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Add initial IGV_HaplotypeViz WDL workflow for generating IGV screenshots #468

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Add initial IGV_HaplotypeViz WDL workflow for generating IGV screenshots #468

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@shadizaheri shadizaheri commented Sep 5, 2024 •
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Summary:
Adding initial IGV_HaplotypeViz WDL to generate IGV screenshots.

  • Introduced the IGV_HaplotypeViz workflow to automate IGV screenshot generation
  • Supports both BAM/BAI file alignment and haplotype bam files sequence visualizations
  • Output IGV screenshots for specified regions in the input BED files
  • Compared to the [IGV-snapshot-automator] (https://github.com/stevekm/IGV-snapshot-automator/tree/master) and GATK-SV IGVSingleGenomeScatter workflow, this workflow allows flexibility in BED file formats and includes support for sequence visualizations with haplotype files.

@shadizaheri
Add initial IGV_HaplotypeViz WDL workflow for generating IGV screenshots
43774f0
@shadizaheri
Add new workflow for parallel processing of large BED files
7cb3c7e
@shadizaheri
fix the workflow name
27f85d6
@shadizaheri
update the docker
6249a7c
@shadizaheri
updating docker and fixing the igv command
c2ac959
@shadizaheri
fixing the docker and igv command
dd2dfc9
@shadizaheri
fixing the runtime
c0fa633
@shadizaheri
fixing the runtime
fafa429
@shadizaheri
new wdl for taking the igv screenshots
9f0d53b
@shadizaheri
update docker and the script to use only one bam
9682125
@shadizaheri
Updated Python script and WDL for IGV snapshot automation
f574936
@shadizaheri
Update WDL and Python script to support IGV 2.18.2 with igv.sh
1c11914
@shadizaheri
update the directory to the python script
d10a140
@shadizaheri
update bai
09154ed
@shadizaheri
checking for bai
4aedff1
@shadizaheri
new wdl-the script has been tested on the vm
bd53b9c
@shadizaheri
technically the same script as IGV_HaplotypeViz but will locate the i…
d533e40 
…nput bai as well
@shadizaheri
modify the runtime attributes
76009fe
@shadizaheri
fixing the issue with bai
11f78ee
@shadizaheri
fix the issue with output directory
0b70896
@shadizaheri
fix bai
7ac3c54
@shadizaheri
updates for bai
3f7005d
@shadizaheri
reverting baclk
c36a899
@shadizaheri
playing with bai definition
6b9baf7
@shadizaheri
fai
889c1fd
@shadizaheri
fai
b2c0836
@shadizaheri
updated the cmmand section
814c24e
@shadizaheri
modify fai
1fa0947
@shadizaheri
fix
965bf77
@shadizaheri
gs input
4712c35
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@SHuang-Broad SHuang-Broad Awaiting requested review from SHuang-Broad

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@shadizaheri