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makePairs workflow cleanup #1068

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WardDeb opened this issue Oct 9, 2024 · 0 comments

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WardDeb commented Oct 9, 2024

alignerThreads is set under config, but should respect predefined 'maxThreads' directives
non-fqc, but mainly alternative trimming modes are not tested and most likely do not work due to hardcoded fastp path
memory for rules should be set properly (or rely on default, or have explicit specifications in profile)
cool/mcool output missing in allelic mode
include an assert to verify --strains are actually present in vcffile

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