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PIP-1593-filter-type-value (#231)
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paul-sud authored Feb 8, 2022
1 parent 472f5dc commit 7d45dc8
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Showing 9 changed files with 95 additions and 1 deletion.
2 changes: 1 addition & 1 deletion accession/accession_steps.py
Original file line number Diff line number Diff line change
Expand Up @@ -111,4 +111,4 @@ def __init__(self, file_params: Dict[str, Any]):
"maybe_preferred_default", False
)
self.filter_type: Optional[str] = file_params.get("filter_type")
self.filter_value: Optional[int] = file_params.get("filter_value")
self.filter_value: Optional[Union[float, int]] = file_params.get("filter_value")
12 changes: 12 additions & 0 deletions accession_steps/atac_steps.json
Original file line number Diff line number Diff line change
Expand Up @@ -207,6 +207,8 @@
"file_format": "bed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks",
"quality_metrics": [
"atac_replication",
Expand Down Expand Up @@ -249,6 +251,8 @@
"file_format": "bed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks",
"quality_metrics": [
"atac_replication",
Expand Down Expand Up @@ -297,6 +301,8 @@
"file_format": "bed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks",
"quality_metrics": [
"atac_replication",
Expand All @@ -320,6 +326,8 @@
"file_format": "bigBed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak_bb",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks"
}
],
Expand All @@ -340,6 +348,8 @@
"file_format": "bigBed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak_bb",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks"
}
],
Expand All @@ -363,6 +373,8 @@
"file_format": "bigBed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak_bb",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks"
}
],
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14 changes: 14 additions & 0 deletions accession_steps/dnase_no_footprints_steps.json
Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,8 @@
],
"file_format": "starch",
"filekey": "analysis.tenth_of_one_percent_peaks_starch",
"filter_type": "false discovery rate percentage",
"filter_value": 0.1,
"output_type": "peaks",
"quality_metrics": []
}
Expand All @@ -109,6 +111,8 @@
"file_format": "bed",
"file_format_type": "bed3+",
"filekey": "analysis.five_percent_allcalls_bed_gz",
"filter_type": "false discovery rate percentage",
"filter_value": 5.0,
"output_type": "FDR cut rate",
"quality_metrics": [
"five_percent_allcalls_qc"
Expand Down Expand Up @@ -156,6 +160,8 @@
"file_format": "bigBed",
"file_format_type": "bed3+",
"filekey": "analysis.five_percent_allcalls_bigbed",
"filter_type": "false discovery rate percentage",
"filter_value": 5.0,
"output_type": "FDR cut rate",
"quality_metrics": []
}
Expand All @@ -181,6 +187,8 @@
"file_format": "bed",
"file_format_type": "narrowPeak",
"filekey": "analysis.five_percent_narrowpeaks_bed_gz",
"filter_type": "false discovery rate percentage",
"filter_value": 5.0,
"output_type": "peaks",
"quality_metrics": [
"five_percent_narrowpeaks_qc"
Expand Down Expand Up @@ -208,6 +216,8 @@
"file_format": "bed",
"file_format_type": "narrowPeak",
"filekey": "analysis.tenth_of_one_percent_narrowpeaks_bed_gz",
"filter_type": "false discovery rate percentage",
"filter_value": 0.1,
"maybe_preferred_default": true,
"output_type": "peaks",
"quality_metrics": [
Expand All @@ -231,6 +241,8 @@
"file_format": "bigBed",
"file_format_type": "narrowPeak",
"filekey": "analysis.tenth_of_one_percent_narrowpeaks_bigbed",
"filter_type": "false discovery rate percentage",
"filter_value": 0.1,
"maybe_preferred_default": true,
"output_type": "peaks",
"quality_metrics": []
Expand All @@ -252,6 +264,8 @@
"file_format": "bigBed",
"file_format_type": "narrowPeak",
"filekey": "analysis.five_percent_narrowpeaks_bigbed",
"filter_type": "false discovery rate percentage",
"filter_value": 5.0,
"output_type": "peaks",
"quality_metrics": []
}
Expand Down
18 changes: 18 additions & 0 deletions accession_steps/dnase_steps.json
Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,8 @@
],
"file_format": "starch",
"filekey": "analysis.tenth_of_one_percent_peaks_starch",
"filter_type": "false discovery rate percentage",
"filter_value": 0.1,
"output_type": "peaks",
"quality_metrics": []
}
Expand All @@ -109,6 +111,8 @@
"file_format": "bed",
"file_format_type": "bed3+",
"filekey": "analysis.five_percent_allcalls_bed_gz",
"filter_type": "false discovery rate percentage",
"filter_value": 5.0,
"output_type": "FDR cut rate",
"quality_metrics": [
"five_percent_allcalls_qc"
Expand Down Expand Up @@ -145,6 +149,8 @@
"file_format": "bed",
"file_format_type": "bed3+",
"filekey": "analysis.one_percent_footprints_bed_gz",
"filter_type": "false discovery rate percentage",
"filter_value": 1.0,
"output_type": "footprints",
"quality_metrics": [
"footprints_quality_metric"
Expand All @@ -168,6 +174,8 @@
"file_format": "bigBed",
"file_format_type": "bed3+",
"filekey": "analysis.one_percent_footprints_bigbed",
"filter_type": "false discovery rate percentage",
"filter_value": 1.0,
"output_type": "footprints",
"quality_metrics": []
}
Expand Down Expand Up @@ -213,6 +221,8 @@
"file_format": "bigBed",
"file_format_type": "bed3+",
"filekey": "analysis.five_percent_allcalls_bigbed",
