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Add new component: deeptools/bamcompare#11572

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oliverdrechsel wants to merge 10 commits intonf-core:masterfrom
oliverdrechsel:deeptools_bamcompare
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Add new component: deeptools/bamcompare#11572
oliverdrechsel wants to merge 10 commits intonf-core:masterfrom
oliverdrechsel:deeptools_bamcompare

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@oliverdrechsel
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This Pull Request adds a module for deeptools/bamcompare. The code was mostly generated with SeqeraAI. Errors were fixed and format requirements from nf-core added.

PR checklist

Closes #11146

  • 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.
  • Broadcast software version numbers to topic: versions - See version_topics
  • 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

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@JoseEspinosa JoseEspinosa left a comment

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Some suggestions but looks pretty nice! 😄

Comment thread modules/nf-core/deeptools/bamcompare/meta.yml Outdated
Comment thread modules/nf-core/deeptools/bamcompare/meta.yml Outdated
Comment thread modules/nf-core/deeptools/bamcompare/meta.yml Outdated
Comment thread modules/nf-core/deeptools/bamcompare/meta.yml Outdated
Comment thread modules/nf-core/deeptools/bamcompare/meta.yml Outdated
Comment thread modules/nf-core/deeptools/bamcompare/meta.yml Outdated
Comment thread modules/nf-core/deeptools/bamcompare/meta.yml Outdated
Comment thread modules/nf-core/deeptools/bamcompare/main.nf Outdated
Comment thread modules/nf-core/deeptools/bamcompare/main.nf Outdated
type: eval
description: The expression to obtain the version of the tool
authors:
- "@seqeraai"
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Here, we only allow for valid GitHub users by the moment, if you want you could raise it on slack to see what others think

Suggested change
- "@seqeraai"

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Good point.
I asked the Slack community and would wait a little to collect opinions.

I'd like to credit the AI somehow. The format is less important to me.

oliverdrechsel and others added 9 commits May 8, 2026 20:40
Add identifier

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
fix ontology for bam1

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
fix ontology for bai

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
fix ontology for bai2

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
fix ontology for bam2

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
fix ontology for bigwig

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
fix ontology for bedgraph

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
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new module: deeptools/bamcompare

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