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Add CRAM compression option #62

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priyanka-surana opened this issue Mar 16, 2023 · 0 comments · Fixed by #68
Closed

Add CRAM compression option #62

priyanka-surana opened this issue Mar 16, 2023 · 0 comments · Fixed by #68
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@muffato
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feature Requests for new features user request Requests made by users and public
Milestone
1.2.0

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@priyanka-surana
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priyanka-surana commented Mar 16, 2023 •
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Description of feature

To close this issue:

  1. Add the updated nf-core/crumble (0.9.1) to the pipeline.
  2. Move samtools_view from workflow to new subworkflow alignment_output.
  3. Integrate nf-core/crumble into alignment_output.
  4. Add custom module configurations to run for different technologies with different settings. (difficult)
@priyanka-surana priyanka-surana added the enhancement Improvement of the existing features label Mar 16, 2023
@priyanka-surana priyanka-surana added this to the 1.2.0 milestone Mar 16, 2023
@priyanka-surana priyanka-surana self-assigned this Mar 16, 2023
@priyanka-surana priyanka-surana pinned this issue Mar 16, 2023
@priyanka-surana priyanka-surana added feature Requests for new features user request Requests made by users and public labels Jun 27, 2023
@priyanka-surana priyanka-surana linked a pull request Jul 11, 2023 that will close this issue
Add read group back and crumble for HiFi #68
Merged
@muffato muffato moved this from Todo to In Progress in Genome After Party Nov 10, 2023
@muffato muffato removed this from the 1.2.0 milestone Dec 8, 2023
@muffato muffato added this to the 1.3.0 milestone Feb 12, 2024
@muffato muffato self-assigned this Jun 1, 2024
@muffato muffato removed the enhancement Improvement of the existing features label Jun 1, 2024
@muffato muffato moved this to To do in readmapping Jun 5, 2024
@muffato muffato modified the milestones: 1.3.0, 1.2.0 Jun 6, 2024
@muffato muffato closed this as completed Jun 6, 2024
@github-project-automation github-project-automation bot moved this from In Progress to Done in Genome After Party Jun 6, 2024
@github-project-automation github-project-automation bot moved this from To do to Done in readmapping Jun 6, 2024
@muffato muffato unpinned this issue Jun 18, 2024
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@muffato muffato

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feature Requests for new features user request Requests made by users and public
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Genome After Party
Status: Done
readmapping
Status: Done
Milestone
1.2.0
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Successfully merging a pull request may close this issue.

Add read group back and crumble for HiFi sanger-tol/readmapping
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@muffato @priyanka-surana