beardymcjohnface / nektool Goto Github PK

per title, implement the recent build fixes documentation that were pushed to snaketool

Hi @beardymcjohnface
thanks for developing and maintaining Nektool! It seems that there are not so many examples with nextflow (yet). I was giving it a try with the test workflow convert2fasta when it failed:

my_nektool run --use-conda --input my_nektool/workflow/tiny.fastq -entry convert2fasta 

ERROR ~ Error executing process > 'convert2fasta:any2fasta (1)'

Caused by:
  Process `convert2fasta:any2fasta (1)` terminated with an error exit status (1)


Command executed:

  which any2fasta
  any2fasta tiny.fastq

which is due probably to the invocation to use conda. The cli doc (https://www.nextflow.io/docs/stable/cli.html) indicates -with-conda instead of --use-conda.

I'll try a PR.
Best,