nhoffman / dada2-nf

A Nextflow pipeline for processing 16S rRNA sequences using dada2
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Unable to parse config error #31

Closed mwohl closed 1 year ago

mwohl commented 3 years ago

On a fresh clone of the repo and install of nextflow, there is an error parsing the config:

mmwohl@unicorn:/molmicro/working/molly/dev/sandbox/dada2-nf$ ./nextflow run main.nf -params-file params-minimal.json
N E X T F L O W  ~  version 21.04.1
Launching `main.nf` [hopeful_franklin] - revision: 21354c4fd2
Unable to parse config file: '/mnt/disk15/molmicro/working/molly/dev/sandbox/dada2-nf/nextflow.config'

  Compile failed for sources FixedSetSources[name='/groovy/script/ScriptE88A3F40E1803CCA0B78D111A0D630B4/_nf_config_2707c0a4']. Cause: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
  /groovy/script/ScriptE88A3F40E1803CCA0B78D111A0D630B4/_nf_config_2707c0a4: 16: Unexpected input: '{' @ line 16, column 10.
     profiles {
              ^

  1 error

@dhoogest noticed that there is a comment introduced in this commit that uses the incorrect syntax (# instead of //).