Support for NuGen Ovation RRBS libraries - #379

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zifornd:nugen-ovation
Open

Support for NuGen Ovation RRBS libraries#379
jma1991 wants to merge 3 commits into
nf-core:devfrom
zifornd:nugen-ovation

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@jma1991jma1991 commented Feb 14, 2024

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This pull request introduces an initial implementation for processing NuGen Ovation RRBS libraries, drawing guidance from the commands outlined in the NuMetRRBS repository. Currently, the focus is on integrating fundamental steps such as adapter trimming and diversity trimming. Although there's an optional component for deduplicating reads via molecular tags, I'm not sure how to implement this right now. Lastly, let me know if I should submit some Ovation data to the test-datasets repository.

PR checklist

  • 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 pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/methylseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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The suggested diversity trimming looks good to me, but do we have specific test data for this?

@jma1991

jma1991 commented Feb 27, 2024

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The suggested diversity trimming looks good to me, but do we have specific test data for this?

I have some Ovation test data, shall I submit it to the test-datasets repository?

@ewels

ewels commented Feb 27, 2024

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@jma1991 could you please update / rebase this PR off the latest nf-core dev branch please?

@sateeshperi

sateeshperi commented Sep 17, 2024

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@jma1991 checking in here - did you get some test data into the test-datasets repo ?

@sateeshperisateeshperi added the WIP Work in progress label Sep 23, 2024
@sateeshperisateeshperi added the stale Will eventually be closed due to divergence and compatibility issues. label Aug 13, 2025
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Support for NuGen Ovation RRBS libraries - #379
Open
jma1991 wants to merge 3 commits into
nf-core:devfrom 
zifornd:nugen-ovation
Open
Support for NuGen Ovation RRBS libraries#379
jma1991 wants to merge 3 commits into
nf-core:devfrom 
zifornd:nugen-ovation
Conversation
@jma1991
@jma1991jma1991
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Feb 14, 2024

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This pull request introduces an initial implementation for processing NuGen Ovation RRBS libraries, drawing guidance from the commands outlined in the NuMetRRBS repository. Currently, the focus is on integrating fundamental steps such as adapter trimming and diversity trimming. Although there's an optional component for deduplicating reads via molecular tags, I'm not sure how to implement this right now. Lastly, let me know if I should submit some Ovation data to the test-datasets repository.
PR checklist
  •  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 pipeline conventions in the contribution docs
  •  If necessary, also make a PR on the nf-core/methylseq branch on the nf-core/test-datasets repository.
  •  Make sure your code lints (nf-core lint).
  •  Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  •  Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  •  Usage Documentation in docs/usage.md is updated.
  •  Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).
@jma1991
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The suggested diversity trimming looks good to me, but do we have specific test data for this?
@jma1991
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Feb 27, 2024

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The suggested diversity trimming looks good to me, but do we have specific test data for this?
I have some Ovation test data, shall I submit it to the test-datasets repository?
@ewels
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Feb 27, 2024

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@jma1991 could you please update / rebase this PR off the latest nf-core dev branch please?
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@jma1991 checking in here - did you get some test data into the test-datasets repo ?
@sateeshperisateeshperi
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@sateeshperisateeshperi
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Skip to content
Support for NuGen Ovation RRBS libraries - #379
Open
jma1991 wants to merge 3 commits into
nf-core:devfrom 
zifornd:nugen-ovation
Open
Support for NuGen Ovation RRBS libraries#379
jma1991 wants to merge 3 commits into
nf-core:devfrom 
zifornd:nugen-ovation
Conversation
@jma1991
@jma1991jma1991
commented
Feb 14, 2024

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This pull request introduces an initial implementation for processing NuGen Ovation RRBS libraries, drawing guidance from the commands outlined in the NuMetRRBS repository. Currently, the focus is on integrating fundamental steps such as adapter trimming and diversity trimming. Although there's an optional component for deduplicating reads via molecular tags, I'm not sure how to implement this right now. Lastly, let me know if I should submit some Ovation data to the test-datasets repository.
PR checklist
  •  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 pipeline conventions in the contribution docs
  •  If necessary, also make a PR on the nf-core/methylseq branch on the nf-core/test-datasets repository.
  •  Make sure your code lints (nf-core lint).
  •  Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  •  Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  •  Usage Documentation in docs/usage.md is updated.
  •  Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).
@jma1991
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The suggested diversity trimming looks good to me, but do we have specific test data for this?
@jma1991
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Feb 27, 2024

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The suggested diversity trimming looks good to me, but do we have specific test data for this?
I have some Ovation test data, shall I submit it to the test-datasets repository?
@ewels
ewels
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Feb 27, 2024

