nf-core/demultiplex: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

1.5.2 - 2024-10-07

`Changed`

#263 Updated all modules and subworkflows, and added new bclconvert test profile.

1.5.1 - 2024-08-20

`Fixed`

#253 Fixed mkfastq output channels.
#265 Fixed adapter removal for input samplesheets without lane information.

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.

1.4.1 - 2024-02-27

`Changed`

#167 Updated template to nf-core/tools v2.12
#162 Updated template to nf-core/tools v2.11
#163 Updated template to nf-core/tools v2.11.1

1.4.0 - 2023-12-14

`Added`

#148 Update CODEOWNERS to use GitHub teams

`Changed`

#141 Updated template to nf-core/tools v2.10
#152 Updated bclconvert module to 4.2.4

`Fixed`

#127 Add singularity.registry = 'quay.io' and bump NF version to 23.04.0
#140 Make it possible to skip MultiQC, fix error raising
#145 Fix MultiQC report generation
#152 Close #150
#157 Fix bcl2fastq and bclconvert publishDir
#158 Update all modules
#201 Fix samplesheet documentation issues

`Removed`

#130 Remove public_aws_ecr profile.

1.3.2 - 2023-06-07

`Fixed`

#125 Move containers for pipeline to quay.io

1.3.1 - 2023-06-05

`Fixed`

#103 -profile test failing due to relative path in flowcell_input.csv
#122 Fails gracefully if an error is encountered

1.3.0 - 2023-05-31

`Added`

Add public_aws_ecr profile for using ECR containers.
Bump fastp module to v0.23.4

`Changed`

#115 Add public_aws_ecr profile

`Fixed`

v1.2.0 - 2023-04-24

`Added`

#91 Add sgdemux
#99 Add fqtk
#107 Add test_full

`Changed`

#94 update documentation
#95 add Codeowners
#108 update modules (untar is now in bcl2fastq and bclconvert modules)

`Fixed`

#96 fix logo
#97 bcl2fastq installation error (@matthdsm)

v1.1.0 - 2023-01-23

`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 (@edmundmiller)

`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 (@edmundmiller)
#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 & @edmundmiller)

v1.0.0 - 2022-10-06

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

`Added`

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

`Fixed`

`Deprecated`