Workflow exits after TrimGalore with “successful” status but no alignments produced

Description of the bug

The workflow terminates after the TrimGalore step with a successful exit status, but no alignment files are generated. TrimGalore completes normally and its output files are present in the expected work directory (verified manually). However, no downstream alignment process is executed. In the .nextflow.log file, there is an unusual debug message stating: Skipping output binding because one or more optional files are missing.

Dec-09 14:34:27.550 [TaskFinalizer-3] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_METHYLSEQ:METHYLSEQ:TRIMGALORE > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>

After TrimGalore, the pipeline proceeds directly to MultiQC and then exits with a successful completion message:

-[nf-core/methylseq] Pipeline completed successfully-
Completed at: 09-Dec-2025 14:35:42
Duration : 19m 15s
CPU hours : 3.6
Succeeded : 4

Despite this, no alignment output is present, indicating that the alignment step is being skipped without an error being raised.

Command used and terminal output

~/bin/nextflow run nf-core/methylseq \
-r 4.1.0 -resume -profile singularity \
  --input samplesheet.csv \
  --comprehensive \
  --outdir results \
  --bismark_index /nas/longleaf/home/sant/data/genomes/medaka

Relevant files

samplesheet.csv
slurm_bismark_410_test_23922691.console.log

nextflow.log

System information

Nextflow version: version 25.04.8
Hardware: HPC
Executor: Slurm
Container engine: Singularity
OS: RHEL9
Version of nf-core/methylseq: 4.1.0

Start with the attached nextflow.log and console log, then compare them with samplesheet.csv. Trace the NFCORE_METHYLSEQ:METHYLSEQ:TRIMGALORE output binding and the downstream process invocation, focusing on the message about missing optional files. Done means the workflow does not skip alignment and produces the expected alignment files.