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Commit 0ed97a3b authored by aknecht2's avatar aknecht2
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Started updating peak call.yal

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chipathlon/jobs/modules/peak_call.yaml
+ 122
− 143
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......@@ -3,180 +3,159 @@ peak_call:
- narrow[peak_type]:
- music_narrow:
inputs:
- prefix:
type: string
- control.bed:
type: file
- signal.bed:
type: file
additional_inputs:
- mapp_files:
type: list
prefix:
param_name: prefix
control.bed:
param_name: control.bed
signal.bed:
param_name: signal.bed
outputs:
- sorted_scale_129_all.bed:
type: file
final_result: true
- sorted_scale_194_all.bed:
type: file
final_result: true
- sorted_scale_291_all.bed:
type: file
final_result: true
sorted_scale_129_all.bed:
param_name: scale_129.bed
final_result: true
sorted_scale_194_all.bed:
param_name: scale_194.bed
final_result: true
sorted_scale_291_all.bed:
param_name: scale_291.bed
final_result: true
- punctate[peak_type]:
- music_punctate:
inputs:
- prefix:
type: string
- control.bed:
type: file
- signal.bed:
type: file
additional_inputs:
- mapp_files:
type: list
prefix:
param_name: prefix
control.bed:
param_name: control.bed
signal.bed:
param_name: signal.bed
outputs:
- sorted_scale_129_all.bed:
type: file
final_result: true
- sorted_scale_194_all.bed:
type: file
final_result: true
- sorted_scale_291_all.bed:
type: file
final_result: true
- sorted_scale_437_all.bed:
type: file
final_result: true
- sorted_scale_656_all.bed:
type: file
final_result: true
- sorted_scale_985_all.bed:
type: file
final_result: true
- sorted_scale_1477_all.bed:
type: file
final_result: true
- sorted_scale_2216_all.bed:
type: file
final_result: true
sorted_scale_129_all.bed:
param_name: scale_129.bed
final_result: true
sorted_scale_194_all.bed:
param_name: scale_194.bed
final_result: true
sorted_scale_291_all.bed:
param_name: scale_291.bed
final_result: true
sorted_scale_437_all.bed:
param_name: scale_437.bed
final_result: true
sorted_scale_656_all.bed:
param_name: scale_656.bed
final_result: true
sorted_scale_985_all.bed:
param_name: scale_985.bed
final_result: true
sorted_scale_1477_all.bed:
param_name: scale_1477.bed
final_result: true
sorted_scale_2216_all.bed:
param_name: scale_2216_all.bed
final_result: true
- broad[peak_type]:
- music_broad:
inputs:
- prefix:
type: string
- control.bed:
type: file
- signal.bed:
type: file
additional_inputs:
- mapp_files:
type: list
prefix:
param_name: prefix
control.bed:
param_name: control.bed
signal.bed:
param_name: signal.bed
outputs:
- sorted_scale_1459_all.bed:
type: file
final_result: true
- sorted_scale_2189_all.bed:
type: file
final_result: true
- sorted_scale_3284_all.bed:
type: file
final_result: true
- sorted_scale_4926_all.bed:
type: file
final_result: true
- sorted_scale_7389_all.bed:
type: file
final_result: true
- sorted_scale_11084_all.bed:
type: file
final_result: true
- sorted_scale_16626_all.bed:
type: file
final_result: true
sorted_scale_1459_all.bed:
param_name: scale_1459.bed
final_result: true
sorted_scale_2189_all.bed:
param_name: scale_2189.bed
final_result: true
sorted_scale_3284_all.bed:
param_name: scale_3284.bed
final_result: true
sorted_scale_4926_all.bed:
param_name: scale_4926.bed
final_result: true
sorted_scale_7389_all.bed:
param_name: scale_7389.bed
final_result: true
sorted_scale_11084_all.bed:
param_name: scale_11084.bed
final_result: true
sorted_scale_16626_all.bed:
param_name: scale_16626.bed
final_result: true
- peakranger[tool]:
- narrow[peak_type]:
- peakranger_callpeak:
inputs:
- exp.bed:
type: file
- control.bed:
type: file
- prefix:
type: string
additional_inputs: null
prefix:
param_name: prefix
control.bed:
param_name: control.bed
signal.bed:
param_name: signal.bed
outputs:
- details:
type: file
- region.bed:
type: file
- summit.bed:
type: file
- peakranger.log:
type: stdout
region.bed:
param_name: region_bed
summit.bed:
param_name: summit_bed
details:
param_name: details
peakranger.log:
param_name: log
- peakranger_format_bed:
inputs:
- region.bed:
type: file
additional_inputs: null
region.bed:
param_name: result_peaks
outputs:
- region_sorted.bed:
type: file
final_result: true
region_sorted.bed:
param_name: sorted_peaks
- peakranger_format_bed:
inputs:
- summit.bed:
type: file
additional_inputs: null
summit.bed:
param_name: result_peaks
outputs:
- summit_sorted.bed:
type: file
final_result: true
summit_sorted.bed:
param_name: sorted_peaks
- ccat[tool]:
- broad[peak_type]:
- ccat_callpeak:
inputs:
- exp.bed:
type: file
- control.bed:
type: file
- chrom.sizes:
type: file
- conf.txt:
type: file
- prefix:
type: string
additional_inputs: null
prefix:
param_name: prefix
control.bed:
param_name: control.bed
signal.bed:
param_name: signal.bed
chrom.sizes:
param_name: chrom.sizes
outputs:
- significant.peak:
type: file
prefix_join: "."
- significant.region:
type: file
prefix_join: "."
- top100000.peak:
type: file
prefix_join: "."
- log:
type: stdout
prefix_join: "."
significant.peak:
param_name: significant_peak
prefix_join: "."
significant.region:
param_name: significant_region
prefix_join: "."
top100000.peak:
param_name: top_100000_peak
prefix_join: "."
log:
param_name: ccat_log
prefix_join: "."
- ccat_format_bed:
inputs:
- significant.region:
type: file
additional_inputs: null
significant.region:
param_name: result_peaks
outputs:
- region_sorted.bed:
type: file
final_result: true
region_sorted.bed:
param_name: sorted_peaks
- ccat_format_bed:
inputs:
- significant.peak:
type: file
additional_inputs: null
significant.peak:
param_name: result_peaks:
outputs:
- peak_sorted.bed:
type: file
final_result: true
peak_sorted.bed:
param_name: sorted_peaks
- gem[tool]:
- narrow[peak_type]:
- gem_callpeak:
......
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