v2.0.4 - Fiery Falcon

What's Changed

• Add support for mouse genome mm10 for vivar compatibility by @matthdsm in #121
• v2.0.4 by @matthdsm in #122

Full Changelog: v2.0.3...v2.0.4

v2.0.3 - Ethereal Eagle

What's Changed

• Re-enable nf-core lint by @matthdsm in #111
• Bump/modules by @matthdsm in #110
• Fix test profile by @nvnieuwk in #113
• Fix groupTuple by @nvnieuwk in #115
• add missing igenomes conf by @nvnieuwk in #116
• small doc updates by @nvnieuwk in #118
• Fix tests by @nvnieuwk in #119
• Dev by @matthdsm in #120

Full Changelog: v2.0.2...v2.0.3

v2.0.2 - Dreamy Dragon

• Drop unsed params
• Set aligner to star for RNA-seq
• Finetune resources
• Fix some bugs for different input tags
• Update modules

Full Changelog: v2.0.1...v2.0.2

v2.0.1 - Cosmic Cheetah

• Fix syntax according to new rules
• Drop usage of check_max function in favour of resourceLimits
• Bump nf-schema to v2.1.0
• Add configuration profiles for several datatypes
• Fix usage of --run_coverage parameter
• Update modules

Pull requests

• Add analysis presets and remote cluster configs by @matthdsm in #95
• syntax validation by @matthdsm in #96
• make coverage optional by @matthdsm in #98
• Enable default help messages and add nice beforetext by @nvnieuwk in #99
• Preprocessing v2.0.1 by @matthdsm in #100

Full Changelog: v2.0.0...v2.0.1

Bold Bear

• Move repo to nf-cmgg organisation
• Overhaul reference data handling. All data is now sourced from the igenomes config file and dynamically loaded based on the organism metadata field.
• Drop support for bam/cram inputs
• Update to nf-core template v2.13.1
• Drop fgbio/fastqtosam in favour of samtools/import
• Add samtools/coverage for coverage analysis
• Add testing with nf-test
• Overhaul panel coverage analysis
• Add support for STAR aligner for RNA-seq
• Replace CSV sampleinfo definition with validated JSON/YAML
• Update modules

Terrible Tiger

• Add fix for sample replicates with different split sizes
• Add option to use samtools for duplicate marking
• Updated modules
• Updated to nf-core template v2.8
• Fix issue where unaligned samples were not merged and fixed naming
• Add minimal support for sample "tags" in sample sheet
• Add panel coverage analysis
• Limit panel coverage analyses to samples with WES/WGS tags
• Make BAM_ARCHIVE accept channels with cram files
• Drop ELPREP support
• Add support for cram and index outputs in SAMTOOLS_SORMADUP
• Add option to disable marking duplicates
• Update to nf-core template v2.9
• Start using nf-validation for input parsing
• Drop support for generating aligner indices

What's Changed

• re-add metro map by @nvnieuwk in #52
• bump modules by @matthdsm in #53
• Fix/unbalanced chunks by @matthdsm in #55
• add samtools markdup by @matthdsm in #56
• bump modules by @matthdsm in #57
• Template merge by @matthdsm in #58
• fix unaliged issue, fixed #60 by @matthdsm in #63
• Feat/expand coverage by @matthdsm in #65
• Template merge by @matthdsm in #69
• Fix typo in nextflow.config by @nvnieuwk in #70
• Nf validation by @matthdsm in #71
• Template merge by @matthdsm in #72
• Cleanup by @matthdsm in #73
• Update all modules to the latest version by @nvnieuwk in #75
• Release PR by @matthdsm in #59

New Contributors

• @nvnieuwk made their first contribution in #52

Full Changelog: v1.1.2...v1.2.0

Rational Raccoon

Support for bamprocessing with ELPREP
Improved sample grouping
Meta value clean up
bump modules
fix multiqc report to include all results
fix duplicate marking with bamsormadup
drop post alignment sorting, doesn't make sense as we do sort/markdup afterwards
Add option to use elprep for alignment postprocessing

What's Changed

• Feature/elprep by @matthdsm in #41
• bump modules bcl2fastq, bclconvert, dragmap by @matthdsm in #49
• Fix elprep/bamsormadup issues by @matthdsm in #48
• Feat/split by @matthdsm in #51
• dev by @matthdsm in #50

Full Changelog: v1.1.1...v1.1.2

Hotfix

hotfix release for faulty sample grouping with flowcell inputs

What's Changed

• HOTFIX for sample grouping with flowcell inputs by @matthdsm in #47
• dev by @matthdsm in #45

Full Changelog: v1.1.0...v1.1.1

Workflow restructure and optimizations

Optimize the workflow structure and unblock the processes post alignment.
Update the default reference genome and reconfigure iGenomes.conf to use on-prem S3.

What's Changed

• Feature/cram input by @matthdsm in #24
• update modules structure by @matthdsm in #27
• Feat/nfcore subwf by @matthdsm in #29
• Feat/nfcore subwf by @matthdsm in #31
• Revert "Feat/nfcore subwf" by @matthdsm in #32
• Wf restructure by @matthdsm in #33
• Feat/ugent igenomes by @matthdsm in #42
• Dev by @matthdsm in #37

Full Changelog: v1.0.1...v1.1.0

v1.0.1

Small bugfixes and module updates

What's Changed

• Bug/fastqtosam by @matthdsm in #25
• Dev by @matthdsm in #26

Full Changelog: v1.0.0...v1.0.1