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Recent Releases of nf-gwas

nf-gwas - 1.0.9

What's Changed

  • Add docker-build action to take advantage of caching and use sharding by @lukfor in https://github.com/genepi/nf-gwas/pull/105
  • Add Step 1 logs by @krferrier and @seppinho in https://github.com/genepi/nf-gwas/pull/109

Full Changelog: https://github.com/genepi/nf-gwas/compare/v1.0.8...v1.0.9

- Nextflow
Published by seppinho about 1 year ago

nf-gwas - 1.0.8

  • rsID file is not required by default.

- Nextflow
Published by seppinho almost 2 years ago

nf-gwas - 1.0.7

  • Install awscli tool

- Nextflow
Published by seppinho almost 2 years ago

nf-gwas - 1.0.6

  • Install AWS CLI tools

- Nextflow
Published by seppinho almost 2 years ago

nf-gwas - 1.0.5

What's Changed

  • Update nf-test to v0.8.2 by @AmstlerStephan in https://github.com/genepi/nf-gwas/pull/91
  • Integration of VCF and BGEN for gene-based testing by @filosi in https://github.com/genepi/nf-gwas/pull/92
  • Update regenie version to 3.4 by @filosi in https://github.com/genepi/nf-gwas/pull/93

New Contributors

  • @AmstlerStephan made their first contribution in https://github.com/genepi/nf-gwas/pull/91

Full Changelog: https://github.com/genepi/nf-gwas/compare/v1.0.4...v1.0.5

- Nextflow
Published by lukfor about 2 years ago

nf-gwas - 1.0.4

  • Fix annotation process when downloading rsID files

- Nextflow
Published by seppinho over 2 years ago

nf-gwas - 1.0.3

What's Changed

  • Update to latest regenie version by @seppinho in https://github.com/genepi/nf-gwas/pull/88
  • Feature/regenie optional params by @seppinho in https://github.com/genepi/nf-gwas/pull/89

Full Changelog: https://github.com/genepi/nf-gwas/compare/v1.0.2...v1.0.3

- Nextflow
Published by seppinho over 2 years ago

nf-gwas - 1.0.2

What's Changed

  • Create subworkflows by @seppinho in https://github.com/genepi/nf-gwas/pull/86
  • Add nf-validations by @seppinho in https://github.com/genepi/nf-gwas/pull/87

Full Changelog: https://github.com/genepi/nf-gwas/compare/v1.0.1...v1.0.2

- Nextflow
Published by seppinho over 2 years ago

nf-gwas - 1.0.1

What's Changed

  • Update nf-test and fix problem with filtering of N/A values by @seppinho in https://github.com/genepi/nf-gwas/pull/85

Full Changelog: https://github.com/genepi/nf-gwas/compare/v1.0.0...v1.0.1

- Nextflow
Published by seppinho over 2 years ago

nf-gwas - 1.0.0

What's Changed

  • Includes best-practices parallelization of REGENIE Step 1 by phenotype (LOCO predictions) by @lukfor and @seppinho
  • Includes parallelization of REGENIE Step 2 (regression model) into genomic chunks by @seppinho and @lukfor. Chunk size and chunk strategy (variants / range) can be specified by users.
  • Includes updated interactive Manhattan Plot to visualize millions of points by @lukfor and @johsr.
  • Optimized parameter configuration to run on public clouds for hundreds of phenotypes by @seppinho in https://github.com/genepi/nf-gwas/pull/84.
  • Delete unused modules
  • Parallelize gwas-report-index by @lukfor in https://github.com/genepi/nf-gwas/pull/83
  • Update to latest regenie version v3.2.9

