diff --git a/chipathlon/jobs/params/macs2_broad.yaml b/chipathlon/jobs/params/macs2_broad.yaml new file mode 100644 index 0000000000000000000000000000000000000000..5f79d9f7d01d4a60ee8e06ec152e5fd80c3f6f2f --- /dev/null +++ b/chipathlon/jobs/params/macs2_broad.yaml @@ -0,0 +1,105 @@ +macs2_broad: + inputs: + - name: signal_bed + type: file + file_type: bed + + - name: control_bed + type: file + file_type: bed + + - name: prefix + type: string + additional_inputs: null + outputs: + - name: result_peak + type: file + file_type: bed + + - name: excel_result + type: file + file_type: xls + + - name: result_summit + type: file + file_type: bed + command: macs2 + arguments: + - callpeak: + type: string + changeable: false + required: true + has_value: false + - "-t": + type: file + changeable: false + required: true + has_value: true + default: $inputs.0 + - "-c": + type: file + changeable: false + required: true + has_value: true + default: $inputs.1 + - "-f": + type: string + changeable: false + required: true + has_value: true + default: "BED" + - "-n": + type: string + changeable: false + required: true + has_value: true + default: $inputs.2 + - "-g": + type: string + changeable: true + required: false + has_value: true + default: "hs" + - "-p": + type: numeric + changeable: true + required: false + has_value: true + default: 0.01 + - "--nomodel": + type: string + changeable: false + required: true + has_value: false + - "--shift": + type: numeric + changeable: true + required: false + has_value: true + default: 0 + - "--extsize": + type: numeric + changeable: true + required: false + has_value: true + default: 110 + - "--SPMR": + type: string + changeable: false + required: true + has_value: false + - "--broad": + type: string + changeable: false + required: true + has_value: false + - "--broad-cutoff": + type: numeric + changeable: true + required: true + has_value: true + default: 0.1 + walltime: 480 + memory: 16000 + cores: 1 + nodes: 1 diff --git a/chipathlon/jobs/params/macs2_callpeak.yaml b/chipathlon/jobs/params/macs2_narrow.yaml similarity index 92% rename from chipathlon/jobs/params/macs2_callpeak.yaml rename to chipathlon/jobs/params/macs2_narrow.yaml index c9156c28c1b9a6987747e7adfd5c0d0795595ea0..175c8e5304d111afa8efbdeed7b1b0d010727139 100644 --- a/chipathlon/jobs/params/macs2_callpeak.yaml +++ b/chipathlon/jobs/params/macs2_narrow.yaml @@ -1,4 +1,4 @@ -macs2_callpeak: +macs2_narrow: inputs: - name: signal_bed type: file @@ -83,17 +83,12 @@ macs2_callpeak: required: false has_value: true default: 110 - - "-B": - type: string - changeable: false - required: true - has_value: false - "--SPMR": type: string changeable: false required: true has_value: false - walltime: 2000 - memory: 8000 + walltime: 480 + memory: 16000 cores: 1 nodes: 1