unable to override of custom.config

[SunSun1324]

Description of the bug

I tried to override custom.config to run nf-core/rnaseq.
(specifically, DUPRADAR, STRINGTIE, QUALIMAP, PICARD_MARKDUPLICATES)

However, when I ran with my custom.config file, the configFiles line was empty (my custom.config was not applied)

is there any way to fix it? any help is appreciated.

Command used and terminal output

Command used:

/home/ohoh/.local/bin/nextflow run nf-core/rnaseq \
  -profile docker \
  -c /media/ohoh/4TB_DATA_2/custom.config \
  --input /media/ohoh/4TB_DATA_2/fetchngs_result/samplesheet/samplesheet.csv \
  --outdir /media/ohoh/T7/nf_core/rnaseq_result \
  --fasta /media/ohoh/T7/nf_core/GCF_003573695.1_ASM357369v1_genomic.fna \
  --gtf /media/ohoh/T7/nf_core/genomic_fixed_fixed.gtf \
  --aligner star_rsem \
  -w /media/ohoh/T7/nf_core/work

Terminal output:

Input/output options
  input          : /media/ohoh/4TB_DATA_2/fetchngs_result/samplesheet/samplesheet.csv
  outdir         : /media/ohoh/T7/nf_core/rnaseq_result

Reference genome options
  fasta          : /media/ohoh/T7/nf_core/GCF_003573695.1_ASM357369v1_genomic.fna
  gtf            : /media/ohoh/T7/nf_core/genomic_fixed_fixed.gtf

Alignment options
  aligner        : star_rsem

Core Nextflow options
  revision       : master
  runName        : furious_miescher
  containerEngine: docker
  launchDir      : /home/ohoh
  workDir        : /media/ohoh/T7/nf_core/work
  projectDir     : /home/ohoh/.nextflow/assets/nf-core/rnaseq
  userName       : ohoh
  profile        : docker
  configFiles    :

Relevant files

My custom.config file is like below (file name is custom.config):

process {

resourceLimits = [
    cpus  : 24,
    memory: 150.GB,
    time  : 96.h
]

withName: 'NFCORE_RNASEQ:RNASEQ:DUPRADAR' {
    cpus   = { 12 * task.attempt }
    memory = { 84.GB * task.attempt }
    time   = { 48.h * task.attempt }
}

withName: 'NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE' {
    cpus   = { 12 * task.attempt }
    memory = { 84.GB * task.attempt }
    time   = { 48.h * task.attempt }
}

withName: 'NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ' {
    cpus   = { 12 * task.attempt }
    memory = { 84.GB * task.attempt }
    time   = { 48.h * task.attempt }
}

withName: 'NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES' {
    cpus   = { 12 * task.attempt }
    memory = { 84.GB * task.attempt }
    time   = { 48.h * task.attempt }
}

}

System information

Nextflow: version 24.10.5
Hardware: Desktop
Container: Docker
OS: ubuntu
Version of nf-core/rnaseq: 3.18.0