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update malt/build module #6994

Merged
merged 23 commits into from
Nov 27, 2024
Merged

update malt/build module #6994

merged 23 commits into from
Nov 27, 2024

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LilyAnderssonLee
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@LilyAnderssonLee LilyAnderssonLee commented Nov 14, 2024 •
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PR checklist

Fixes nf-core/createtaxdb#29

  • 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

mashehu
mashehu approved these changes Nov 14, 2024
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please double check any pipelines using this module and inform them about the change of input type.

@jfy133
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jfy133 commented Nov 21, 2024

please double check any pipelines using this module and inform them about the change of input type.

Just me, and I'm informed :=*

@LilyAnderssonLee
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@jfy133 Amazing debugging methods and excellent solutions!!!

@jfy133
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jfy133 commented Nov 25, 2024

Java shakes fist - mostly thanks to @mahesh-panchal as always though 😬

@LilyAnderssonLee LilyAnderssonLee added this pull request to the merge queue Nov 26, 2024
@LilyAnderssonLee LilyAnderssonLee removed this pull request from the merge queue due to a manual request Nov 26, 2024
mahesh-panchal
mahesh-panchal reviewed Nov 27, 2024
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So I'm not sure if process.resourceLimits are defined for the runners, but they should be I think. Not here though

modules/nf-core/malt/run/tests/nextflow.config Outdated Show resolved Hide resolved
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@LilyAnderssonLee LilyAnderssonLee added this pull request to the merge queue Nov 27, 2024
Merged via the queue into nf-core:master with commit 47f728e Nov 27, 2024
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@LilyAnderssonLee LilyAnderssonLee deleted the malt_update branch November 27, 2024 13:34
LouisLeNezet pushed a commit to LouisLeNezet/modules that referenced this pull request Dec 4, 2024
@LilyAnderssonLee @jfy133 @mahesh-panchal
update malt/build module (nf-core#6994)
a35192c 
* update malt/build module

* use stageAs for input fasta files

* Try HTTPS rather than s3

* Trying manually restricting memory

* Move config loading to the right place

* Update modules/nf-core/malt/build/tests/main.nf.test

Co-authored-by: Mahesh Binzer-Panchal <[email protected]>

* Update main.nf.test

* Update nextflow.config

* Get tests running

* Adjust to VM minimum

* And MALT_RUN

* use process.resourceLimits defining the memory limit

* Update modules/nf-core/malt/run/tests/nextflow.config

Co-authored-by: Mahesh Binzer-Panchal <[email protected]>

* Update modules/nf-core/malt/run/tests/nextflow.config

Co-authored-by: Mahesh Binzer-Panchal <[email protected]>

* Update modules/nf-core/malt/run/tests/nextflow.config

Co-authored-by: Mahesh Binzer-Panchal <[email protected]>

* Update nextflow.config

---------

Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: Mahesh Binzer-Panchal <[email protected]>
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@mashehu mashehu mashehu approved these changes

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MALT will fail if too many FASTAs due to UNIX command limits
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@LilyAnderssonLee @jfy133 @mashehu @mahesh-panchal