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Recent Releases of preprocessing

preprocessing - v2.0.6 - Heavenly Horse

HeavenlyHorse

What's Changed

  • Update bash options by @jhaezebr in https://github.com/nf-cmgg/preprocessing/pull/129
  • Bump bclconvert by @matthdsm in https://github.com/nf-cmgg/preprocessing/pull/130
  • v2.0.6 Release PR by @matthdsm in https://github.com/nf-cmgg/preprocessing/pull/132

New Contributors

  • @jhaezebr made their first contribution in https://github.com/nf-cmgg/preprocessing/pull/129

Full Changelog: https://github.com/nf-cmgg/preprocessing/compare/v2.0.5...2.0.6

- Nextflow
Published by matthdsm 9 months ago

preprocessing - v2.0.5 - Glimmering Gecko

glimmering_gecko

What's Changed

  • update efficiency of panel coverage by @nvnieuwk in https://github.com/nf-cmgg/preprocessing/pull/123
  • update SAMTOOLS_CONVERT resources by @matthdsm in https://github.com/nf-cmgg/preprocessing/pull/124
  • set markdup to samtools for WGS and edit sormadup settings by @matthdsm in https://github.com/nf-cmgg/preprocessing/pull/126
  • Release PR by @matthdsm in https://github.com/nf-cmgg/preprocessing/pull/127

Full Changelog: https://github.com/nf-cmgg/preprocessing/compare/v2.0.4...v2.0.5

- Nextflow
Published by matthdsm 10 months ago

preprocessing - v2.0.4 - Fiery Falcon

fiery_falcon

What's Changed

  • Add support for mouse genome mm10 for vivar compatibility by @matthdsm in https://github.com/nf-cmgg/preprocessing/pull/121
  • v2.0.4 by @matthdsm in https://github.com/nf-cmgg/preprocessing/pull/122

Full Changelog: https://github.com/nf-cmgg/preprocessing/compare/v2.0.3...v2.0.4

- Nextflow
Published by matthdsm about 1 year ago

preprocessing - v2.0.3 - Ethereal Eagle

ethereal_eagle

What's Changed

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

Full Changelog: https://github.com/nf-cmgg/preprocessing/compare/v2.0.2...v2.0.3

- Nextflow
Published by matthdsm about 1 year ago

preprocessing - v2.0.2 - Dreamy Dragon

DreamyDragon

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

Full Changelog: https://github.com/nf-cmgg/preprocessing/compare/v2.0.1...v2.0.2

- Nextflow
Published by matthdsm over 1 year ago

preprocessing - v2.0.1 - Cosmic Cheetah

596aa114-1385-4958-b231-e5c7dd55699f kopie

  • 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 https://github.com/nf-cmgg/preprocessing/pull/95
  • syntax validation by @matthdsm in https://github.com/nf-cmgg/preprocessing/pull/96
  • make coverage optional by @matthdsm in https://github.com/nf-cmgg/preprocessing/pull/98
  • Enable default help messages and add nice beforetext by @nvnieuwk in https://github.com/nf-cmgg/preprocessing/pull/99
  • Preprocessing v2.0.1 by @matthdsm in https://github.com/nf-cmgg/preprocessing/pull/100

Full Changelog: https://github.com/nf-cmgg/preprocessing/compare/v2.0.0...v2.0.1

- Nextflow
Published by matthdsm over 1 year ago

preprocessing - 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

- Nextflow
Published by nvnieuwk over 1 year ago

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

New Contributors

  • @nvnieuwk made their first contribution in https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/52

Full Changelog: https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/compare/v1.1.2...v1.2.0

- Nextflow
Published by nvnieuwk about 2 years ago

preprocessing - 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 https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/41
  • bump modules bcl2fastq, bclconvert, dragmap by @matthdsm in https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/49
  • Fix elprep/bamsormadup issues by @matthdsm in https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/48
  • Feat/split by @matthdsm in https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/51
  • dev by @matthdsm in https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/50

Full Changelog: https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/compare/v1.1.1...v1.1.2

- Nextflow
Published by matthdsm about 3 years ago

preprocessing - Hotfix

hotfix release for faulty sample grouping with flowcell inputs

What's Changed

  • HOTFIX for sample grouping with flowcell inputs by @matthdsm in https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/47
  • dev by @matthdsm in https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/45

Full Changelog: https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/compare/v1.1.0...v1.1.1

- Nextflow
Published by matthdsm about 3 years ago

preprocessing - 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 https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/24
  • update modules structure by @matthdsm in https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/27
  • Feat/nfcore subwf by @matthdsm in https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/29
  • Feat/nfcore subwf by @matthdsm in https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/31
  • Revert "Feat/nfcore subwf" by @matthdsm in https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/32
  • Wf restructure by @matthdsm in https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/33
  • Feat/ugent igenomes by @matthdsm in https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/42
  • Dev by @matthdsm in https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/37

Full Changelog: https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/compare/v1.0.1...v1.1.0

- Nextflow
Published by matthdsm about 3 years ago

preprocessing - v1.0.1

Small bugfixes and module updates

What's Changed

  • Bug/fastqtosam by @matthdsm in https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/25
  • Dev by @matthdsm in https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/26

Full Changelog: https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/compare/v1.0.0...v1.0.1

- Nextflow
Published by matthdsm over 3 years ago

preprocessing - Version 1.0.0

First full version, feature complete to replace WDL workflow

What's Changed

  • Testing by @matthdsm in https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/1
  • Alignment/readgroups by @matthdsm in https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/10
  • Feature/fastq split by @matthdsm in https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/13
  • Feature/teams hook by @matthdsm in https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/20
  • v1.0 by @matthdsm in https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/18

New Contributors

  • @matthdsm made their first contribution in https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/pull/1

Full Changelog: https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/commits/v1.0.0

- Nextflow
Published by matthdsm over 3 years ago