Add meryl and merqury

[stephenturner]

Merqury is a tool for genome quality assessment that uses k-mer counts from raw sequencing data to evaluate the accuracy and completeness of a genome assembly. Meryl is the companion tool that efficiently counts and stores k-mers from sequencing reads, enabling Merqury to estimate metrics like assembly completeness and base accuracy. These tools provide a k-mer-based approach to assess assembly quality, helping to identify potential errors or gaps.​

• Adds MERYL_COUNT nf-core module, fixes Add meryl count #58
• Adds MERYL_UNIONSUM nf-core module, fixes add meryl union sum #60
• Adds MERQURY_MERQURY nf-core module, fixes Add merqury to pipeline #42
• Optionally supply fastq in samplesheet, fixes Optionally pass in reads #62
• Add processes to genomeqc.nf workflow
• Update nextflow.config and modules.config
• Rebuild nextflow_schema.json adding new params
• new test profiles fixes Add new test_with_merqury profile #67
• updates README.md with info about optional reads in samplesheet, running merqury, fixes Update README.md with merqury info #68

[GallVp]

Nice work @stephenturner

Would be great to support the trio mode with parental reads. This is supported by the assemblyqc pipeline. Maybe, we can extract a sub workflow, put it on nf-core/modules so that the two pipelines can benefit from shared development. Please see the workflow on the assemblyqc repo:

https://github.com/Plant-Food-Research-Open/assemblyqc/blob/cec2728d0785d97e0e9493558c83d83d0b48240e/workflows/assemblyqc.nf#L598-L771

[stephenturner]

Noting that one of the test commands isn't going to run until nf-core/test-datasets#1365 is merged, which updates samplesheets in test-datasets

[chriswyatt1]

Test datasets is merged now