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Add quilt2 first draft implementation#282

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atrigila merged 30 commits into
nf-core:devfrom
atrigila:quilt2
May 19, 2026
Merged

Add quilt2 first draft implementation#282
atrigila merged 30 commits into
nf-core:devfrom
atrigila:quilt2

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@atrigila

@atrigila atrigila commented Apr 3, 2026

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Closes #116

@atrigila atrigila marked this pull request as ready for review April 12, 2026 22:13
@atrigila atrigila requested a review from LouisLeNezet April 12, 2026 22:13

@LouisLeNezet LouisLeNezet left a comment

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I would suggest a few changes to make this integration similar to all the other tools used at the moment.

Comment thread conf/steps/imputation_quilt2.config Outdated
Comment thread conf/test_quilt2.config
Comment thread docs/usage.md Outdated
Comment thread subworkflows/local/bam_impute_quilt2/main.nf
Comment thread workflows/phaseimpute/tests/nextflow.config Outdated
Comment thread workflows/phaseimpute/tests/test_quilt2.nf.test Outdated
Comment thread README.md Outdated
atrigila and others added 5 commits April 15, 2026 18:16
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@atrigila atrigila requested a review from LouisLeNezet May 17, 2026 19:37

@LouisLeNezet LouisLeNezet left a comment

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Just a few comments, but good to go otherwise !
Thanks for this nice addition (I will need to add it to the benchmark 😉).

Comment thread docs/usage.md Outdated
Comment thread conf/test_quilt2.config Outdated
Comment thread subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf
Comment thread conf/steps/initialisation.config
@atrigila atrigila merged commit 006ea62 into nf-core:dev May 19, 2026
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@atrigila atrigila mentioned this pull request May 24, 2026
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3 participants