Full Changelog: https://github.com/genepi/nf-gwas/compare/v0.7.7...v1.0.0

- Nextflow
Published by seppinho over 2 years ago

nf-gwas - 0.7.7

  • Update to genomic-utils v0.7.7 for improved report indexing

- Nextflow
Published by seppinho over 2 years ago

nf-gwas - 0.7.6

  • Update to latest genomic-utils to simplify merge/filter logic

- Nextflow
Published by seppinho over 2 years ago

nf-gwas - 0.7.5

  • Update to genomic-utils v0.3.0

- Nextflow
Published by seppinho over 2 years ago

nf-gwas - 0.7.4

  • Make regenie filter step configurable

- Nextflow
Published by seppinho over 2 years ago

nf-gwas - 0.7.3

What's Changed

  • Update to latest genomic-utils library

- Nextflow
Published by seppinho over 2 years ago

nf-gwas - 0.7.2

What's Changed

  • Add rinted histogram if phenotypesapplyrint is true (Features/histogram rinted) by @johsr in https://github.com/genepi/nf-gwas/pull/67
  • Update sorting by @seppinho in https://github.com/genepi/nf-gwas/pull/79

- Nextflow
Published by seppinho over 2 years ago

nf-gwas - 0.7.1

What's Changed

  • Remove unused tabix-merge.jar file by @ejseqera in https://github.com/genepi/nf-gwas/pull/76
  • Add basic nextflow_schema.json by @robsyme in https://github.com/genepi/nf-gwas/pull/68

New Contributors

  • @ejseqera made their first contribution in https://github.com/genepi/nf-gwas/pull/76
  • @robsyme made their first contribution in https://github.com/genepi/nf-gwas/pull/68

Full Changelog: https://github.com/genepi/nf-gwas/compare/v0.6.4...v0.7.1

- Nextflow
Published by seppinho over 2 years ago

nf-gwas - 0.6.4

What's Changed

  • Fix issue with depreciated params name by @seppinho [cfce9f3078efc1a5c50104abe06906880a43c879]

- Nextflow
Published by seppinho over 2 years ago

nf-gwas - 0.6.3

Full Changelog: https://github.com/genepi/nf-gwas/compare/v0.6.2...v0.6.3

- Nextflow
Published by seppinho almost 3 years ago

nf-gwas - 0.6.2

Full Changelog: https://github.com/genepi/nf-gwas/compare/v0.6.1...v0.6.2

- Nextflow
Published by seppinho almost 3 years ago

nf-gwas - 0.6.1

  • Fix wrong sorting directory which affected SLURM executions

- Nextflow
Published by seppinho almost 3 years ago

nf-gwas - 0.6.0

What's Changed

  • Add rsids to top hits by @lukfor, @salvidm, @johsr and @seppinho in https://github.com/genepi/nf-gwas/pull/59
  • Update top loci table by @lukfor in https://github.com/genepi/nf-gwas/pull/61
  • Features/lift over by @seppinho in https://github.com/genepi/nf-gwas/pull/64
  • Improve report and add index file to improve navigation by @lukfor and @johsr in https://github.com/genepi/nf-gwas/pull/62

Full Changelog: https://github.com/genepi/nf-gwas/compare/v0.5.2...v0.6.0

- Nextflow
Published by seppinho almost 3 years ago

nf-gwas - 0.5.2

What's Changed

  • Feature/interaction testing by @seppinho and @johsr in https://github.com/genepi/nf-gwas/pull/63

Full Changelog: https://github.com/genepi/nf-gwas/compare/v0.5.1...v0.5.2

- Nextflow
Published by seppinho about 3 years ago

nf-gwas - 0.5.1

  • Set version of plink2 in environment.yml

- Nextflow
Published by seppinho about 3 years ago

nf-gwas - 0.5.0

  • Support gene-based testing
  • Update to latest regenie version v3.2.1
  • Improved R-Report (split QQ-Plot by MAF, remove duplicate code)
  • Add new option how to convert VCF to PLINK2
  • Make nf-gwas cloud-ready

- Nextflow
Published by seppinho over 3 years ago

nf-gwas - 0.4.2

  • Fix relative path issue with LOCO predictions on AWS Batch. [7ecd0dfcd82927d1aa07bffdedd0d1d374010ae7]

