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DSL2 - CLASSIFY_MTDNA_HAPLOGROUP#1134

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trianglegrrl wants to merge 73 commits intodevfrom

dsl2-haplogrep3

Commits on May 2, 2025

Commits on May 23, 2025

Add general structure, and generate (not working!) snapshot for basic test profile

jfy133
authored and
VerbalCant
committed
Try adding an ignore zip system, doesn't work atm though...

jfy133
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VerbalCant
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Continue customisation

jfy133
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VerbalCant
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More debugging

jfy133
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VerbalCant
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Get working function

jfy133
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VerbalCant
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Get working function properly, and start integrating into snapshot: problem with collection/name not working

jfy133
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VerbalCant
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Extract names properly

jfy133
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VerbalCant
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Remove unnecesary code

jfy133
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VerbalCant
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Get working string check function!

jfy133
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VerbalCant
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TODO

jfy133
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VerbalCant
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Update MQC so works on gitpod, try to re-add original getAllFilesFromDir (but not working - no md5swum?!)

jfy133
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VerbalCant
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And get it back again

jfy133
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VerbalCant
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Sort output to ensure consistency

jfy133
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VerbalCant
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Sort file name only funciton

jfy133
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VerbalCant
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Start testing preprocessing

jfy133
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VerbalCant
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Start adding preprocessing dir but diff not working so can't ser variability

jfy133
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VerbalCant
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Backing up TODO notes

jfy133
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VerbalCant
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Final snapshots, need to double check all files are covered but I think so

jfy133
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VerbalCant
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Finalise first test

jfy133
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VerbalCant
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Update tests to latest dev

jfy133
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VerbalCant
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Start refactoring to use nft-utils

jfy133
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VerbalCant
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bump nft-utils version

TCLamnidis
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VerbalCant
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start refactoring to use nft-utils

TCLamnidis
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VerbalCant
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update snapshot. Not sure it works yet.

TCLamnidis
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VerbalCant
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add preprocessing

TCLamnidis
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VerbalCant
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fix preprocessing checks

TCLamnidis
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VerbalCant
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reorder and add todos

TCLamnidis
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VerbalCant
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remove versions.ymls from snapshot

TCLamnidis
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VerbalCant
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check bam names instead of content

TCLamnidis
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VerbalCant
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fix result pickup for bam filtering and deduplication

TCLamnidis
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VerbalCant
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add final_bams,mapstats. fix mapping. remove old code

TCLamnidis
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VerbalCant
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simplify bam_input_stats snapshot

TCLamnidis
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VerbalCant
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update snapshot

TCLamnidis
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VerbalCant
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exclude unstable qualimap results.

TCLamnidis
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VerbalCant
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Check existence of Multiqc output files. reorder tests to match alphanumeric ordering of directories in output

TCLamnidis
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VerbalCant
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remove leftover todo

TCLamnidis
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VerbalCant
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add command legend, and align a bit more

TCLamnidis
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VerbalCant
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Fix test. and snapshot.

TCLamnidis
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VerbalCant
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bump nft-bam version

TCLamnidis
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VerbalCant
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Start over with new output directory structure

TCLamnidis
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VerbalCant
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bump nft-bams to latest

TCLamnidis
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VerbalCant
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remove premature snapshot

TCLamnidis
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VerbalCant
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WIP test reimplementation

TCLamnidis
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VerbalCant
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add all remaining sections. tests still fail.

TCLamnidis
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VerbalCant
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Slightly improved docs phrasing and structure

jfy133
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VerbalCant
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Add some TODOs

jfy133
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VerbalCant
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Add ebugging prints

jfy133
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VerbalCant
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Fix var name

jfy133
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VerbalCant
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Update test snapshot to exclude directories and contained files

jfy133
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VerbalCant
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Add missing bam and flagstat files

jfy133
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VerbalCant
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remove unused nft-bam plugin

TCLamnidis
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VerbalCant
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cleanup unused code and debug output

TCLamnidis
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VerbalCant
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add bamfiltering_savefilteredbams again

TCLamnidis
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VerbalCant
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remve duplicate Qualimap config

TCLamnidis
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VerbalCant
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update test. add genotyping and metagenomics

TCLamnidis
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VerbalCant
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update snapshot

TCLamnidis
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VerbalCant
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exclude unstable files from md5sum

TCLamnidis
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VerbalCant
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Stricter checking of VCF file checksums using nft-vcf.

TCLamnidis
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VerbalCant
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add to unstable file list

TCLamnidis
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VerbalCant
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better comments

TCLamnidis
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VerbalCant
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add 5p_misincorporation to ignore list

TCLamnidis
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VerbalCant
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Pass phylotree through to haplogrep3 module
VerbalCant
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Update testing docs with new params
VerbalCant
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Merge branch 'dev' into dsl2-haplogrep3
TCLamnidis
authored

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