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

nf-core / ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2

https://nf-co.re/ampliseq

MIT License

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standardize the samplesheet for ampliseq to the other nf-core pipelines #790

Open jenmuell opened 3 weeks ago

jenmuell commented 3 weeks ago

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.

d4straub commented 3 weeks ago

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

jenmuell commented 3 weeks ago

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