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Count duplicate reads using alignment from Bowtie2 #70

Merged
merged 26 commits into from
Oct 16, 2024
Merged

Count duplicate reads using alignment from Bowtie2 #70

merged 26 commits into from
Oct 16, 2024

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harmonbhasin
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Implemented a script in rust that counts duplicate reads using the alignment from bowtie2 once it has been converted to a tsv.

EC2 Default User added 17 commits October 8, 2024 17:00
Count duplicate reads using bowtie alignment
aaeaa44
Rust script that counts duplicates, and allows for fuzzy matching
4bc40f0
Allow for custom container for bbtools so that we can use our custom …
898abb0 
…script for finding dedup group clashes
Adjusting clumpify single to test if I can get the duplicate file to …
ddd0daf 
…render properly
Add duplicates from sam file to hv directory
66a6386
Export the duplicates identified from bowtie to the main workflow so …
486cf7d 
…that I can put them in the publish directory.
Updated the tsv file to include the quality score of the forward and …
2355f92 
…reverse read
Changed the name of this binary
9ba3ef2
Turned on moduleBinaries so that we could put bin folders in each ind…
eae517b 
…ividual folder. https://www.nextflow.io/docs/latest/module.html#module-binaries
Merged duplicate counts from alignment to hv hits
a41aea5
Renamed this to countAlignmentDuplicates
e01b9c6
Included line to call coundAlignmentDuplicates, another line to merge…
083ad35 
… the tsvs, and updated collapseHV to take this file as input
Stopped publishing duplicate counts into publish directory, it's now …
7d901bd 
…in hv_hits
Count duplicates using the genome_id, start position of forward read,…
a0d069f 
… and start position of reverse read from the bowtie2 alignment. We've additionally added functionality for fuzzy matching, however for now this will default to 0.
Added option for fuzzy matching to config
74b5983
Passing fuzzy parameter to hv workflow
3bdb00b
Passing fuzzy parameter to module
19e6a99
@harmonbhasin harmonbhasin self-assigned this Oct 15, 2024
This was linked to issues Oct 15, 2024
Implement duplication analysis #56
Closed
Implement fragment-length analysis #57
Closed
@jeffkaufman
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Is the base branch set correctly here? This is showing up as a PR to merge 42 commits, with a ton of modified lines, which is usually a sign that something is set wrong,

@willbradshaw
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It looks like this includes changes from #60 and #67.

Base automatically changed from remove_concat_gzipped to dev October 15, 2024 17:35
@willbradshaw willbradshaw merged commit 1a5ff8b into dev Oct 16, 2024
@willbradshaw willbradshaw deleted the dedup-sam branch October 16, 2024 14:48
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@willbradshaw willbradshaw willbradshaw approved these changes

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Implement fragment-length analysis Implement duplication analysis
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@harmonbhasin @jeffkaufman @willbradshaw