Dev#1

Merged

mhoban merged 40 commits intomainfrom

Mar 17, 2026

Commits on Jul 18, 2025

add fst SD as error bars in line graph instead of separate trace
mykle hoban
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Commits on Jul 24, 2025

report updates, postprocess cleanup
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Commits on Jul 30, 2025

extract sequences, update report, fix caching issues
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cut some extra junk out
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Commits on Aug 2, 2025

conver fisher test and sequence extract to use data.table
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convert poolfstat to use data.table
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convert joinfreq to data.table
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update containers and conda environments for data.table conversions
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Commits on Aug 4, 2025

small fixes to fisher & poolfstat
mykle hoban
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convert report to data.table
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remove commented-out dplyr code from R scripts
mykle hoban
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small tweak to report
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add na.rm to quantile
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add na.rm where necessary
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Commits on Aug 5, 2025

use args2 for gawk processes, as theyre supposed to
mykle hoban
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change column to log_fisher
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change pops to factors in fst table (maybe causes memory error in pandoc?)
mykle hoban
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Commits on Aug 7, 2025

add sync input option, tweak report, etc.
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update fisher plot to use global slider
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Merge branch 'sync_input' into dev
mykle hoban
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remove svg device from fisher plots
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Commits on Aug 8, 2025

adding suggested default options yaml file
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update publish directories
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svg output for correlation plots
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Commits on Aug 11, 2025

update to mulled containers
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Commits on Mar 16, 2026

modified editorconfig
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update citations
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Commits on Mar 17, 2026

fix input schema to allow ?thing=whatever on urls
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update test profile
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update input schema to allow ?thing=whatever for vcf index
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update documentation for non-official version
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remove bcftools-reheader module
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fix test data url in schema
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fix unchanged email template
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various linting fixes, mostly addressing TODOs
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ignore manifest.homePage in linting
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remove some ignore lines in .nf-core.yml
mykle hoban
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removing nf-core/ from various things
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remove nf-core/ prefix from various references to the pipeline name
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fix case
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