- Nextflow
Published by seppinho over 3 years ago

nf-gwas - 0.4.1

  • Fix sorting by position in final regenie file [4cc3ae667b1570085e5a5352b980ac23012dbda9]

- Nextflow
Published by seppinho over 3 years ago

nf-gwas - 0.4.0

  • Adding Azure support [ e13dd0727c3ecab303cebabc67b04a48ec862a13]
  • Updating pipeline to Regenie version v3.0.1

- Nextflow
Published by seppinho over 3 years ago

nf-gwas - 0.3.5

  • Update pruning default values

- Nextflow
Published by seppinho almost 4 years ago

nf-gwas - 0.3.4

- Nextflow
Published by seppinho almost 4 years ago

nf-gwas - 0.3.3

- Nextflow
Published by seppinho almost 4 years ago

nf-gwas - 0.3.2

- Nextflow
Published by seppinho almost 4 years ago

nf-gwas - 0.3.1

  • Check for NA string when filtering regenie results

- Nextflow
Published by seppinho almost 4 years ago

nf-gwas - 0.3.0

  • Update to regenie 3.0

- Nextflow
Published by seppinho almost 4 years ago

nf-gwas - 0.2.2

  • Restructure merge step and use tuples to save resources
  • Read correct data type in R-Report

- Nextflow
Published by seppinho about 4 years ago

nf-gwas - 0.2.1

- Nextflow
Published by seppinho about 4 years ago

nf-gwas - 0.2.0

  • Introduce process and name labels

- Nextflow
Published by seppinho about 4 years ago

nf-gwas - 0.1.15

  • Tabix regenie results to use with Locuszoom

- Nextflow
Published by seppinho about 4 years ago

nf-gwas - 0.1.14

  • Use protein_coding genes for annotation
  • Annotate genes directly in Manhattan Plot
  • Enable/disbale annotation in Manhattan plot
  • Add first test-cases using nf-test

- Nextflow
Published by seppinho about 4 years ago

nf-gwas - 0.1.14-rc1

- Nextflow
Published by seppinho about 4 years ago

nf-gwas - 0.1.13

  • Support slurm profiles

- Nextflow
Published by seppinho over 4 years ago

nf-gwas - 0.1.12

  • Add regenieforcestep1 parameter
  • Publish log of pruning for better investigation

- Nextflow
Published by seppinho over 4 years ago

nf-gwas - 0.1.11

Major changes: - Apply pruning (if set) on QCed genotyped files - Set y-limit for QQ-Plot - Output log files for better investigation - Set default value for parallelization to 1. This must be set depending on the architecture (cluster executor vs local executor).

- Nextflow
Published by seppinho over 4 years ago

nf-gwas - 0.1.10

  • Annotate all hits with logp value >= 5 (can also be set using the annotation_min_log10p parameter)
  • Restructure R-Report

- Nextflow
Published by seppinho over 4 years ago

nf-gwas - 0.1.9

- Nextflow
Published by seppinho over 4 years ago

nf-gwas - 0.1.8

- Nextflow
Published by seppinho over 4 years ago

nf-gwas - 0.1.7

- Nextflow
Published by seppinho over 4 years ago

nf-gwas - 0.1.6

  • Add annotation task with bedtools

- Nextflow
Published by seppinho over 4 years ago

nf-gwas - 0.1.5

  • Migrate to DSL2

- Nextflow
Published by seppinho over 4 years ago

nf-gwas - 0.1.4

- Nextflow
Published by seppinho over 4 years ago

nf-gwas - 0.1.3

- Nextflow
Published by seppinho over 4 years ago

nf-gwas - 0.1.2

- Nextflow
Published by seppinho over 4 years ago

nf-gwas - 0.1.1

  • Set docker image to remote location

- Nextflow
Published by seppinho over 4 years ago

nf-gwas - 0.1.0

  • Init release

- Nextflow
Published by seppinho over 4 years ago