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Nanomonsv get#2849

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awgymer wants to merge 4 commits into
nf-core:masterfrom
awgymer:nanomonsv-get
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Nanomonsv get#2849
awgymer wants to merge 4 commits into
nf-core:masterfrom
awgymer:nanomonsv-get

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@awgymer awgymer commented Feb 7, 2023 •
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Adding the get command for nanomonsv.
Data has been added to the test-datasets repo for testing.

Test is currently rather slow as it pulls in a reference genome :/

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:
    • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

matthdsm
matthdsm reviewed Mar 7, 2023
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Comment thread modules/nf-core/nanomonsv/get/main.nf
@@ -0,0 +1,61 @@
// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
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Please remove all TODO's

matthdsm
matthdsm reviewed Mar 7, 2023
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Comment thread modules/nf-core/nanomonsv/get/main.nf
matthdsm
matthdsm reviewed Mar 7, 2023
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Comment thread modules/nf-core/nanomonsv/get/main.nf
matthdsm
matthdsm reviewed Mar 7, 2023
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Comment thread modules/nf-core/nanomonsv/get/meta.yml
@@ -0,0 +1,51 @@
name: "nanomonsv_get"
## TODO nf-core: Add a description of the module and list keywords
description: write your description here
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Add description

matthdsm
matthdsm reviewed Mar 7, 2023
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Comment thread modules/nf-core/nanomonsv/get/meta.yml
## TODO nf-core: Add a description of the module and list keywords
description: write your description here
keywords:
- sort
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Add keywords

matthdsm
matthdsm reviewed Mar 7, 2023
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Comment thread modules/nf-core/nanomonsv/get/meta.yml
- sort
tools:
- "nanomonsv":
## TODO nf-core: Add a description and other details for the software below
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Remove TODO's

matthdsm
matthdsm reviewed Mar 7, 2023
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Comment thread modules/nf-core/nanomonsv/get/meta.yml
pattern: "*.{bam,cram,sam}"

## TODO nf-core: Add a description of all of the variables used as output
output:
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Describe outputs

matthdsm
matthdsm requested changes Mar 7, 2023
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Good start, but still needs some work!

@edmundmiller edmundmiller requested review from a team and edmundmiller October 19, 2023 16:26
@edmundmiller edmundmiller removed their request for review February 19, 2024 21:27
@edmundmiller edmundmiller added the stale Stale label Feb 19, 2024
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awgymer commented Feb 20, 2024

I have abandoned this tool so I'm closing this MR as we no longer use the module.

@awgymer awgymer closed this Feb 20, 2024
@awgymer awgymer deleted the nanomonsv-get branch September 2, 2025 06:52
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manascripts commented May 4, 2026

@awgymer, I wanted to create this module for my pipeline, is there a specific reason why you abandoned it? Just wondering if the reason is relevant for me. If you don't mind, can you also say what exactly you used as an alternative? Severus?

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awgymer commented May 5, 2026

I abandoned trying to get the nanomonsv modules into nf-core (I still had them locally in a pipeline) mostly because I couldn't get reasonable sized test data without more work than I was willing to do at the time and then we did subsequently move to using Severus.

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manascripts commented May 27, 2026 •
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I see, I am thinking of giving it a try. Do you have any test-data that you can share? I see that you mentioned about some test data at the start

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awgymer commented May 28, 2026

I do not I'm afraid.

@manascripts manascripts mentioned this pull request May 29, 2026
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manascripts commented May 29, 2026

Okay thanks for confirming, turned out to be possible without it.

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