Hi all. I am using the methylseq pipeline but now stuck with this error. I worked well initially for a fewer set of samples. Help in this regard will be greatly appreciated. Thanks! Command run:

$nextflow run nf-core/methylseq --input /mnt/e/jvsfn6_methylation_new/samplesheet.csv --outdir /mnt/e/jvsfn6_methylation_new/results --genome GRCm38 --max_memory '48.GB' --max_cpus '16' --rrbs -resume -profile conda

Caused by:
 Process NFCORE_METHYLSEQ:METHYLSEQ:QUALIMAP_BAMQC (Saline200) terminated with an error exit status (127)


Command executed:

 unset DISPLAY
 mkdir -p tmp
 export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp
 qualimap \
     --java-mem-size=29491M \
     bamqc \
     -gd MOUSE \
     -bam Saline200.sorted.bam \
      \
     -p non-strand-specific \
     --collect-overlap-pairs \
     -outdir Saline200 \
     -nt 6

 cat <<-END_VERSIONS > versions.yml
 "NFCORE_METHYLSEQ:METHYLSEQ:QUALIMAP_BAMQC":
     qualimap: $(echo $(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*$//')
 END_VERSIONS

Command exit status:
 127

Command output:
 (empty)

Command error:
 .command.sh: line 6: qualimap: command not found

Work dir:
 /mnt/e/jvsfn6_methylation_new/work/1d/9d62271081ca5c943ee6e45349d6a5

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

-- Check '.nextflow.log' file for details
has context menu

It seems there’s a problem with qualimap in conda. Have you tried using docker/singularity?