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Recent Releases of germline-structuralv-nf

germline-structuralv-nf - v1.2.0

What's Changed

  • Remove harcoded GRCh38 version for AnnotSv by @juanesarango in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/76

New Contributors

  • @juanesarango made their first contribution in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/76

Full Changelog: https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/compare/v1.0.0...v1.2.0

- Nextflow
Published by georgiesamaha over 1 year ago

germline-structuralv-nf - v1.1.0

What's Changed

  • workflow structure 1st push by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/1
  • Svcallers by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/4
  • fixed manta process- all sv callers done by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/6
  • Variant calling processes complete by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/7
  • clean .vscode by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/8
  • v1.0 release by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/11
  • backup, annotSV todo by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/12
  • Betarelease by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/15
  • fix typo by @SarahBeecroft in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/25
  • Added manta container, fixed some spacing by @SarahBeecroft in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/21
  • Create setonix.config by @SarahBeecroft in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/22
  • Create SLURMsetonixrunpipeline.sh by @SarahBeecroft in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/23
  • Add info about reference files by @SarahBeecroft in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/24
  • added setonix.config to this file by @SarahBeecroft in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/28
  • added gadi config by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/29
  • remove dummy account variable by @SarahBeecroft in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/31
  • add newer tidbit container by @SarahBeecroft in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/32
  • include specific timings for jobs by @SarahBeecroft in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/36
  • run small jobs with local executor by @SarahBeecroft in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/37
  • run small jobs with small slurm allocation by @SarahBeecroft in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/38
  • Flexible AnnotSV annotation mode by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/39
  • Apply additional flags to AnnotSV by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/40
  • Create trace timestamp by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/41
  • Flexible customisation options by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/42
  • Add tower.yml and params.json for tower configurations by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/44
  • remove tower.yml by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/45
  • Tidy up parameters for tower integration by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/46
  • Fix parameters for tower by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/47
  • tower implementation fixes by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/48
  • fix manta container, fix pbs script by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/49
  • Fix indenting of nextflow.config by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/50
  • Update nextflow_schema.json for tower by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/51
  • Update nextflow_schema.json by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/52
  • Fix gadi.config beforeScript by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/53
  • Remove beforeScript by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/54
  • Update gadi.config by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/55
  • Tower Gadi implementation by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/56
  • Add gdata to gadi config by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/58
  • Gadi local jobs failing to access 10Gb memory by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/59
  • Finalise Tower integration with scalable run on Gadi by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/61
  • Fix issue #65: mix up of pbs and gadi parameters by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/66
  • Fixed *.config & queue in PBSgadirunpipeline.sh by @chlu0571 in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/67
  • change nextflow.config & hashed beforeScript in gadi.config by @chlu0571 in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/68
  • Final release of workflow v1.0.0 by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/73

New Contributors

  • @georgiesamaha made their first contribution in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/1
  • @SarahBeecroft made their first contribution in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/25
  • @chlu0571 made their first contribution in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/67

Full Changelog: https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/commits/v1.1.0

- Nextflow
Published by georgiesamaha over 1 year ago

germline-structuralv-nf - v1.0.0

What's Changed

  • workflow structure 1st push by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/1
  • Svcallers by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/4
  • fixed manta process- all sv callers done by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/6
  • Variant calling processes complete by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/7
  • clean .vscode by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/8
  • v1.0 release by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/11
  • backup, annotSV todo by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/12
  • Betarelease by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/15
  • fix typo by @SarahBeecroft in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/25
  • Added manta container, fixed some spacing by @SarahBeecroft in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/21
  • Create setonix.config by @SarahBeecroft in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/22
  • Create SLURMsetonixrunpipeline.sh by @SarahBeecroft in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/23
  • Add info about reference files by @SarahBeecroft in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/24
  • added setonix.config to this file by @SarahBeecroft in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/28
  • added gadi config by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/29
  • remove dummy account variable by @SarahBeecroft in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/31
  • add newer tidbit container by @SarahBeecroft in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/32
  • include specific timings for jobs by @SarahBeecroft in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/36
  • run small jobs with local executor by @SarahBeecroft in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/37
  • run small jobs with small slurm allocation by @SarahBeecroft in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/38
  • Flexible AnnotSV annotation mode by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/39
  • Apply additional flags to AnnotSV by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/40
  • Create trace timestamp by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/41
  • Flexible customisation options by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/42
  • Add tower.yml and params.json for tower configurations by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/44
  • remove tower.yml by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/45
  • Tidy up parameters for tower integration by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/46
  • Fix parameters for tower by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/47
  • tower implementation fixes by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/48
  • fix manta container, fix pbs script by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/49
  • Fix indenting of nextflow.config by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/50
  • Update nextflow_schema.json for tower by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/51
  • Update nextflow_schema.json by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/52
  • Fix gadi.config beforeScript by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/53
  • Remove beforeScript by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/54
  • Update gadi.config by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/55
  • Tower Gadi implementation by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/56
  • Add gdata to gadi config by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/58
  • Gadi local jobs failing to access 10Gb memory by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/59
  • Finalise Tower integration with scalable run on Gadi by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/61
  • Fix issue #65: mix up of pbs and gadi parameters by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/66
  • Fixed *.config & queue in PBSgadirunpipeline.sh by @chlu0571 in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/67
  • change nextflow.config & hashed beforeScript in gadi.config by @chlu0571 in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/68
  • Final release of workflow v1.0.0 by @georgiesamaha in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/73

New Contributors

  • @georgiesamaha made their first contribution in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/1
  • @SarahBeecroft made their first contribution in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/25
  • @chlu0571 made their first contribution in https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/pull/67

Full Changelog: https://github.com/Sydney-Informatics-Hub/Germline-StructuralV-nf/commits/v1.0.0

- Nextflow
Published by georgiesamaha about 2 years ago