These are chat archives for nextflow-io/nextflow

29th
Oct 2017
Ghost
@ghost~598345d2d73408ce4f6ff925
Oct 29 2017 19:00

I'm trying to use gzipped reads with my aligner but it seems I'm not getting the format right. I first load the paired gzipped reads like so

    Channel
      .fromPath(params.reads).splitCsv(header: true)
      .map {row -> [row.Sample_Name, [row.Read1, row.Read2]]}
      .ifEmpty {error "File ${params.reads} not parsed properly"}
      .into {gzipped_reads}

And then send them to my mapping process where I've omitted everything except the input.

    process map_gzipped_reads {

      input:
      set sampleid, file (reads:'*') from gzipped_reads

      output:

      script:

My error is the aligner says it doesn't recognize the files as gzipped fastq. Any suggestions?