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Tcoffee tcs #5288

Merged
merged 11 commits into from
Mar 20, 2024
Merged

Tcoffee tcs #5288

merged 11 commits into from
Mar 20, 2024

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alessiovignoli
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PR checklist

Closes #XXX

  • 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

@alessiovignoli alessiovignoli requested a review from a team as a code owner March 19, 2024 16:59
@alessiovignoli alessiovignoli requested review from LeuThrAsp and removed request for a team March 19, 2024 16:59
@alessiovignoli alessiovignoli added the enhancement New feature or request label Mar 19, 2024
@alessiovignoli
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Description:

This module uses t_coffee to compute the Transient Consistency Score (TCS). A metric used to assest the quality and conservation of the given MSA. It expects a msa as input and optionally a msa library. It outputs the TCS file in the score_ascii format of t_coffee and a simple csv reporting the overall TCS value for the given msa.

itrujnara
itrujnara reviewed Mar 20, 2024
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Looking good, just some minor remarks

modules/nf-core/tcoffee/tcs/main.nf

input:
tuple val(meta), path(msa)
tuple val(meta2), path(lib)
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Why 2 input channels? It seems meta2 is not even used in the script

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You can optionally pass a lib file. And if you doyou pass it through a channel that created such library in an alignment step before, so it will have it is own meta anyway. It is not used because not needed. But it will be passed in case with the lib file.

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Okay, should be fine as is

modules/nf-core/tcoffee/tcs/main.nf
def lib_arg = lib ? "-lib ${lib}" : ""
def header = meta.keySet().join(",")
def values = meta.values().join(",")
def unzipped_name = msa.toString() - '.gz'
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Align equal signs

@lrauschning
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Hm weird, locally prettier runs without any issues.

itrujnara
itrujnara approved these changes Mar 20, 2024
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I see everything's fixed, good to go.

@alessiovignoli alessiovignoli added this pull request to the merge queue Mar 20, 2024
@alessiovignoli alessiovignoli mentioned this pull request Mar 20, 2024
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@github-merge-queue github-merge-queue bot removed this pull request from the merge queue due to failed status checks Mar 20, 2024
@lrauschning lrauschning added this pull request to the merge queue Mar 20, 2024
Merged via the queue into nf-core:master with commit 2d5ea49 Mar 20, 2024
11 checks passed
jvfe added a commit to jvfe/modules that referenced this pull request Mar 20, 2024
@jvfe
Merge branch 'master' into nf-test_islandpath
f01d48c 
* master:
  Tcoffee tcs (nf-core#5288)
  Add and update - picard/gatk4 - addorreplacereadgroups (nf-core#5302)
  New module svtypersso (nf-core#5311)
jvfe added a commit that referenced this pull request Mar 20, 2024
@jvfe
Merge branch 'master' into nf-test_phispy
a2bedc0 
* master:
  Add module nanofilt (#5290)
  Tcoffee tcs (#5288)
  Add and update - picard/gatk4 - addorreplacereadgroups (#5302)
  New module svtypersso (#5311)
tucano pushed a commit to tucano/modules that referenced this pull request Mar 20, 2024
@alessiovignoli @tucano
Tcoffee tcs (nf-core#5288)
1e4c5eb 
* right ater execution of nf-core modules create

* added compression compatibility

* allocated for otional lib file and created scores csv file based on tcs output

* compiled the meta.yml

* added the test for msa and msa compressed

* removed lib only option

* fixed issue with filename extension after ungzip, wrote test for input lib and modified test for compressed

* added direct export of TEMP dir, hopefully fixes error ongithub singularity

* fixing trailing whitespaces
jennylsmith pushed a commit to RSC-RP/modules that referenced this pull request Mar 20, 2024
@alessiovignoli @jennylsmith
Tcoffee tcs (nf-core#5288)
31aaed8 
* right ater execution of nf-core modules create

* added compression compatibility

* allocated for otional lib file and created scores csv file based on tcs output

* compiled the meta.yml

* added the test for msa and msa compressed

* removed lib only option

* fixed issue with filename extension after ungzip, wrote test for input lib and modified test for compressed

* added direct export of TEMP dir, hopefully fixes error ongithub singularity

* fixing trailing whitespaces
alexnater pushed a commit to alexnater/nf-core-modules that referenced this pull request Mar 21, 2024
@alessiovignoli
Tcoffee tcs (nf-core#5288)
2f22395 
* right ater execution of nf-core modules create

* added compression compatibility

* allocated for otional lib file and created scores csv file based on tcs output

* compiled the meta.yml

* added the test for msa and msa compressed

* removed lib only option

* fixed issue with filename extension after ungzip, wrote test for input lib and modified test for compressed

* added direct export of TEMP dir, hopefully fixes error ongithub singularity

* fixing trailing whitespaces
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@itrujnara itrujnara itrujnara approved these changes

@LeuThrAsp LeuThrAsp Awaiting requested review from LeuThrAsp LeuThrAsp was automatically assigned from nf-core/nf-test

@lrauschning lrauschning Awaiting requested review from lrauschning

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@alessiovignoli @lrauschning @itrujnara