Includes template nextflow config file with defaults for large (100s) and huge(1000s) numbers of samples
Better merging/clustering of VCF records at the start of the pipeline, meaning it can handle 1000s of samples without graph explosions
More efficient making huge VCF at the end of the pipeline, using ivcfmerge. Can now complete on huge data sets instead of crashing from using too much RAM.
Note: "normal" single sample run of minos also now uses the the new merging/clustering.
Closes several issues, either by directly fixing them or making them irrelevant because the pipeline has been rewritten:
closes #95
closes #88 (because can now handle a lot of variants)
closes #75
closes #74
closes #69
Regenotyping pipeline rewrite from scratch.
Note: "normal" single sample run of minos also now uses the the new merging/clustering.
Closes several issues, either by directly fixing them or making them irrelevant because the pipeline has been rewritten: closes #95 closes #88 (because can now handle a lot of variants) closes #75 closes #74 closes #69