Create a full command line executable workflow for RNA-Seq on PBMC Samples. Open a new pull request (on a separate branch) and comment the PR number here when you're done

[rohan-uiuc]

Experiment Type: RNA-Seq Sequencing of total cellular RNA

Workflow Management: Bash/SLURM Scripting and job scheduling

Software Stack: FastQC MultiQC STAR RSEM samtools DESeq2

What else to know about the pipeline? I am working PBMC samples collected from patients that are undergoing immunotherapy.

Use the data files existing in Report_WholeBrain as input for this workflow.

You should write a series of bash scripts and R scripts that can accomplish this task. Open a PR with those scripts when you're done.

[lil-jr-dev[bot]]

Thanks for opening a new issue! I'll now try to finish this implementation and open a PR for you to review.

You can monitor the LangSmith trace here.

Feel free to comment in this thread to give me additional instructions, or I'll tag you in a comment if I get stuck. If I think I'm successful I'll 'request your review' on the resulting PR. Just watch for emails while I work.

[lil-jr-dev[bot]]

Error in handle_issue_opened: name 'human_tools' is not defined Traceback

Traceback (most recent call last):
  File "/app/github_webhook_handlers.py", line 96, in handle_issue_opened
    bot = WorkflowAgent(run_id_in_metadata=langsmith_run_id)
  File "/app/ml4bio_agent.py", line 30, in __init__
    self.agent = self.make_agent()
  File "/app/ml4bio_agent.py", line 41, in make_agent
    tools = get_tools()
  File "/app/tools.py", line 86, in get_tools
    tools: list[BaseTool] = human_tools + browser_tools + github_tools + search + docs_tools + file_management + [shell]
NameError: name 'human_tools' is not defined