scrnaseq will not recognize my genome file path

[jjovelc]

Description of the bug

I am trying to run the scrnaseq nextflow workflow with the following error message:

ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:GTF_GENE_FILTER ([])'

Caused by:
Process NFCORE_SCRNASEQ:SCRNASEQ:GTF_GENE_FILTER ([]) terminated with an error exit status (2)

Command executed:

filter_gtf_for_genes_in_genome.py
--gtf gencode.v32.primary_assembly.annotation.gtf
--fasta
-o []_genes.gtf
cat <<-END_VERSIONS > versions.yml
"NFCORE_SCRNASEQ:SCRNASEQ:GTF_GENE_FILTER":
python: $(python --version | sed 's/Python //g')
END_VERSIONS

Command exit status:
2

Command output:
(empty)

Command error:
WARNING: DEPRECATED USAGE: Environment variable SINGULARITYENV_TMPDIR will not be supported in the future, use APPTAINERENV_TMPDIR instead
WARNING: DEPRECATED USAGE: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR will not be supported in the future, use APPTAINERENV_NXF_TASK_WORKDIR instead
WARNING: DEPRECATED USAGE: Environment variable SINGULARITYENV_NXF_DEBUG will not be supported in the future, use APPTAINERENV_NXF_DEBUG instead
usage: filter_gtf_for_genes_in_genome.py [-h] [--gtf GTF] [--fasta FASTA]
[-o OUTPUT]
filter_gtf_for_genes_in_genome.py: error: argument --fasta: expected one argument

Command used and terminal output

No response

Relevant files

#!/usr/bin/bash

eval "$(conda shell.bash hook)"
conda activate nextflow

export DIR=$(pwd)
export JAVA_HOME="/home/juan.jovel/mambaforge/envs/nextflow"
export PATH="$JAVA_HOME/bin:$PATH"

REFS="/work/vetmed_data/jj/db/ensembl/GRCh38/reference_sources"

# Run the Nextflow pipeline with the specified configuration and input
nextflow run /work/vetmed_data/jj/projects/juanJovel/pipelines/nextflow/scrnaseq/scrnaseq/main.nf \
    -profile singularity \
    -c "${DIR}/jj_arc_scrnaseq.config" \
    --input "${DIR}/samplesheet.csv" \
    --genome_fasta "${REFS}/Homo_sapiens.GRCh38.dna.primary_assembly.fa" \
    --gtf "${REFS}/gencode.v32.primary_assembly.annotation.gtf" \
    --outdir "${DIR}/results" \
    --aligner alevin \
    --protocol 10XV2 \
    -resume

I could pinpoint that the problem is in file .command.sh in the working directory. Namely, the PATH of my genome fasta file was not included here:

#!/bin/bash -euo pipefail
filter_gtf_for_genes_in_genome.py \
    --gtf gencode.v32.primary_assembly.annotation.gtf \
    --fasta  \
    -o []_genes.gtf
cat <<-END_VERSIONS > versions.yml
"NFCORE_SCRNASEQ:SCRNASEQ:GTF_GENE_FILTER":
    python: $(python --version | sed 's/Python //g')
END_VERSIONS

System information

My nextflow version:

N E X T F L O W
  version 23.04.2 build 5870
  created 08-06-2023 08:29 UTC (02:29 MDT)
  cite doi:10.1038/nbt.3820
  http://nextflow.io

MY config file:

params {
outdir = "${baseDir}/results"
input = "${baseDir}/samplesheet.csv"
genome_fasta = "/work/vetmed_data/jj/db/ensembl/GRCh38/reference_sources/Homo_sapiens.GRCh38.dna.primary_assembly.fa"
gtf = "/work/vetmed_data/jj/db/ensembl/GRCh38/reference_sources/gencode.v32.primary_assembly.annotation.gtf"
aligner = "alevin"
protocol = "10XV2"
}

singularity {
enabled = true
}

process {
executor = 'slurm'
memory = '128 GB'
cpus = 24
time = '48h'
}

singularity {
enabled = true
autoMounts = true
}

docker {
enabled = false
}

timeline {
enabled = true
file = "${params.outdir}/pipeline_timeline.html"
overwrite = true
}

report {
enabled = true
file = "${params.outdir}/pipeline_report.html"
overwrite = true
}

trace {
enabled = true
file = "${params.outdir}/pipeline_trace.txt"
overwrite = true
}

params {
max_cpus = 24
max_memory = '128 GB'
}

executor {
queueSize = 100
maxForks = 4
}

workDir = '/work/vetmed_data/jj/projects/juanJovel/pipelines/nextflow/scrnaseq'

[jjovelc]

We solved the issue. The problem is that in the github page, the flag for passing the genome file to the pipeline appear as --genome_fasta GRCm38.p6.genome.chr19.fa. This is wrong, the correct way to pass the genome file is: --fasta GRCm38.p6.genome.chr19.fa.

[grst]

Thanks for reporting back! Let's keep this issue open then as a reminder to fix the documentation :)