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@jma1991 could you please update / rebase this PR off the latest nf-core dev branch please?
@sateeshperi
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@jma1991 checking in here - did you get some test data into the test-datasets repo ?
@sateeshperisateeshperi
added
the 
WIP
Work in progress
label
Sep 23, 2024
@sateeshperisateeshperi
added
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stale
Will eventually be closed due to divergence and compatibility issues.
label
Aug 13, 2025
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Skip to content
Support for NuGen Ovation RRBS libraries - #379
Open
jma1991 wants to merge 3 commits into
nf-core:devfrom 
zifornd:nugen-ovation
Open
Support for NuGen Ovation RRBS libraries#379
jma1991 wants to merge 3 commits into
nf-core:devfrom 
zifornd:nugen-ovation
Conversation
@jma1991
@jma1991jma1991
commented
Feb 14, 2024

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This pull request introduces an initial implementation for processing NuGen Ovation RRBS libraries, drawing guidance from the commands outlined in the NuMetRRBS repository. Currently, the focus is on integrating fundamental steps such as adapter trimming and diversity trimming. Although there's an optional component for deduplicating reads via molecular tags, I'm not sure how to implement this right now. Lastly, let me know if I should submit some Ovation data to the test-datasets repository.
PR checklist
  •  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 pipeline conventions in the contribution docs
  •  If necessary, also make a PR on the nf-core/methylseq branch on the nf-core/test-datasets repository.
  •  Make sure your code lints (nf-core lint).
  •  Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  •  Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  •  Usage Documentation in docs/usage.md is updated.
  •  Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).
@jma1991
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requested a review
from a team
as a code ownerFebruary 14, 2024 14:53
FelixKrueger
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The suggested diversity trimming looks good to me, but do we have specific test data for this?
@jma1991
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Feb 27, 2024

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The suggested diversity trimming looks good to me, but do we have specific test data for this?
I have some Ovation test data, shall I submit it to the test-datasets repository?
@ewels
ewels
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Feb 27, 2024

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@jma1991 could you please update / rebase this PR off the latest nf-core dev branch please?
@sateeshperi
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Sep 17, 2024

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@jma1991 checking in here - did you get some test data into the test-datasets repo ?
@sateeshperisateeshperi
added
the 
WIP
Work in progress
label
Sep 23, 2024
@sateeshperisateeshperi
added
the 
stale
Will eventually be closed due to divergence and compatibility issues.
label
Aug 13, 2025
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Skip to content
Support for NuGen Ovation RRBS libraries - #379
Open
jma1991 wants to merge 3 commits into
nf-core:devfrom 
zifornd:nugen-ovation
Open
Support for NuGen Ovation RRBS libraries#379
jma1991 wants to merge 3 commits into
nf-core:devfrom 
zifornd:nugen-ovation
Conversation
@jma1991
@jma1991jma1991
commented
Feb 14, 2024

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This pull request introduces an initial implementation for processing NuGen Ovation RRBS libraries, drawing guidance from the commands outlined in the NuMetRRBS repository. Currently, the focus is on integrating fundamental steps such as adapter trimming and diversity trimming. Although there's an optional component for deduplicating reads via molecular tags, I'm not sure how to implement this right now. Lastly, let me know if I should submit some Ovation data to the test-datasets repository.
PR checklist
  •  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 pipeline conventions in the contribution docs
  •  If necessary, also make a PR on the nf-core/methylseq branch on the nf-core/test-datasets repository.
  •  Make sure your code lints (nf-core lint).
  •  Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  •  Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  •  Usage Documentation in docs/usage.md is updated.
  •  Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).
@jma1991
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requested a review
from a team
as a code ownerFebruary 14, 2024 14:53
FelixKrueger
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The suggested diversity trimming looks good to me, but do we have specific test data for this?
@jma1991
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Feb 27, 2024

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The suggested diversity trimming looks good to me, but do we have specific test data for this?
I have some Ovation test data, shall I submit it to the test-datasets repository?
@ewels
ewels
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Feb 27, 2024

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@jma1991 could you please update / rebase this PR off the latest nf-core dev branch please?
@sateeshperi
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Sep 17, 2024

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@jma1991 checking in here - did you get some test data into the test-datasets repo ?
@sateeshperisateeshperi
added
the 
WIP
Work in progress
label
Sep 23, 2024
@sateeshperisateeshperi
added
the 
stale
Will eventually be closed due to divergence and compatibility issues.
label
Aug 13, 2025
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try {
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Skip to content
Support for NuGen Ovation RRBS libraries - #379
Open
jma1991 wants to merge 3 commits into
nf-core:devfrom 
zifornd:nugen-ovation
Open
Support for NuGen Ovation RRBS libraries#379
jma1991 wants to merge 3 commits into
nf-core:devfrom 
zifornd:nugen-ovation
Conversation
@jma1991
@jma1991jma1991
commented
Feb 14, 2024

