ngless-toolkit / ngless-toolkit/ngless

Filetype in external modules does not enforce number of inputs passed

Open
#54 0 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Rust
Stars
152
Forks
23
PR merge metrics
No merged PRs in 30d

Description

When using external modules one can specify

        arg1:
            atype: 'readset'
            can_gzip: true

which passes one (.1.fq), two (.1.fq, .2.fq), or three (.1.fq, .2.fq, .single.fq) files depending on what the caller used or produced, fastq(), paired() or paired(singles=), respectively.

Current API specifies that you can add a filetype annotation/constraint to have ngless pass the expected format:

        arg1:
            atype: 'readset'
            filetype: 'fq3'
            can_gzip: true

This didn't work as expected. In the example above, even though fq3 (.1.fq, .2.fq, .single.fq) was specified ngless still passed either one, two or three .fq files.

The same happens if instead of fq3, fq1 is defined. Up to three files are still passed.

A testcase can be found here

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the linked testcase gist and trace how external module arguments interpret the filetype annotation for readset values. Verify the handling of fq1 and fq3 against callers using fastq(), paired(), and paired(singles=), and confirm that the passed file count matches the declared constraint.

Written by the indexing model from the issue text.

Assessment

Tech stack
rust
Domain
bioinformatics, compilers
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.