Rc peakcall 2797 #1478
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Rc peakcall 2797 #1478
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…into aa-peakcall
🔍Changelog Validation Results: |
🔍Version Validation Results: |
…warp into rc_peakcall_2797
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Remember to squash merge! |
🔍Changelog Validation Results: |
🔍Version Validation Results: |
ekiernan
reviewed
Jan 31, 2025
pipelines/skylab/atac/atac.wdl
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| atac_data_mod.uns[key] = atac_data_mod.uns[key].to_pandas() | ||
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| print("Write into h5ad file") | ||
| atac_data_mod.write_h5ad("~{bam_base_name}.peaks.h5ad") |
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Suggested change
| atac_data_mod.write_h5ad("~{bam_base_name}.peaks.h5ad") | |
| atac_data_mod.write_h5ad("~{bam_base_name}.bin.h5ad") |
ekiernan
reviewed
Jan 31, 2025
pipelines/skylab/atac/atac.wdl
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| print("Write into h5ad file") | ||
| atac_data_mod.write_h5ad("~{bam_base_name}.peaks.h5ad") | ||
| peak_matrix.write_h5ad("~{bam_base_name}.matrix.h5ad") |
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Suggested change
| peak_matrix.write_h5ad("~{bam_base_name}.matrix.h5ad") | |
| peak_matrix.write_h5ad("~{bam_base_name}.peaks.h5ad") |
ekiernan
reviewed
Jan 31, 2025
pipelines/skylab/atac/atac.wdl
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| output { | ||
| File peaks_h5ad = "~{bam_base_name}.peaks.h5ad" | ||
| File matrix_h5ad = "~{bam_base_name}.matrix.h5ad" |
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| File matrix_h5ad = "~{bam_base_name}.matrix.h5ad" | |
| File matrix_h5ad = "~{bam_base_name}.bins.h5ad" |
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Remember to squash merge! |
🔍Version Validation Results: |
🔍Changelog Validation Results: |
ekiernan
reviewed
Jan 31, 2025
pipelines/skylab/atac/atac.wdl
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| # peak calling using SnapATAC2 | ||
| task PeakCalling { | ||
| input { | ||
| File bam |
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Remember to squash merge! |
🔍Changelog Validation Results: |
🔍Version Validation Results: |
|
Remember to squash merge! |
🔍Changelog Validation Results: |
🔍Version Validation Results: |
|
Remember to squash merge! |
🔍Changelog Validation Results: |
🔍Version Validation Results: |
ekiernan
reviewed
Jan 31, 2025
| } | ||
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| output { | ||
| File peaks_h5ad = "~{output_base_name}.cellbybin.h5ad" |
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Should we adjust output variable name as well?
ekiernan
reviewed
Jan 31, 2025
| output { | ||
| File bam_aligned_output = bam_aligned_output_atac | ||
| File fragment_file = fragment_file_atac | ||
| File fragment_file_index = fragment_file_index_atac | ||
| File snap_metrics = snap_metrics_atac | ||
| File library_metrics_file = library_metrics | ||
| File? peakcall_h5ad_file = PeakCalling.peaks_h5ad |
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Should we add both peak calling output files? The cellbybin matrix and the cellbypeak matrix?
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Description
Added the peakcalling step in ATAC.
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 team by tagging @broadinstitute/warp-admins in a comment on this PR.