bwameth pipeline skipping all bwameth steps when --fasta, --fasta_index, and --bwa_meth_index are provided.

[drothen15]

Description of the bug

I have previously processed the GRCh38 genome with bwameth for a different pipeline that I'm trying to compare with the nf-core. So I provide the following with the input command:
--fasta
--fasta_index
--bwa_meth_index

However, everytime I do this the pipeline just skips all the bwameth steps in the pipeline and then completes without error (screenshot).

Command used and terminal output

nextflow run /shared-storage/data/ngs/methylseq-test --input SampleSheet.csv --outdir /shared-storage/home/drothenheber/meth_testing/20240404_nf-core_bwameth --em_seq --comprehensive --aligner bwameth -profile apptainer --fasta test.fa --fasta_index test.fa.fai --bwa_meth_index /path/to/bwameth/indices/

Relevant files

nextflow.log

System information

Nextflow version: 23.10.1
Hardware: HPC
Executor: slurm
Container engine: apptainer
OS: Linux
MethylSeq version: 2.6.0

[npatel-ah]

I created the bismark index and kept the reference file within the folder ( not soft link), then re-ran it using --bismark_index and that seems to solve it for now.