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Str conda #232

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Str conda #232

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This branch has fixes related to #142

  • created new conda envs to install R and Python packages for rules related to EHDN
  • EHDN version is old and unavailable from conda or Github, hence keeping it hard-coded in config.yaml
  • Moved all required scripts of str.smk to crg2/scripts/str
  • Using rules for each steps instead of one single Bash scripts
  • Tested with NA12878

Changes are summarized in crg2/documentation/str.md

@aarthi-mohan
yaml for EHDN report rule with required R and python packages
8af0718
@aarthi-mohan
added conda env for rule EHdn_report
478acf8
@aarthi-mohan
readme for str scripts
c28b23c
@aarthi-mohan
move str scripts to script/str directory
54e5ff3
@aarthi-mohan
fixed a bug: missing 2nd argument for 1000G counts per STR and correc…
431436e 
…ted wrong order of std and median while parsing file
@aarthi-mohan
ehdn: split script into new rules, and add env
072caf9
@aarthi-mohan
moved hardcoded paths in various EHDN script to config_hpf.yaml
d2f96be
@aarthi-mohan
split the ehdn_report rule into outlier detection and annotation with…
e9f1f6d 
… annovar
@aarthi-mohan
added missing scripts reqd for ehdn
2322850
@aarthi-mohan
yaml for dbscan outlier step + small var fix + removed hard-coded pat…
13380b8 
…hs from crg.ehdn script
@aarthi-mohan
minor fix and added missing package to yaml
2701159
@aarthi-mohan
Merge remote-tracking branch 'origin/master' into str-conda
8d8f458
@aarthi-mohan
added and updated references from "arun" folder to "ccm_dccforge/dccd…
33e6e26 
…ipg" for DBSCAN R scripts
@aarthi-mohan
changed hard-coded paths to arguments; removed dates from out filenames
de9d8ed
@aarthi-mohan
split dbscan rule into two: dbscan outlier and merge epxansion
3e2b5d3
@aarthi-mohan
summary of the changes done
586bf49
@aarthi-mohan
fixed output path
db5429a
@aarthi-mohan
updated changes
2a3f247
@aarthi-mohan
updated md
32ed7af
@aarthi-mohan aarthi-mohan linked an issue Oct 15, 2024 that may be closed by this pull request
EHDN and EHDN report rules have hardcoded hpf paths and no environment #142
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@Madelinehazel Madelinehazel Awaiting requested review from Madelinehazel

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EHDN and EHDN report rules have hardcoded hpf paths and no environment
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@aarthi-mohan