MODKIT_BEDGRAPH produces empty output when pileup run with --combine-mods

Start with modules/local/bed2bedgraphs/modkit_bedgraphs/main.nf and inspect the awk filter against pileup output produced with --combine-mods. Reproduce the command from the issue, verify the column format and strand/mod conditions, and confirm that the resulting bedgraph files contain methylation data rather than zero lines.

Description of the bug

I ran the ONT workflow (pipeline version 2.0.0) with --combine-mods in the pileup step. The bedgraph output files came out empty for all 4 of my samples. There was no error or warning, they just have 0 lines.

Command I used for pileup (matches what the pipeline ran internally):

modkit pileup --motif CG 0 --combine-mods --ref <reference.fa> <input.bam>

What I think might be happening is that with --combine-mods, modkit writes just a bare base letter (e.g. C) into column 4 of the pileup output, instead of a base,context,offset triplet like C,CG,0.

The bedgraph conversion script (modules/local/bed2bedgraphs/modkit_bedgraphs/main.nf) filters on column 4 expecting that triplet format:

awk -v strand=$strand -v mod=$mod 'BEGIN{OFS="\t"} (($4==mod) && ($6==strand)) && ($5 >= 5) {print $1,$2,$3,$11,$12,$13}' ${in_bed}

where mod is one of "C,CHH,0", "C,CHG,0", "C,CG,0", "A,A,0".

Since column 4 in my pileup output is just "C", it never matches any of those triplets, so the filter drops every row. This happens consistently across all 4 of my samples and all 8 output files (positive/negative strand × 4 mod/context combos).

To reproduce:

1. Run the ONT workflow with --combine-mods set in the pileup step.
2. Check the resulting *.bedgraph.gz files, they'll have 0 lines.

Expected: bedgraph files should contain the methylation data from the pileup step.
Actual: bedgraph files are empty, with no error reported anywhere in the log.
Workaround: I pulled methylation data directly from the pileup .bed.gz output instead, which seems unaffected by this issue.

Command used and terminal output

Relevant files

No response

System information

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