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nf-core / smrnaseq

A small-RNA sequencing analysis pipeline
https://nf-co.re/smrnaseq
MIT License
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Missing output folders #285

Closed andrewdchen closed 7 months ago

andrewdchen commented 12 months ago

Description of the bug

The pipeline on my data ran successfully but I'm missing several results folders including edgeR.

Currently I only have the output folders:

fastp
genome
index
pipeline_info

I'm only skipping fastqc and multiqc in the pipeline command. Seems like the awsmegatests are also missing a couple of output folders.

Command used and terminal output

nextflow run nf-core/smrnaseq \
    -r 2.2.3 \
    -profile singularity \
    --input clean_samplesheet.csv \
    --skip_fastqc \
    --skip_multiqc \
    --genome 'GRCh37' \
    --mirtrace_species 'hsa' \
    --protocol 'illumina' \
    --outdir 'Processed'

Relevant files

No response

System information

Nextflow version: 23.04.1 Hardware: HPC Executor: Sun Grid Engine Container engine: Singularity OS: AlmaOS 8 Linux Version of nf-core/smrnaseq: v2.2.3-g18d6c84

apeltzer commented 7 months ago

Dev should be fine now