rrwick / Unicycler

hybrid assembly pipeline for bacterial genomes
GNU General Public License v3.0
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Trouble with --spades_options --careful #342

Open JasonBeardSanger opened 3 weeks ago

JasonBeardSanger commented 3 weeks ago
#!/bin/bash -euo pipefail
unicycler \
      --threads 8 \
      -1 46872_2#248_1.fastq.gz -2 46872_2#248_2.fastq.gz \
      --spades_options "--careful"\
\
      --out ./
  mv assembly.fasta 46872_2#248.assembly.fa
  mv assembly.gfa 46872_2#248.assembly.gfa
  mv unicycler.log 46872_2#248.unicycler.log

I'm having problems passing --careful to spades through my nexflow pipline, --spades_options "--phred-offset 33" and --spades_options "--cov-cutoff auto" were no problem but --careful throws the error: [--spades_options was expecting an argument](unicycler: error: argument --spades_options: expected one argument) as a note using double quotes, no quotes, and with or without a space at the end didn't seem to help Passing like this also fails but with a different error

#!/bin/bash -euo pipefail
unicycler \
    --threads 8 \
    -1 46872_2#248_1.fastq.gz -2 46872_2#248_2.fastq.gz \
    "--spades_options --careful ''" \
     \
    --out ./
mv assembly.fasta 46872_2#248.assembly.fa
mv assembly.gfa 46872_2#248.assembly.gfa
mv unicycler.log 46872_2#248.unicycler.log

spades.py: error: Please specify option (e.g. -1, -2, -s, etc)) for the following paths: --careful, '' Using a single dash -careful triggers the same error

JasonBeardSanger commented 20 hours ago

It seems unicycler uses --isolate as a deafult which is in compatable with --careful . There seems to be no way to change this without changing the code myself, future updates maybe?