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TRUST4 module #316

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TRUST4 module #316

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mapo9
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@mapo9 mapo9 commented Mar 25, 2024

This PR adds the TRUST4 module in a new subworkflow.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/airrflow branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@mapo9 mapo9 requested a review from ggabernet March 25, 2024 08:28
@mapo9 mapo9 marked this pull request as draft March 25, 2024 08:28
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mapo9 commented Mar 25, 2024

Currently we have the problem that (for single cell data), the workflow fails at the SINGLE_CELL_QC_AND_FILTERING:SINGLE_CELL_QC step with the following error

  Quitting from lines 210-213 [removeDoublets] (_main.Rmd)
  Error in removeDoublets():
  ! The column cell_id contains no data
  Backtrace:
   1. enchantr::removeDoublets(...)
  Warning messages:
  1: replacing previous import 'data.table::first' by 'dplyr::first' when loading 'enchantr' 
  2: replacing previous import 'data.table::last' by 'dplyr::last' when loading 'enchantr' 
  3: replacing previous import 'data.table::between' by 'dplyr::between' when loading 'enchantr' 
  Execution halted

Work dir:
  /home/kymmp01/workdir/pipeline_dev/trust42airrflow/airrflow/test_flow/work/40/5d32e7d034d6123f08d2cc50bda49f

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

 -- Check '.nextflow.log' file for details
ERROR ~ Corruption: 
        Descriptor does not contain a meta-nextfile entry
        Descriptor does not contain a meta-lognumber entry
        Descriptor does not contain a last-sequence-number entry

 -- Check '.nextflow.log' file for details

I am pretty sure this happens because ! The column cell_id contains no data.
Currently, I am using the OUT_airr.tsv to feed the TRUST4 results into the immcantation workflow.
Here, each sequence is one row.

TRUST4 also provides a out_barcode_airr.tsv for single cell data where each cell_id is one row.
So basically this gives clonotypes for a barcode with "consensus_count" being the number of reads/UMI supporting this contig. Obviously, the barcode_airr is a lot larger and contains many redundant junctions when different cells present the same clone.

I think we have 2 options now:

  1. use barcode_airr.tsv for analysis
  2. use the OUT_airr.tsv and give the "sequence_id" as "cell_id"

The discussion with the TRUST4 developers about this can be found here.

This might also help understand:
Screenshot 2024-03-22 at 16 45 28

@nf-core nf-core deleted a comment from github-actions bot Apr 11, 2024
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github-actions bot commented Apr 11, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 6f9e5af

+| ✅ 206 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   1 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

  • nextflow_config - Config default value incorrect: params.umi_position is set as R1 in nextflow_schema.json but is null in nextflow.config.

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-12 08:11:43

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mapo9 commented Apr 11, 2024

I worked some more on this issue and tested the barcode_airr file now as well. This contains cell_ids and the Immcantation frameworks in airrflow runs through fine using this file.
I am adding the test airr files here as well.

Here you can also find the respective airrflow results.

It would be great, if you could have a look whether the results look reasonable for you like this or if we need to find another solution for the integration of TRUST4.

@mapo9 mapo9 closed this May 6, 2024
@mapo9 mapo9 mentioned this pull request May 16, 2024
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