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nf-cmgg / germline

A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data
https://nf-cmgg.github.io/germline/
MIT License
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Convert the scattering and header merging to processes #52

Closed nvnieuwk closed 1 year ago

nvnieuwk commented 1 year ago

Description of feature

Convert the scattering and header merging to processes

nvnieuwk commented 1 year ago

Negates #51

nvnieuwk commented 1 year ago

Convert the pipeline groovy functions to processes: SCATTER

  1. CLI: https://medium.com/@tambapps/groovy-parsing-command-line-arguments-with-clibuilder-44eaad1be4b4 => Inputs: bed, prefix, scatter_size
  2. Write a check for gzipped or unzipped
  3. Write the bed files

HEADER MERGE

  1. CLI: https://medium.com/@tambapps/groovy-parsing-command-line-arguments-with-clibuilder-44eaad1be4b4 => Inputs: vcf, ped_vcf, prefix
  2. Write the vcf with merged header

docker: https://hub.docker.com/layers/library/groovy/jdk17-alpine/images/sha256-70d532c7045c99b7a5fe7346a80c3c151cc50eaeb7954905cf65e9196a75bd06?context=explore

nvnieuwk commented 1 year ago

Added in #56