/demultiplex/pull/122
Move test data from pipeline to testdatasets by @drpatelh in https://github.com/nf-core/demultiplex/pull/123
Dev -> Master for 1.3.1 patch release by @drpatelh in https://github.com/nf-core/demultiplex/pull/124

Full Changelog: https://github.com/nf-core/demultiplex/compare/1.3.0…1.3.1

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[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 https://github.com/nf-core/demultiplex/pull/113
Important! Template update for nf-core/tools v2.8 by @nf-core-bot in https://github.com/nf-core/demultiplex/pull/114
Update all modules and specify container registry using docker.registry default by @adamrtalbot in https://github.com/nf-core/demultiplex/pull/115
Bump fastp by @matthdsm in https://github.com/nf-core/demultiplex/pull/117
Re-add aws_tower config for running on Tower by @adamrtalbot in https://github.com/nf-core/demultiplex/pull/119
Release candidate 1.3.0 by @adamrtalbot in https://github.com/nf-core/demultiplex/pull/118

Full Changelog: https://github.com/nf-core/demultiplex/compare/1.2.0…1.3.0

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What’s Changed

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

New Contributors

@sam-white04 made their first contribution in https://github.com/nf-core/demultiplex/pull/91
@nh13 made their first contribution in https://github.com/nf-core/demultiplex/pull/94
@maxulysse made their first contribution in https://github.com/nf-core/demultiplex/pull/107

Full Changelog: https://github.com/nf-core/demultiplex/compare/1.1.0…1.2.0

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`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)