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standardize the samplesheet for ampliseq to the other nf-core pipelines

Open jenmuell opened this issue 1 year ago • 2 comments

Description of feature

The samplesheet of ampliseq looks different to the other nf-core pipelines. I would propose the standardization of the headers of the samplesheet in ampliseq for:

  • [ ] sampleID to sample
  • [ ] forwardReads to fastq_1
  • [ ] reverseReads to fastq_2
  • [ ] coordinate/adapt the testdata to support the old and new samplesheet layout

Maybe it would be good to have an adaption from tab to csv as well since with nf-core schema it already supports them.

jenmuell avatar Oct 29 '24 09:10 jenmuell

Thanks!

Maybe it would be good to have an adaption from tab to csv as well since with nf-core schema it already supports them.

--input should already accept tsv, csv, yml as detailed in https://nf-co.re/ampliseq/2.11.0/docs/usage/#samplesheet-input

d4straub avatar Oct 29 '24 10:10 d4straub

Yes it does. I have tested it just to be sure before I implemented the autogeneration of the samplesheet in fetchngs as csv

jenmuell avatar Oct 29 '24 16:10 jenmuell