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nf-core / rnasplice

rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
https://nf-co.re/rnasplice
MIT License
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make contrasts file names consistent with those of the differentialabundance pipeline #106

Open adomingues opened 10 months ago

adomingues commented 10 months ago

Description of feature

Motivation

Many projects will use a combination of differentialabundance and rnasplice analysis, using as input the processed data from rnaseq. Thus keeping the workflows as consistent as possible would facilitate reusing files, for the user, and code, for developers.

Suggestion

The column names in the contrasts file are different from those of the differentialabundance pipeline. Would it possible to uniformize them?

in this pipeline contrast,treatment,control would becomes id,reference,target as in differentialabundance This would allow the re-use of the contrast file across the two nf-core pipelines for at least the simplest comparisons.

I am suggesting the change here because it seems to me that that differentialabundance is the more mature of the two and thus change there would result in more things breaking.

jma1991 commented 10 months ago

Hello @adomingues

I agree, using the same column names would be great - we'll look into this for either the next major/minor release.

Thanks