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This pull request introduces an initial implementation for processing NuGen Ovation RRBS libraries, drawing guidance from the commands outlined in the NuMetRRBS repository. Currently, the focus is on integrating fundamental steps such as adapter trimming and diversity trimming. Although there's an optional component for deduplicating reads via molecular tags, I'm not sure how to implement this right now. Lastly, let me know if I should submit some Ovation data to the test-datasets repository.
PR checklist
  •  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 pipeline conventions in the contribution docs
  •  If necessary, also make a PR on the nf-core/methylseq branch on the nf-core/test-datasets repository.
  •  Make sure your code lints (nf-core lint).
  •  Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  •  Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  •  Usage Documentation in docs/usage.md is updated.
  •  Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).
@jma1991
jma1991
requested a review
from a team
as a code ownerFebruary 14, 2024 14:53
FelixKrueger
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reviewed
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The suggested diversity trimming looks good to me, but do we have specific test data for this?
@jma1991
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Feb 27, 2024

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The suggested diversity trimming looks good to me, but do we have specific test data for this?
I have some Ovation test data, shall I submit it to the test-datasets repository?
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@jma1991 could you please update / rebase this PR off the latest nf-core dev branch please?
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@jma1991 checking in here - did you get some test data into the test-datasets repo ?
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Skip to content
Support for NuGen Ovation RRBS libraries - #379
Open
jma1991 wants to merge 3 commits into
nf-core:devfrom 
zifornd:nugen-ovation
Open
Support for NuGen Ovation RRBS libraries#379
jma1991 wants to merge 3 commits into
nf-core:devfrom 
zifornd:nugen-ovation
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@jma1991
@jma1991jma1991
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Feb 14, 2024

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This pull request introduces an initial implementation for processing NuGen Ovation RRBS libraries, drawing guidance from the commands outlined in the NuMetRRBS repository. Currently, the focus is on integrating fundamental steps such as adapter trimming and diversity trimming. Although there's an optional component for deduplicating reads via molecular tags, I'm not sure how to implement this right now. Lastly, let me know if I should submit some Ovation data to the test-datasets repository.
PR checklist
  •  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 pipeline conventions in the contribution docs
  •  If necessary, also make a PR on the nf-core/methylseq branch on the nf-core/test-datasets repository.
  •  Make sure your code lints (nf-core lint).
  •  Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  •  Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  •  Usage Documentation in docs/usage.md is updated.
  •  Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).
@jma1991
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The suggested diversity trimming looks good to me, but do we have specific test data for this?
@jma1991
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Feb 27, 2024

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The suggested diversity trimming looks good to me, but do we have specific test data for this?
I have some Ovation test data, shall I submit it to the test-datasets repository?
@ewels
ewels
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Feb 27, 2024

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@jma1991 could you please update / rebase this PR off the latest nf-core dev branch please?
@sateeshperi
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Sep 17, 2024

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@jma1991 checking in here - did you get some test data into the test-datasets repo ?
@sateeshperisateeshperi
added
the 
WIP
Work in progress
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Sep 23, 2024
@sateeshperisateeshperi
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stale
Will eventually be closed due to divergence and compatibility issues.
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Aug 13, 2025
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Skip to content
Support for NuGen Ovation RRBS libraries - #379
Open
jma1991 wants to merge 3 commits into
nf-core:devfrom 
zifornd:nugen-ovation
Open
Support for NuGen Ovation RRBS libraries#379
jma1991 wants to merge 3 commits into
nf-core:devfrom 
zifornd:nugen-ovation
Conversation
@jma1991
@jma1991jma1991
commented
Feb 14, 2024

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This pull request introduces an initial implementation for processing NuGen Ovation RRBS libraries, drawing guidance from the commands outlined in the NuMetRRBS repository. Currently, the focus is on integrating fundamental steps such as adapter trimming and diversity trimming. Although there's an optional component for deduplicating reads via molecular tags, I'm not sure how to implement this right now. Lastly, let me know if I should submit some Ovation data to the test-datasets repository.
PR checklist
  •  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 pipeline conventions in the contribution docs
  •  If necessary, also make a PR on the nf-core/methylseq branch on the nf-core/test-datasets repository.
  •  Make sure your code lints (nf-core lint).
  •  Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  •  Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  •  Usage Documentation in docs/usage.md is updated.
  •  Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).
@jma1991
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as a code ownerFebruary 14, 2024 14:53
FelixKrueger
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The suggested diversity trimming looks good to me, but do we have specific test data for this?
@jma1991
jma1991
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Feb 27, 2024

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The suggested diversity trimming looks good to me, but do we have specific test data for this?
I have some Ovation test data, shall I submit it to the test-datasets repository?
@ewels
ewels
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Feb 27, 2024

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@jma1991 could you please update / rebase this PR off the latest nf-core dev branch please?
@sateeshperi
sateeshperi
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Sep 17, 2024

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@jma1991 checking in here - did you get some test data into the test-datasets repo ?
@sateeshperisateeshperi
added
the 
WIP
Work in progress
label
Sep 23, 2024
@sateeshperisateeshperi
added
the 
stale
Will eventually be closed due to divergence and compatibility issues.
label
Aug 13, 2025
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