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Add RTNI_TNI module #5320

Merged
merged 22 commits into from
May 23, 2024
Merged

Add RTNI_TNI module #5320

merged 22 commits into from
May 23, 2024

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mribeirodantas
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@mribeirodantas mribeirodantas commented Mar 20, 2024 •
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PR checklist

Closes #5319

This PR adds a new module to nf-core: RTN/TNI for Regulatory Transcriptional Network Inference from expression data.

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@mribeirodantas
Initial work towards a module for RTN TNI
39ee2bb 
Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas mribeirodantas self-assigned this Mar 20, 2024
@mribeirodantas mribeirodantas added the new module Adding a new module label Mar 20, 2024
mribeirodantas and others added 7 commits May 13, 2024 12:54
@mribeirodantas
Make it a simple PoC
2a4c017 
Tests are passing. From now on, I can make it more complex and
closer to what I want this module to do in the end.
@mribeirodantas
Add two more steps in the module
69c5743
@mribeirodantas
Prettify file
905af60
@mribeirodantas
Merge branch 'master' into rtn_tni
bd6d549
@mribeirodantas
Merge branch 'master' into rtn_tni
d7e90e6
@mribeirodantas
Merge branch 'master' into rtn_tni
68b4d43
@mribeirodantas
Use test data, add remaining steps/collect output in TNI
89a5014 
Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas mribeirodantas marked this pull request as ready for review May 22, 2024 16:05
@mribeirodantas mribeirodantas requested a review from a team as a code owner May 22, 2024 16:05
@mribeirodantas mribeirodantas requested review from kpadm and removed request for a team May 22, 2024 16:05
mribeirodantas and others added 5 commits May 22, 2024 12:09
@mribeirodantas
Fix DOI in meta.yml
53840f3 
Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Some ongoing changes
9f41dba 
Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Rename rtn_tni.R to rtn_tni.r
e18a351
@mribeirodantas
Fix snapshot mismatch issue
0019c36 
Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Merge branch 'master' into rtn_tni
53c9c3d
adamrtalbot
adamrtalbot reviewed May 22, 2024
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  • Remove the todos
  • Can you check the output contents a bit deeper? I think we can get the md5s with a snapshot.

modules/nf-core/rtn/tni/main.nf Outdated Show resolved Hide resolved
modules/nf-core/rtn/tni/tests/main.nf.test Show resolved Hide resolved
mribeirodantas and others added 3 commits May 22, 2024 16:16
@mribeirodantas
Add --n_permutations + tests
ae72091 
Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Merge branch 'master' into rtn_tni
a3d94d4
@mribeirodantas
Get rid of the TODOs
8be4c61 
Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
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The RDS are binary files, so it's tricky to check content. Also, the snapshots mismatch for some reason :(

@mribeirodantas
Use different dataset (real gene ids)
a9a7a33 
Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Add support to --tfs + tests
cd1b672 
Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas
Fix indentation for ECLint check
e2c6819 
Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
@mribeirodantas mribeirodantas added this pull request to the merge queue May 23, 2024
Merged via the queue into master with commit 8667d59 May 23, 2024
16 checks passed
tstoeriko pushed a commit to tstoeriko/nf-core-modules that referenced this pull request May 23, 2024
@mribeirodantas @tstoeriko
Add RTNI_TNI module (nf-core#5320)
a8ad801 
* Initial work towards a module for RTN TNI

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>

* Make it a simple PoC

Tests are passing. From now on, I can make it more complex and
closer to what I want this module to do in the end.

* Add two more steps in the module

* Prettify file

* Use test data, add remaining steps/collect output in TNI

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>

* Fix DOI in meta.yml

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>

* Some ongoing changes

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>

* Rename rtn_tni.R to rtn_tni.r

* Fix snapshot mismatch issue

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>

* Add --n_permutations + tests

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>

* Get rid of the TODOs

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>

* Use different dataset (real gene ids)

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>

* Add support to --tfs + tests

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>

* Fix indentation for ECLint check

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>

* Remove quotes from environment dependencies for conda

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>

---------

Signed-off-by: Marcel Ribeiro-Dantas <mribeirodantas@seqera.io>
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@adamrtalbot adamrtalbot adamrtalbot approved these changes

@kpadm kpadm Awaiting requested review from kpadm kpadm is a code owner automatically assigned from nf-core/nf-test

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new module: RTN/TNI
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