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Np batch snm3c PD-2482 #1193

Merged
merged 29 commits into from
Feb 15, 2024
Merged

Np batch snm3c PD-2482 #1193

merged 29 commits into from
Feb 15, 2024

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nikellepetrillo
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@nikellepetrillo nikellepetrillo commented Feb 2, 2024

Description

This pr includes the merging of several tasks:

  • Separate_unmapped_reads & Split_unmapped_reads
  • Merge_original_and_split_bam_and_sort_all_reads_by_name_and_position & dedup_unique_bam_and_index_unique_bam
  • Unique_reads_allc & Unique_reads_cgn_extraction
  • Hisat_single_end_r1_r2_mapping_dna_mode_and_merge_sort_split_reads_by_name & Remove_overlap_read_parts

This pr removed several outputs of the pipeline. @kayleemathews does this pr need doc updates?


Checklist

If you can answer "yes" to the following items, please add a checkmark next to the appropriate checklist item(s) and notify our WARP documentation team by tagging either @ekiernan or @kayleemathews in a comment on this PR.

  • Did you add inputs, outputs, or tasks to a workflow?
  • Did you modify, delete or move: file paths, file names, input names, output names, or task names?
  • If you made a changelog update, did you update the pipeline version number?

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github-actions bot commented Feb 2, 2024

Remember to squash merge!

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github-actions bot commented Feb 2, 2024

Remember to squash merge!

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github-actions bot commented Feb 5, 2024

Remember to squash merge!

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github-actions bot commented Feb 6, 2024

Remember to squash merge!

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Remember to squash merge!

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Remember to squash merge!

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Remember to squash merge!

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Remember to squash merge!

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Remember to squash merge!

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Remember to squash merge!

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Remember to squash merge!

@nikellepetrillo nikellepetrillo marked this pull request as ready for review February 14, 2024 13:47
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@kevinpalis kevinpalis left a comment

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LGTM

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@ekiernan ekiernan left a comment

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Thanks @nikellepetrillo ! LGTM as long as summary file matches after changes. I had just one question about the contact summary tar.

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Remember to squash merge!

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Remember to squash merge!

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Remember to squash merge!

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@kayleemathews kayleemathews left a comment

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@nikellepetrillo Docs are updated! If you can review them before you merge that would be great!

@nikellepetrillo
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retest this please

@nikellepetrillo nikellepetrillo merged commit f130cd0 into develop Feb 15, 2024
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5 participants