8000 Fixes for self-complementary AAV and workflow configuration by dougnukem · Pull Request #94 · formbio/laava · GitHub
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Fixes for self-complementary AAV and workflow configuration #94

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Merged
merged 9 commits into from
Apr 9, 2025
Merged

Fixes for self-complementary AAV and workflow configuration #94

merged 9 commits into from
Apr 9, 2025

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dougnukem
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@dougnukem dougnukem commented Apr 3, 2025 •
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Summary

  • Fixed sc-AAV itr-partial type classification to properly identify and classify itr-partial reads
  • Fixed Azenta out of range error in sequence processing
  • Added configuration parameters to customize machine type, CPU count, and memory allocation
  • Default settings now configurable: 'e2-highmem-8', 8 CPUs, and 64GB memory

Test plan

  • Verify correct classification of sc-AAV itr-partial reads using test samples
  • Confirm Azenta samples process without range errors
  • Test custom resource configurations to ensure they override defaults correctly

Tested with different CPU count, it runs succesfully if you want to validate the generated report/data
--cpus=8(default)
--cpus=7
--cpus=48

Test commands

NOTE: To reference a container version in a pull-request or branch you can use the following
https://github.com/formbio/laava/pkgs/container/laava/388068909?tag=pr-94

--container_version=pr-94

You can also reference the branch name itself with / converted to - e.g.
https://github.com/formbio/laava/pkgs/container/laava/388068909?tag=alpha-sc-fixes

--container_version=alpha-sc-fixes

formbio workflow run \
--run-name 'xam-laava-4.0_CPU_48' \
--org form-bio-solutions \
--project laava-validation \
--repo formbio/laava \
--workflow formbio/laava \
--version alpha/sc-fixes  \
--execution-engine nextflow \
--github true \
-- \
--cpus=48 \
--container_version=pr-94 \
--flipflop_name='AAV2' \
--helper_name='pHelper' \
--host_fa='formbio://form-bio-solutions/laava-validation/reference/hs1.chm13.fa' \
--itr_label_1='itr-l' \
--itr_label_2='itr-r' \
--lambda_name='Lambda' \
--max_allowed_missing_flanking=100 \
--max_allowed_outside_vector=100 \
--min_supp_joint_coverage=0.8 \
--packaging_fa='formbio://form-bio-solutions/laava-validation/PacBio-example-AAV/2021-scAAV-CBA-eGFP/package.fa' \
--repcap_name='pRep2Cap9' \
--sample_display_name='xam' \
--sample_unique_id='demux.xam' \
--seq_reads_file='formbio://form-bio-solutions/laava-validation/PacBio-example-AAV/2022-ssAAV-pAV-CMF-GFP/0-reads/xam.bam' \
--target_gap_threshold=200 \
--ui_source_type='file_source' \
--vector_bed='formbio://form-bio-solutions/laava-validation/PacBio-example-AAV/2022-ssAAV-pAV-CMF-GFP/pAV-CMV-GFP.bed' \
--vector_fa='formbio://f
8000
orm-bio-solutions/laava-validation/PacBio-example-AAV/2022-ssAAV-pAV-CMF-GFP/pAV-CMV-GFP.fasta' \
--vector_type='ss'

@dougnukem dougnukem changed the title Alpha/sc fixes Fixes for self-complementary AAV and workflow configuration Apr 3, 2025
@dougnukem
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@alphabdiallo lgtm merging in

@dougnukem dougnukem merged commit 9412f98 into main Apr 9, 2025
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@dougnukem dougnukem deleted the alpha/sc-fixes branch April 9, 2025 16:38
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@alphabdiallo alphabdiallo Awaiting requested review from alphabdiallo

@mcrocker-bioborg mcrocker-bioborg Awaiting requested review from mcrocker-bioborg

@colossalpat colossalpat Awaiting requested review from colossalpat

@vijayformbio vijayformbio Awaiting requested review from vijayformbio

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