Requesting support with error "Explicit 'name separator' in class"

[josruirod]

Hi,

Thanks for your kind support in the past. I've been using mpgap routinely in our projects, but now I've been struggling for a while with a new installation... maybe trivial but I'm stuck and wondered if you could comment on it. I'm using singularity. Everything seems to be working, and the pipeline starts, but then ends with the error:

Explicit 'name separator' in class near index 8 [dataset/pacbio.fastq] ^ -- Check script '/.nextflow/assets/fmalmeida/mpgap/./workflows/parse_samples.nf' at line: 66 or see '.nextflow.log' file for more details

I believe I've used the same syntax as always, and the one suggested in the manual in the yml samplesheet: samplesheet:

• id: Sol_test_1 pacbio:
  • 'dataset/pacbio.fastq' genome_size: 39.11m wtdbg2_technology: rs corrected_long_reads: false

I'm attaching the nextflow.log. May be something trivial and nextflow-related... but could you comment please? I've unsuccesfully tried to use different quotes in the yml file, or even placing the file on the same folder.

Thanks!

[fmalmeida]

Hi @josruirod , Thanks for using the tool. I am a bit busy recently but I can give it a try tonight.

could you share with me the yml file you’re using? Not just copy and paste but the file itself? So I can download some pacbio data and try with it to see if I can reproduce.

but indeed, sounds that for some reason it is not parsing correctly

😬

[fmalmeida]

Before I actually try, I saw two things:

You have like this:

- id: Sol_test_1
  pacbio: 
    - 'dataset/pacbio.fastq'
  genome_size: 39.11m
  wtdbg2_technology: rs
  corrected_long_reads: false 

but the line breaked syntax is used for Illumina that can expect SE, PE or both reads. As long reads is always one, I think I wrote to expect in one line:

See here

- id: Sol_test_1
  pacbio: dataset/pacbio.fastq
  genome_size: 39.11m
  wtdbg2_technology: rs
  corrected_long_reads: false 

Also, I think is best that in the samplesheet you use the absolute paths to files to avoid the pipeline not finding it :)

[josruirod]

Hi, and thanks for the quick and kind support. My fault 100% and you are completely right. It was that silly mistake in the syntax. Apologies for any inconvenience.

Best wishes!

[fmalmeida]

Awesome. Great to hear that it worked 😄 Have fun with it 💯