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nf-core / differentialabundance

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
https://nf-co.re/differentialabundance
MIT License
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Unable to run pipeline – please provide test data #358

Open febedtu opened 6 days ago

febedtu commented 6 days ago

Description of the bug

I have been able to successfully run the pipeline test

nextflow run nf-core/differentialabundance \ --outdir test \ -profile test,docker

Unfortunately, I remain unsuccessfull with my own data. Would it be possible to provide the data used in the test as well as the test command to determine what parameters and/or inputs are incorrect in my own application?

Command used and terminal output

Relevant files

No response

System information

No response

WackerO commented 20 hours ago

Hello @febedtu,

the test profile simply runs the pipeline with all the parameters in defined in this file: https://github.com/nf-core/differentialabundance/blob/master/conf/test.config

The test.config also calls the https://github.com/nf-core/differentialabundance/blob/master/conf/rnaseq.config settings; you can either provide those manually or call them with -profile rnaseq, so if you want to reproduce the analysis locally, after downloading the files from the test.config (or just using the online links), you could so something like this:

nextflow run nf-core/differentialabundance -profile docker,rnaseq --input SRP254919.samplesheet.csv etc.