bwameth symlink bug

Description of the bug

Hello,

I have tried using the bwameth workflow but encountered an issues with the BWAMETH_ALIGN related with how it handles symlinks:

ln -sf \$(readlink ${fasta}) ${index}/${fasta}

My workaround was to modify main.nf of that process in my local copy of the pipeline. I replace the code above with this:

 if [ ! -f ${index}/${fasta} ]; then
        ln -sf \$(readlink ${fasta}) ${index}/${fasta}
    fi

Since the genome was already present in the index folder, the script now sees the file and skips the ln command entirely. This allows the script to proceed straight to bwameth.py without ever trying to modify the staged directory, keeping the Linux kernel and Nextflow happy.

Command used and terminal output

I ran the following command:

nextflow run nf-core/methylseq -r 4.2.0 --input EM005_starterSheet.csv --fasta /NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa --fasta_index /NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa.fai  --aligner bwameth --run_qualimap true -profile crukmi --outdir final_results

And had this output:

Error executing process > 'NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BWAMETH:BWAMETH_ALIGN (0462_L004)'

Caused by:
  Process `NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BWAMETH:BWAMETH_ALIGN (0462_L004)` terminated with an error exit status (1)


Command executed:

  export BWA_METH_SKIP_TIME_CHECKS=1
  ln -sf $(readlink genome.fa) BwamethIndex/genome.fa
  
  bwameth.py \
       \
       \
      -t 48 \
      --reference BwamethIndex/genome.fa \
      0462_L004_1_val_1.fq.gz 0462_L004_2_val_2.fq.gz \
      | samtools view  -@ 48 -bhS -o 0462_L004.bam -
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BWAMETH:BWAMETH_ALIGN":
      bwameth: $(bwameth.py --version | cut -f2 -d" ")
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  ln: BwamethIndex/genome.fa: File exists

Work dir:
  /scratch/wsspaces/achelu-methylseq-EM005/EM005/work/13/0f83ef7c27dced7ab5479f45162422

Container:
  /lmod/nextflow_software/depot.galaxyproject.org-singularity-bwameth-0.2.9--pyh7e72e81_0.img

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

Relevant files

No response

System information

• Nextflow version: 25.04.4
• Hardware, executor and container engine details are in crukmi profile
• Methylseq version 4.2.0

Start in main.nf at the BWAMETH_ALIGN process and inspect the command that stages genome.fa into BwamethIndex. Reproduce the supplied Nextflow command or run the generated task command from the reported work directory, then verify that an existing indexed genome no longer causes the File exists failure and that bwameth.py proceeds.