update ncbi-scrub task (version 2.2.1)

[cimendes]

Closes

🛠️ Changes Being Made

• ncbi_scrub
  • Update docker container to us-docker.pkg.dev/general-theiagen/ncbi/sra-human-scrubber:2.2.1
  • Update task so paired-end reads are processed as interleaved files

🧠 Context and Rationale

For ncbi_scrub, the latest version solves the issue of paired reads not being correctly masked, according to their documentation . The reads are still processed individually in the task, so the phenomenon might still persist if we do not change the tasks to first interleave the reads, then process them using ncbi-scrub, and then split them again.

I've also altered the ncbi_scrub_pe task to first interleave the reads for processing with HRRT, and then split the resulting file back to forward and reverse read files.

📋 Workflow/Task Steps

N/A

Inputs

N/A

Outputs

• read1_human_spots_removed and read2_human_spots_removed were removed (this isn't actually a final output of any of the workflows)
• human_spots_removed was added with the stats containing the number of spots removed for the interleaved files

🧪 Testing

Locally

Tests passed locally with miniwdl for the individual task.

Terra

Tests under way...

🔬 Quality checks

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• The workflow/task has been tested locally and on Terra
• The CI/CD has been adjusted and tests are passing
• Everything follows the style guide

---

• To see the specific tasks where the Asana app for GitHub is being used, see below:
  • https://app.asana.com/0/0/1207183337014876

[frankambrosio3]

testing wf here: https://app.terra.bio/#workspaces/theiagen-validations/ambrosio_validation_sandbox/job_history/62526fbe-07f0-48a3-afb6-8e8cc418bf0e

[kevinlibuit]

Will this work if there are uneven reads in ~{read1} and ~{read2}?

[kevinlibuit]

Seeing failures in workflows utilizing the task ncbi_scrub_se. Unclear from GHA log files as to why this is occurring. Also seeing many failures in the Terra runs posted by @frankambrosio3 above

[sam-baird]

Seeing failures in workflows utilizing the task ncbi_scrub_se. Unclear from GHA log files as to why this is occurring. Also seeing many failures in the Terra runs posted by @frankambrosio3 above

This error may be occurring in ncbi_scrub_se because the -n option for scrub.sh was removed as of 2.0.0 and its functionality made the default. I'm using code from this pull request to add read scrubbing to a workflow, and removing -n (and adding -i) fixed it for me.

[cimendes]

Closing PR as stale

[cimendes]

⚠️ Please do not delete the branch! Thank you! ⚠️