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Making PROFILE take in ONT data#199

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simonleandergrimm wants to merge 31 commits intodevnaobservatory/mgs-workflow:devfrom simon-ont-profile-v2naobservatory/mgs-workflow:simon-ont-profile-v2Copy head branch name to clipboard

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Commits on Feb 8, 2025

• Adding a manual flag for human read filtering.

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  bb278f3

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• Adding stand-alone containers for minimap2 and samtools.

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  0aab9dd

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• Adding code for filtering out human reads on ont.

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  79cff17

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• Added optional human read filtering to subsetTrim

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• Added human_read_filtering param to subset_trim

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Commits on Feb 11, 2025

• Merge branch 'dev' into simon-human-read-filtering

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• added comment to human read filtering.

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• dropping second human read filtering.

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  acdafe9

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• added dislcaimer re ONT

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Commits on Feb 12, 2025

• Added a test for minimap2

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• Added a work in progress test for samtools. Doesn't yet work properly.

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• Merge branch 'dev' into simon-human-read-filtering

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  5950650

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• Added samtools and profile edits to make handling ONT data in PROFILE possible.

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  9707939

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• fixed human read filtering flag in run.config

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• Added proper tests and streaming.

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  a730568

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• added resource specification to samtools

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• adding comments to main.nf.test samtools

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• Merge branch 'dev' into simon-human-read-filtering

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  5b44d38

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• Merge branch 'simon-human-read-filtering' into simon-ont-profile-v2

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• added streaming to samtools.

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• Merge branch 'simon-human-read-filtering' into simon-ont-profile-v2

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  cb3afbb

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• fixed testing for samtools

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• adding ribo index testing.

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Commits on Feb 14, 2025

• Reverting the edits that were introduced through merging human_read_filtering branch.

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• WIP change save, still need to fix reference generation.

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  683bd95

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• Created custom container for samtools and minimap2

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Commits on Feb 15, 2025

• fixing minimap2 reference name.

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  666b0bb

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Commits on Feb 16, 2025

• fixed subset input params.

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Commits on Feb 17, 2025

• amended profile to use output of new minmap2 process.

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• dropped samtools process and tests

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• resetting style of subset_trim input variable order.

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