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nf-core/phaseimpute: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v1.0dev - [date]

Initial release of nf-core/phaseimpute, created with the nf-core template.

Added

  • #20 - Added automatic detection of vcf contigs for the reference panel and automatic renaming available
  • #22 - Add validation step for concordance analysis. Input channels changed to match inputs steps. Outdir folder organised by steps. Modules config by subworkflows.
  • #26 - Added QUILT method
  • #47 - Add possibility to remove samples from reference panel. Add glimpse2 chunking method. Add full-size test parameters.
  • #58 - Add external params posfile and chunks. Add glimpse2 phasing and imputation.
  • #67 - Export CSVs from each step.
  • #71 - Allow external panel to be used in step impute.
  • #97 - Add dog reference panel and config to test pipeline with other species.
  • #102 - Add dog panel test.
  • #119 - Add dog test with panelprep and imputation.
  • #118 - Explain how to customize arguments in the pipeline.
  • #111 - Add nf-test for all sbwf, wf, modules and functions.
  • #131 - Set normalisation as optional. Fix extension detection function. Add support for validation with vcf files. Concatenate vcf only if more than one file. Change --phased to --phase for consistency.

Changed

  • #18
    • Maps and region by chromosome
    • update tests config files
    • correct meta map propagation
    • Test impute and test sim works
  • #19 - Changed reference panel to accept a csv, update modules and subworkflows (glimpse1/2 and shapeit5)
  • #40 - Add STITCH method. Reorganize panelprep subworkflows.
  • #51 - Update all process and fix linting errors. Remove fastqc added by the template.
  • #56 - Move to nf-test to check the output files names generated. Fix validation and concatenation by chromosomes missing. Add dedicated GLIMPSE1 subworkflow. Fix posfile generation to be done once for glimpse and stitch.
  • #68 - QUILT can handle external params chunks and hap-legend files.
  • #78 - Separate validate step from panel preparation.
  • #84 - Change depth computation to use SAMTOOLS_DEPTH and make separation by chromosome only if regions are specified.
  • #85 - Use external params in individual tests for tools.
  • #86 - Move bcftools_convert to vcf_sites_extract_bcftools.
  • #88 - Improve multiqc report with more information.
  • #91 - Update metro map with all steps and remove deprecated ones.
  • #93 - Add support for CRAM file.
  • #93 - Check contigs name at workflow level for BAM and VCF.
  • #93 - Samples remove with multiallelics records.
  • #93 - Samtools merge in BAM_REGION sbwf.
  • #93 - Fix glimpse2_phase output file names.
  • #93 - Fix fai combination to fasta.
  • #96 - Simplify csv export
  • #96 - Use only legend file as posfile for all imputation workflow.
  • #100 - Update bcftools, samtools, ... nf-core modules. All indexing is now done with the file creation for most of them.
  • #101 - Set --compute_freq as false by default.
  • #102 - Compute chr name from whole vcf.
  • #102 - Only warn the user if some contigs are absent from files, the regions to compute is now the intersection of regions, panel, posfile, chunks, map.
  • #102 - Update all test and recompute snapshot to match new version of the phaseimpute test dataset.
  • #103 - Update Glimpse2 phase, gunzip and multiqc

Fixed

  • #15 - Changed test csv files to point to nf-core repository
  • #16 - Removed outdir from test config files
  • #65 - Separate stitch output by individuals
  • #75 - Set frequency computation with VCFFIXUP process as optional with --compute_freq. Use Glimpse_chunk on panel vcf to compute the chunk and not makewindows on fasta.
  • #117 - Fix directories in CSV.

Dependencies

Deprecated