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nf-core / scrnaseq

A single-cell RNAseq pipeline for 10X genomics data
https://nf-co.re/scrnaseq
MIT License
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test_full-profile not running out-of-the-box #366

Open asp8200 opened 2 months ago

asp8200 commented 2 months ago

Description of the bug

The test_full-profile doesn’t run out-of-the-box on scrnaseq v.2.7.1:

nextflow run nf-core/scrnaseq -r 2.7.1 -profile test_full,singularity --outdir results
...
ERROR ~ Must provide a genome fasta file ('--fasta') and a gtf file ('--gtf') if no index is given!. Expression: (star_index || (genome_fasta && gtf)). Values: star_index = [], genome_fasta = [], gtf = []

So I added --genome GRCh38, but it still didn’t work.

Then I removed the initialisation of fasta and gtf from nextflow.config which was introduced here in v2.7.1.

And the test_full-profil ran OK.

Having removed the initialisation of fasta and gtf, I got the following warnings which are also kind of misleading, since, in this case, fasta and gtf are being set through igenomes.config:

WARN: Access to undefined parameter `gtf` -- Initialise it to a default value eg. `params.gtf = some_value`
WARN: Access to undefined parameter `fasta` -- Initialise it to a default value eg. `params.fasta = some_value`

Issue first report on Slack here.

Command used and terminal output

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Relevant files

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System information

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wzheng0520 commented 1 month ago

Hi @asp8200 I also meet same issue and I think it cause by params.fasta = getGenomeAttribute('fasta') and params.gtf = getGenomeAttribute('gtf') update in scrnaseq.nf cannot be accepted. Once you defined them on nextflow.config as null, any updated in workflow cannot really make them to be updated into correct path.