"filter_type": "false discovery rate percentage",
"filter_value": 5.0,
"output_type": "FDR cut rate",
"quality_metrics": []
}
Expand All @@ -238,6 +248,8 @@
"file_format": "bed",
"file_format_type": "narrowPeak",
"filekey": "analysis.five_percent_narrowpeaks_bed_gz",
"filter_type": "false discovery rate percentage",
"filter_value": 5.0,
"output_type": "peaks",
"quality_metrics": [
"five_percent_narrowpeaks_qc"
Expand Down Expand Up @@ -265,6 +277,8 @@
"file_format": "bed",
"file_format_type": "narrowPeak",
"filekey": "analysis.tenth_of_one_percent_narrowpeaks_bed_gz",
"filter_type": "false discovery rate percentage",
"filter_value": 0.1,
"maybe_preferred_default": true,
"output_type": "peaks",
"quality_metrics": [
Expand All @@ -288,6 +302,8 @@
"file_format": "bigBed",
"file_format_type": "narrowPeak",
"filekey": "analysis.tenth_of_one_percent_narrowpeaks_bigbed",
"filter_type": "false discovery rate percentage",
"filter_value": 0.1,
"maybe_preferred_default": true,
"output_type": "peaks",
"quality_metrics": []
Expand All @@ -309,6 +325,8 @@
"file_format": "bigBed",
"file_format_type": "narrowPeak",
"filekey": "analysis.five_percent_narrowpeaks_bigbed",
"filter_type": "false discovery rate percentage",
"filter_value": 5.0,
"output_type": "peaks",
"quality_metrics": []
}
Expand Down
2 changes: 2 additions & 0 deletions accession_steps/jsonnet/atac_chip.jsonnet
Original file line number Diff line number Diff line change
Expand Up @@ -149,6 +149,8 @@
local shared_file_props_no_qc = {
file_format_type: file_format_type,
output_type: 'IDR thresholded peaks',
filter_type: 'IDR',
filter_value: 0.05,
},
local shared_file_props = shared_file_props_no_qc {
quality_metrics: (if is_atac then ['atac_replication', 'atac_peak_enrichment'] else [
Expand Down
12 changes: 12 additions & 0 deletions accession_steps/tf_chip_bwa_control_fastqs_steps.json
Original file line number Diff line number Diff line change
Expand Up @@ -311,6 +311,8 @@
"file_format": "bed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks",
"quality_metrics": [
"chip_replication",
Expand Down Expand Up @@ -372,6 +374,8 @@
"file_format": "bed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks",
"quality_metrics": [
"chip_replication",
Expand Down Expand Up @@ -435,6 +439,8 @@
"file_format": "bed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks",
"quality_metrics": [
"chip_replication",
Expand All @@ -461,6 +467,8 @@
"file_format": "bigBed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak_bb",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks"
}
],
Expand All @@ -484,6 +492,8 @@
"file_format": "bigBed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak_bb",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks"
}
],
Expand All @@ -508,6 +518,8 @@
"file_format": "bigBed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak_bb",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks"
}
],
Expand Down
12 changes: 12 additions & 0 deletions accession_steps/tf_chip_pbam_steps.json
Original file line number Diff line number Diff line change
Expand Up @@ -193,6 +193,8 @@
"file_format": "bed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks",
"quality_metrics": [
"chip_replication",
Expand Down Expand Up @@ -254,6 +256,8 @@
"file_format": "bed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks",
"quality_metrics": [
"chip_replication",
Expand Down Expand Up @@ -317,6 +321,8 @@
"file_format": "bed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks",
"quality_metrics": [
"chip_replication",
Expand All @@ -343,6 +349,8 @@
"file_format": "bigBed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak_bb",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks"
}
],
Expand All @@ -366,6 +374,8 @@
"file_format": "bigBed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak_bb",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks"
}
],
Expand All @@ -390,6 +400,8 @@
"file_format": "bigBed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak_bb",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks"
}
],
Expand Down
12 changes: 12 additions & 0 deletions accession_steps/tf_chip_peak_call_only_steps.json
Original file line number Diff line number Diff line change
Expand Up @@ -152,6 +152,8 @@
"file_format": "bed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks",
"quality_metrics": [
"chip_replication",
Expand Down Expand Up @@ -213,6 +215,8 @@
"file_format": "bed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks",
"quality_metrics": [
"chip_replication",
Expand Down Expand Up @@ -276,6 +280,8 @@
"file_format": "bed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks",
"quality_metrics": [
"chip_replication",
Expand All @@ -302,6 +308,8 @@
"file_format": "bigBed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak_bb",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks"
}
],
Expand All @@ -325,6 +333,8 @@
"file_format": "bigBed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak_bb",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks"
}
],
Expand All @@ -349,6 +359,8 @@
"file_format": "bigBed",
"file_format_type": "narrowPeak",
"filekey": "bfilt_idr_peak_bb",
"filter_type": "IDR",
"filter_value": 0.05,
"output_type": "IDR thresholded peaks"
}
],
Expand Down
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