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daviesdrew / variantcalling

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Reference genome specified in CLI not accepted as input for any processes #15

Open peterk87 opened 4 years ago

peterk87 commented 4 years ago

The reference genome(s) need to be accepted as a parameter from the command-line. It's not ever going to be a static file included with the workflow - it's going to be dependent on the users needs given their dataset and the questions they wish to answer. Also, it should be possible to specify multiple reference genomes with --refs "/path/to/reference_genomes/*.fasta" when running the workflow.

In the workflow body, you'll need to create a Channel for the reference genome files:

workflow {
  ch_refs = Channel.fromPath(params.refs)
  // combine all read sets with each reference
  ch_reads_and_refs = ch_reads | combine(ch_refs)
  // each value in ch_reads_and_refs will contain [ sample_id, reads1, reads2, ref_fasta ]
  MAP(ch_reads_and_refs)
}