The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
- #389 Bump to version 1.7.1.
- #388 Improve functions nf-test.
- #387 Use nf-schema 2.7.0.
- #379 Enable workflow outputs.
- #372 Remove local subworkflows with less than 2 modules.
- #371 Bump checkqc
- #354 Bump version and note mgikit addition in 1.7.0 Changelog
- #355 Template update for nf-core/tools v3.5.1
- #357 Update MultiQC to 1.33
- #359 Update FASTP module
- #363 Use samshee only for validating samplesheet, not for formatting the samplesheet that's used by the demultiplexers.
- #368 Port nf-tests to
UTILS.groovy
- #385 Fix publish statements cannot be mixed with other statements in a dynamic publish path.
- #389 Fix
ConcurrentModificationExceptionerror in CI.
| Dependency | Old version | New version |
|---|---|---|
| falco | 1.2.1 | 1.2.5 |
| fastp | 1.0.1 | 1.1.0 |
| multiqc | 1.31 | 1.33 |
| multiqcsav | 1.9.0 | |
| samshee | 0.2.10 | 0.2.13 |
- #299 Added mgikit
- #334 Template update for nf-core/tools v3.3.2
- #335 Generated samplesheets now point to trimmed fastq files when they exist.
- #336 Updated nf-core modules to most recent versions except fqtk.
- #346 Template update for nf-core/tools v3.4.1
- #347 Updated cellranger mkfastq module to most recent version.
- #349 Updated bases2fastq
- #335 Samplesheet generation no longer has a tag (was previously every fastq file name)
- #347 Updated cellranger mkfastq module to most recent version to fix issues with downtream FALCO processing.
- #336 bclconvert now works when using fusion
| Dependency | Old version | New version |
|---|---|---|
| bases2fastq | 1.8.0.1260801529 | 2.3.0.2116803307 |
| coreutils | 8.30 | 9.5 |
| fastp | 0.23.4 | 0.24.0 |
| fqtk | 0.2.1 | 0.3.1 |
| kraken2 | 2.1.3 | 2.1.5 |
| mgikit | 2.1.0 | |
| multiqc | 1.29 | 1.31 |
| md5sum | 8.3 | 9.5 |
- #306 Update template to v3.2.0.
- #323 Update
samsheeto 0.2.10. - #327 Changed the manifest to new style and added contributors.
- #315 Fix adapter removal tests for various samplesheet formats
- #316 Fixed fastp module to properly respect the
trim_fastqparameter and not run when set to false
- #308 Add samplesheet generation for nf-core/sarek and nf-core/methylseq.
- #310 Replace [] with null as default
- #288 Fix
test_fullby validating parameters inlenientModeand fix workflow megatest workflow dispatch. - #294 Fix workflow.onComplete email sending feature.
- #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.
- #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
publishDirsubdirectory structure. - #281 Update cellranges/mkfastq module to fix missing reports and stats outputs.
- #282 Fixed downstream samplesheet paths and
publishDirconfig.
- #263 Updated all modules and subworkflows, and added new bclconvert test profile.
- #253 Fixed mkfastq output channels.
- #265 Fixed adapter removal for input samplesheets without lane information.
- #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.
- #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
- #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
- #148 Update CODEOWNERS to use GitHub teams
- #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
- #130 Remove
public_aws_ecrprofile.
- #125 Move containers for pipeline to quay.io
- #103
-profile testfailing due to relative path inflowcell_input.csv - #122 Fails gracefully if an error is encountered
- Add
public_aws_ecrprofile for using ECR containers. - Bump
fastpmodule to v0.23.4
- #115 Add public_aws_ecr profile
- #94 update documentation
- #95 add Codeowners
- #108 update modules (untar is now in bcl2fastq and bclconvert modules)
- #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)
- #78 Nextflow minimal version is now
22.10.1
- #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)
Initial release of nf-core/demultiplex, created with the nf-core template.