getting weird "missing output " error when running a nextflow pipeline - nextflow

Question

For my data analysis pipeline I am using nextflow (which is a workflow management system) and I gave all the required arguments in the main command but I am getting a weird error. Basically in the output section I introduce the output but the error is missing output. I have made 3 files to run the pipeline including:
1- the module containing the main code to run the tool (ASEReadCounter) and named ASEReadCounter.nf :
process ASEReadCounter {
input:
file vcf_file
file bam_file
path(genome_fasta)
output:
file "${vcf_file}.ASE.csv"
script:
"""
gatk ASEReadCounter \\
-R ${params.genome} \\
-V ${params.vcf_infile} \\
-O ${params.vcf_infile}.txt \\
-I ${params.bam_infile}
"""
}
2- the main file which is used to run the pipeline named main.nf :
#!/usr/bin/env nextflow
nextflow.preview.dsl=2
include ASEReadCounter from './modules/ASEReadCounter.nf'
genome_ch = Channel.fromPath(params.genome)
vcf_file_ch=Channel.fromPath(params.vcf_infile)
bam_infile_ch=Channel.fromPath(params.bam_infile)
workflow {
count_ch=ASEReadCounter(genome_ch, vcf_file_ch, bam_infile_ch)
}
3- config file which is named nextflow.config :
params {
genome = '/hpc/hg38_genome/GRCh38.p13.genome.fa'
vcf_infile = '/hpc/test_data/test/test.vcf.gz'
bam_infile = ‘/hpc/test_data/test/test.sorted.bam'
}
process {
shell = ['/bin/bash', '-euo', 'pipefail']
withName: ASEReadCounter {
container = 'broadinstitute/gatk:latest'
}
}
singularity {
enabled = true
runOptions = '-B /hpc:/hpc -B $TMPDIR:$TMPDIR'
autoMounts = true
cacheDir = '/hpc/diaggen/software/singularity_cache'
}
here is the command I use to run the whole pipeline:
nextflow run -ansi-log false main.nf
Here is the error I am getting:
Error executing process > 'ASEReadCounter (1)'
Caused by:
Missing output file(s) `GRCh38.p13.genome.fa.ASE.csv` expected by process `ASEReadCounter (1)`
Command executed:
gatk ASEReadCounter -R /hpc/hg38_genome/GRCh38.p13.genome.fa \
-V /hpc/test_data/test/test.vcf.gz \
-O /hpc/test_data/test/test.vcf.gz.txt \
-I /hpc/test_data/test/test.sorted.bam
Do you know how I can fix the error?

Answer 1

Your ASEReadCounter process expects a file with the pattern ${vcf_file}.ASE.csv as output, as defined at:
output:
file "${vcf_file}.ASE.csv"
I assume the line -O ${params.vcf_infile}.txt makes it so your gatk ASEReadCounter command writes its output to a file with the pattern $params.vcf_infile}.txt. The expected output and the actual output filenames don't match and nextflow throws an error because it doesn't want to contine since a downstream process might need the output file. You can fix it by matching the expected output and actual output patterns,