dhslab/nf-core-hic ? reverse-engineered prompt

Build me a Nextflow pipeline for Hi C and Capture C data analysis that I can run on local machines, HPC, or cloud with containers. It should take paired FASTQ files plus a sample sheet, a genome fasta, BWA index prefix, chromosome sizes, and optionally a baits BED file for Capture C.

I want three run modes, one for the main Hi C workflow, one for Capture C, and one for a quick QC run that estimates library complexity from shallow sequencing. For the main workflow, trim and clean reads, align them, process the pairs, remove duplicates, merge libraries by sample, and generate a cool style matrix file. For Capture C, do the same early steps, then add bait coverage QC and a BAM output that works with CHiCAGO. For QC, just give me the complexity report.

Please include sensible defaults, clear output files, a test profile, and make the command line simple for a scientist to use. If you need current docs for any tools, look them up online.