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chrisgulvik / wf-assembly-snps

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Workflow can't handle specified reference #17

Open SarahNadeau opened 2 years ago

SarahNadeau commented 2 years ago

Current behavior

Running this:

nextflow run main.nf -profile docker --refpath 16-090.fna.gz --inpath INPUT_DIR/ --outpath OUTPUT_DIR --max_cpus 2 --max_memory '1.GB'

Gives this error:

10:02:41 - INFO - <<Parsnp started>>
  10:02:41 - INFO - No genbank file provided for reference annotations, skipping..
  Traceback (most recent call last):
    File "/parsnp-1.5.6/parsnp", line 815, in <module>
      if hdr[0] != ">":
  IndexError: string index out of range
  [2022-Apr-11 Mon 10:02:41] ERROR: gingr file parsnp/parsnp.ggr absent
  ERROR: Parsnp failed.
    Check parsnp/parsnpAligner.log

Work dir:
  /Users/nadeau/Documents/CDC_ORISE/Projects/wf-assembly-snps/work/04/06d34e16ad6ca11c2289a0569f4571

And the reference file is empty, e.g.:

head /Users/nadeau/Documents/CDC_ORISE/Projects/wf-assembly-snps/work/04/06d34e16ad6ca11c2289a0569f4571/.ref/16-090
# File has no content

Expected behavior

User can specify a reference file from anywhere on their system and it will be used.