[BUG] Cutadapt (trim_galore) issue: ERROR: Running in parallel is not supported on Python 2

[raimondsre]

While running sarek with option --trim_fastq i encounter a following error:

ERROR: Running in parallel is not supported on Python 2

The issue could be with singularity, could you suggest a solution?

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line:

   nextflow run nf-core/sarek \
   --input 1test.tsv \
   --split_fastq 2000000 \
   --tools 'HaploTypeCaller' \
   --skip_qc 'FastQC, MultiQC, bamQC, BCFtools, BaseRecalibrator' \
   --trim_fastq \
   --genome GRCh38 \
   --save_reference \
   --species 'homo_sapiens' \
   -profile singularity 

2. here is the .command.err file:
   .command.err

Log files

The .nextflow.log file .nextflow.log

System

• Hardware: HPC
• Executor: PBS
• OS: CentOS Linux
• Version 3.10.0-957.21.3.el7.x86_64

Nextflow Installation

• Version: 2.7.1

Container engine

• Engine: singularity
• version: 3.2.1-7.1.ohpc.1.3.8
• Image tag: nfcore/sarek:2.7 (?)

[raimondsre]

I found an answer in sarek slack, but it is extremely slow, so better solution is needed. The solution thus far is to add the following code to custom nextflow.config file, but make sure memory variable is correct:

process {
  withName:TrimGalore {
    cpus = 1
    memory = '64 GB'
    time = '24h'
  }
}