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Pipeline does not detect transcriptome_fasta argument #20

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jma1991 opened this issue Dec 17, 2019 · 1 comment
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Pipeline does not detect transcriptome_fasta argument #20

jma1991 opened this issue Dec 17, 2019 · 1 comment
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@jma1991
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jma1991 commented Dec 17, 2019

The pipeline does not detect when I provide a transcriptome fasta file. Instead, it produces the following error:

$ /home/jashmore/anaconda3/envs/nextflow/bin/nextflow run nf-core/scrnaseq --reads 'data/reads/*_R{1,2}.fastq.gz' --type 10x --chemistry V2 --aligner alevin --salmon_index data/genomes/index/salmon --txp2gene data/genomes/txp2gene.csv --transcriptome_fasta data/genomes/transcriptome.fa
N E X T F L O W  ~  version 19.10.0
Launching `nf-core/scrnaseq` [marvelous_mcclintock] - revision: 884e541285 [master]
Neither of --fasta or --transcriptome provided! At least one must be provided to quantify genes

The error message is also slightly wrong as there is actually no argument called "--transcriptome", instead it is "--transcriptome_fasta" in the documentation. I think the error may be caused by a mistake in the variable naming in the main.nf file (lines 107 - 110). Shouldn't the params variable refer to params.transcriptome_fasta not params.transcript_fasta?

if (!params.fasta && !params.transcript_fasta){
  exit 1, "Neither of --fasta or --transcriptome provided! At least one must be provided to quantify genes"
}

Thank you,
James

@apeltzer apeltzer self-assigned this Dec 18, 2019
@apeltzer apeltzer added the bug Something isn't working label Dec 18, 2019
@apeltzer apeltzer added this to the 1.0.1 milestone Dec 21, 2019
@apeltzer apeltzer mentioned this issue Dec 21, 2019
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@apeltzer
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Pull Request #22 should fix this issue - you can for example test using this here and replacing [...] with your parameters of choice:

nextflow run apeltzer/scrnaseq -r dev [....]

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