Error: Unable to parse nextflow.config. Cannot compare java.lang.Boolean with value 'true' and java.lang.Integer with value '0'

[kubu4]

Description of the bug

Pipeline fails immediately with the error in subject line.

This is my first attempt at using Nextflow and the nf-core RNAseq pipeline, so I'm not even sure where to start to debug this.

The goal is to run this on a University HPC node in offline mode.

Command used and terminal output

### Assign Variables

## PROGRAMS ##
# NF Core RNAseq workflow directory
nf_core_rnaseq="/gscratch/srlab/programs/nf-core-rnaseq-3.6/"

# Load Singularity Mox module for NF Core/Nextflow
module load singularity

#####################################

nextflow run ${nf_core_rnaseq} \
--input sample_sheet-"${SLURM_JOB_ID}".csv \
--outdir ${wd} \
--multiqc_title "20220317-pgen-nextflow_rnaseq-tissues-${SLURM_JOB_ID}" \
--fasta ${genome_fasta} \
--gff ${genome_gff} \
--transcript_fasta ${transcriptome_fasta} \
--save_reference \
--gtf_extra_attributes gene_name \
--gtf_group_features gene_id \
--featurecounts_group_type gene_biotype \
--featurecounts_feature_type exon \
--trim_nextseq \
--save_trimmed \
--aligner star_salmon \
--pseudo_aligner salmon \
--min_mapped_reads 5 \
--save_align_intermeds \
--rseqc_modules bam_stat,\
inner_distance,\
infer_experiment,\
junction_annotation,\
junction_saturation,\
read_distribution,\
read_duplication \
-profile singularity \
-c ${nf_core_rnaseq_config}

Error message:

N E X T F L O W  ~  version 21.10.6
Launching `/gscratch/srlab/programs/nf-core-rnaseq-3.6/workflow/main.nf` [prickly_hypatia] - revision: 6b989c60f8
Unable to parse config file: '/gscratch/srlab/programs/nf-core-rnaseq-3.6/workflow/nextflow.config'

  Cannot compare java.lang.Boolean with value 'true' and java.lang.Integer with value '0'

### Relevant files

Custom config file: /gscratch/srlab/programs/nf-core-rnaseq-3.6/conf/base-srlab_500GB_node.config:

[base-srlab_500GB_node.config.zip](https://github.com/nf-core/rnaseq/files/8307506/base-srlab_500GB_node.config.zip)

Nextflow log:

[nextflow.log.zip](https://github.com/nf-core/rnaseq/files/8308359/nextflow.log.zip)

### System information

Nextflow version: `21.10.6`
HPC node: `28 CPUs`, `500GB RAM`
Executor: `local`
Container engine: `Singularity`
OS: `CentOS Linux`
Version of nf-core/rnaseq: `3.6`

[kubu4]

This error is triggered by this option:

--trim_nextseq

It turns out it is expecting an integer. So, when nothing is supplied, this is the error which occurs.

Resolve it with something like:

--trim_nextseq 20