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User-friendly error messages #11

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hoelzer opened this issue Jun 14, 2020 · 1 comment
Open

User-friendly error messages #11

hoelzer opened this issue Jun 14, 2020 · 1 comment
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@hoelzer
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hoelzer commented Jun 14, 2020

Currently, PoSeiDon does not have a user-friendly error control and feedback. This can be implemented using functionalities such as

annotated_reads
    .map{ row -> row[-2]}
    .collect()
    .subscribe onNext: {
        for ( i in it ){
        assert 2 <= it.count(i)
        }
    }, onError: { exit 1, 'You need at least 2 samples per condition to perform a differential gene expression analysis.' }

or

if ( ! (params.tpm instanceof java.lang.Double || params.tpm instanceof java.lang.Float || params.tpm instanceof java.lang.Integer) ) {
    exit 1, "--tpm has to be numeric"
}

(stolen from https://github.com/hoelzer-lab/rnaseq/blob/master/main.nf)

@hoelzer
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hoelzer commented Jun 22, 2020

Added some basic error handling of the input FASTA file including terminal print outs and stop of the workflow if the FASTA is not valid.

Missing: error handling in later steps of the pipeline w/ terminal prints

@hoelzer hoelzer mentioned this issue Jun 22, 2020
@hoelzer hoelzer self-assigned this Jun 22, 2020
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