3.0.2 - Juniper Jackalope

What's Changed

• Drop plugin config in favour of nf-cmgg/configs

Full Changelog: 3.0.1...3.0.2

3.0.1 - Jellylume Jellyfish

What's changed

• Bump minimal nextflow version to 26.04
• Make pipeline fully strict syntax compatible
• Fix bug where Falco wasn't run on fastq samples

Full Changelog: v3.0.0...3.0.1

3.0.1 - Release Candidate 1

What's Changed

• Update nf-teams plugin version to 0.1.1 by @nvnieuwk in #163
• fix mosdepth env issue on gcp by @nvnieuwk in #166
• Add parameter typing by @nvnieuwk in #167
• Bump/template by @matthdsm in #168

Full Changelog: v3.0.0...v3.0.1-RC1

3.0.0 - Icebound Insect

Major release featuring:

• module updates
• faster bclconvert output handling
• modified output structure, featuring qc reports per library and enhanced run qc through multiqc_sav
• fastq output when aligner equals false, with falco report
• per sample analysis definition for more flexibility

Contributions

• Update regex pattern for BED file path validation by @matthdsm in #137
• coverage - filter seqcap genelists by @matthdsm in #133
• only use first versions of modules by @nvnieuwk in #136
• Workflow output definitions by @nvnieuwk in #138
• Fix nextflow lint warnings + template update by @nvnieuwk in #139
• Fix/bclconvert gcp by @matthdsm in #140
• Chore/bump modules by @matthdsm in #142
• output files in library subdir where possible by @matthdsm in #143
• Enable fastq outputs by @matthdsm in #146
• optimize resources for gcp by @matthdsm in #148
• Add splice junctions and junctions to rna output by @nvnieuwk in #150
• Fix splice junctions file name by @nvnieuwk in #151
• Add multiqc_cmgg with custom template by @matthdsm in #152
• migrate analysis and resource profiles to external repo by @matthdsm in #153
• Feat/fastq qc by @matthdsm in #156
• Feat: per sample params by @matthdsm in #155
• Migrate pipeline to topic only by @matthdsm in #157
• Feat: MultiQC SAV by @matthdsm in #160
• Bump modules by @matthdsm in #161
• Update/docs by @matthdsm in #162
• try nf-metro by @matthdsm in #158
• Preprocessing v3.0.0 by @matthdsm in #159

Full Changelog: 2.0.6...v3.0.0

v2.0.6 - Heavenly Horse

What's Changed

• Update bash options by @jhaezebr in #129
• Bump bclconvert by @matthdsm in #130
• v2.0.6 Release PR by @matthdsm in #132

New Contributors

• @jhaezebr made their first contribution in #129

Full Changelog: v2.0.5...2.0.6

v2.0.5 - Glimmering Gecko

What's Changed

• update efficiency of panel coverage by @nvnieuwk in #123
• update SAMTOOLS_CONVERT resources by @matthdsm in #124
• set markdup to samtools for WGS and edit sormadup settings by @matthdsm in #126
• Release PR by @matthdsm in #127

Full Changelog: v2.0.4...v2.0.5

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