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Updates to scATAC-seq preprocessing v1 #334

Merged
merged 36 commits into from
Jun 29, 2021
Merged

Updates to scATAC-seq preprocessing v1 #334

merged 36 commits into from
Jun 29, 2021

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@cflerin cflerin commented Apr 2, 2021

Updates to initial version of scATAC-seq preprocessing

  • Update bwa mapping approach
    • skip samtools sort step, turn off compression for piped commands, reduce samtools threads
    • Re-work add_barcode_as_tag mawk script to include both corrected and uncorrected barcode tags in final bam
    • Split config file into discrete parts that can be loaded separately
  • Update fragments sorting command
  • BAP updates
    • Implement multiplet detection pipeline
    • Fix bap install in Docker image
  • Enable skipping of barcode correction (when whitelist parameters are empty)
  • scATAC-seq docs updates and fixes

cflerin added 30 commits December 11, 2020 10:36
@cflerin
Update archr publish methods
f9d54ba
@cflerin
Add archr qc filtering method and entry point
7606659
@cflerin
Add macs2 callpeaks command to qc_prefilter
162a1b3
@cflerin
Update bwa Dockerfile
60c52a2 
- Revert to the Debian-based image after running into issues with memory
errors in BWA
@cflerin
Refine pycistopic implementation andi compute_qc_stats function.
0cff3a4 
- Switch to local singularity container for development
- Update publishing output
- Add new configuration options for compute_qc_stats and cleanup the
script
- qc_filtering workflow update
@cflerin
Fix row name in mapping summary
fa2401b
@cflerin
Update bwa mapping approach
1d55659 
- Skip samtools sort by name step
- Turn off compression for intermediate samtools steps
- Reduce the number of samtools threads to 6 or ${task.cpus}
@cflerin
Add additional output to cell calling step
77f3a4a
@cflerin
Merge branch 'develop' into develop_atac
d86e2c0 
- Major updates for Nextflow 20.10.0 compatibility
@cflerin
Fix channel naming conflict
adefaf5
@cflerin
Merge branch 'develop' into develop_atac
2633e46
@cflerin
Update fragments file sorting command
350ed25
@cflerin
Cleanup and separation of bap config
af01535
@cflerin
Initial implementation of bap multiplet pipeline
0f2f114
@cflerin
Changes to include corrected barcode in final bam
3692c35
@cflerin
Update bap compute parameters
090a34c
@cflerin
Change default barcode tag in BAP to CB
d33be8d
@cflerin
Implement bap multiplet detection pipeline
0af9541 
- Update container
- Finish multiplet process and publishing steps
- Resolves #246
@cflerin
Update archr steps add option to remove density coloring on cell calling
69e46c3 
plot
@cflerin
Split up the bwamaptools config to enable the use of the index function
21f936b 
without loading the config for mapping
@cflerin
Move sinto publish fragments to parent workflow
1864591
@cflerin
Enable fragments step to take alternate barcode tag
1871c94
@cflerin
Update bap dockerfile
1bcb181 
- Use bap fork with subprocess fix
@cflerin
Fix bap multiplet output file naming
0e3e853
@cflerin
Enable skipping of barcode correction
175d26b 
- Skip when whitelist entries in the params are empty
@cflerin
Update samtools command
befea86
@cflerin
Update singlecelltoolkit default container
82747b4 
- This container has the fix to enable barcode correction with barcodes
longer than 16bp
@cflerin
Update atac-seq docs
032673e
@cflerin
Update atac doc codeblocks
4d979ba
@cflerin
Update links to sctk scripts in docs
41df185
@cflerin
develop_atac cleanup:
9032820 
- Keep qc_filtering methods in a separate branch

Revert "Update archr steps add option to remove density coloring on cell calling"
- This reverts commit 69e46c3.

Revert "Add additional output to cell calling step"
- This reverts commit 77f3a4a.

Revert "Refine pycistopic implementation andi compute_qc_stats function."
- This reverts commit 0cff3a4.

Revert "Add macs2 callpeaks command to qc_prefilter"
- This reverts commit 162a1b3.

Revert "Add archr qc filtering method and entry point"
- This reverts commit 7606659.

Revert "Update archr publish methods"
- This reverts commit f9d54ba.
@cflerin cflerin requested review from dweemx and KrisDavie April 2, 2021 12:32
@cflerin cflerin merged commit f148539 into develop Jun 29, 2021
@cflerin cflerin mentioned this pull request Jun 29, 2021
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@dweemx dweemx Awaiting requested review from dweemx

@KrisDavie KrisDavie Awaiting requested review from KrisDavie

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