(DSL2) Methyldactyl extract does not produce expected bedGraph when using --methylkit param

[TheodoreMarkulin]

Description of the bug

In the DSL2 branch, when using the --methylkit parameter in conjunction with methyldactyl the pipeline fails. This appears to be due to an 'either or' kind of behavior wherein Methyldactyl extract will produce *_CpG.methylKit with --methylkit used or `*.bedGraph without it used but both are never produced from this step.

The step currently fails because it expects a *.bedGraph file. MultiQC also expects the *.bedGraph file to be produced.

Steps to reproduce

1. Run any version of the pipeline within DSL2 with methldactyl with the --methyl_kit parameter set

Expected behaviour

• Production of the *.methyKit files,
• Completion of the pipeline

Command Used

nextflow run $PIPELINE -with-tower '<IP ADDRESS>'  -bucket-dir $BUCKET_DIR  --input $DATA --outdir $OUTPATH_PREFIX/methyldactyl --fasta $REFERENCE --aligner bwameth --clip_r1 20 --clip_r2 15 -c "$CONFIG" --methyl_kit

System

• Hardware: Amazon
• Executor: AWS Batch
• OS: Amazon Linux

Nextflow Installation

• Version: 21.10.06
• Pipeline Version: dsl2 branch, commit- ba50ea9ce3c4c5aea0504d6c4aa07b8516335421

Container engine

• Engine: Docker
• version:
• Image tag: quay.io/biocontainers/methyldackel:0.6.0--h22771d5_0