fixing handling of nanopore samplesheets for viralrecon

src/viralrecon.rs

@@ -98,16 +98,15 @@ impl CollectByPlatform for SeqPlatform {
  Ok(vec![sample_id, fastq1, fastq2].join(","))
  }
  SeqPlatform::Nanopore => {
- // figure out which FASTQ files go with the provided sample_id
- let barcode_fastq = fastq_paths
- .iter()
- .filter_map(|x| x.to_str())
- .find(|x| x.contains(sample_id.as_ref()))
- .ok_or("Sample ID no longer matches a FASTQ.")
- .unwrap_or("");
+ // pull out the barcode
+ let barcode = if sample_id.starts_with("0") {
+ sample_id.replace("barcode", "").chars().skip(1).collect()
+ } else {
+ sample_id.replace("barcode", "")
+ };
 
- // instantiate an illumina line and return it
- Ok(vec![sample_id.as_ref(), barcode_fastq].join(","))
+ // instantiate a Nanopore line and return it
+ Ok(vec![sample_id.as_ref(), &barcode].join(","))
  }
  }
  }