Commit 5189f83a authored by aknecht2's avatar aknecht2
Browse files

Updated all workflow job yaml files for peak calling jobs.

parent f98571d5
cat_awk_sort_peaks:
inputs:
- name: peak_result
peak_results:
type: file
file_type: bed
additional_inputs: null
outputs:
- name: sorted_result
sorted_results:
type: file
file_type: bed
command: chip-job-cat-peak
arguments:
- "$inputs.0":
- "$peak_results":
type: file
changeable: false
required: true
has_value: false
- "$outputs.0":
- "$sorted_results":
type: file
changeable: false
required: true
......
ccat_callpeak:
inputs:
- name: signal_bed
prefix:
type: string
control.bed:
type: file
file_type: bed
- name: control_bed
signal.bed:
type: file
file_type: bed
- name: chrom_sizes
type: file
file_type: chrom_sizes
- name: ccat_configuration
chrom.sizes:
type: file
file_type: ccat_conf
- name: prefix
type: string
additional_inputs: null
file_type: bed
outputs:
- name: significant_peak
significant_peak:
type: file
file_type: bed
- name: significant_region
significant_region:
type: file
file_type: bed
- name: top_100000_peak
top_1000000_peak:
type: file
file_type: bed
- name: ccat_log
ccat_log:
type: stdout
file_type: log
command: CCAT
arguments:
- "$inputs.0":
- "$signal.bed":
type: file
changeable: false
required: true
has_value: false
- "$inputs.1":
- "$control.bed":
type: file
changeable: false
required: true
has_value: false
- "$inputs.2":
- "$chrom.sizes":
type: file
changeable: false
required: true
has_value: false
- "$inputs.3":
- "config_TF.txt":
type: rawfile
file_type: txt
changeable: true
......@@ -60,7 +49,7 @@ ccat_callpeak:
has_value: false
default: config_TF.txt
path: config
- "$inputs.4":
- "$prefix":
type: file
changeable: false
required: true
......
ccat_format_bed:
inputs:
- name: result_peaks
result_peaks:
type: file
file_type: bed
additional_inputs: null
outputs:
- name: sorted_peaks
sorted_peaks:
type: file
file_type: bed
command: chip-job-ccat-format-bed
......@@ -15,13 +14,13 @@ ccat_format_bed:
changeable: false
required: true
has_value: true
default: $inputs.0
default: $result_peaks
- "--output":
type: file
changeable: false
required: true
has_value: true
default: $outputs.0
default: $sorted_peaks
walltime: 60
memory: 8000
cores: 1
......
cp:
inputs:
- name: peak_result
input_file:
type: file
file_type: bed
file_type: any
additional_inputs: null
outputs:
- name: tag_align_result
output_file:
type: file
file_type: bed
file_type: any
command: cp
arguments:
- "$inputs.0":
- "$input_file":
type: file
changeable: false
required: true
has_value: false
- "$outputs.0":
- "$output_file":
type: file
changeable: false
required: true
......
gem_callpeak:
inputs:
- name: chrom_sizes
prefix:
type: string
chrom.sizes:
type: file
file_type: chrom_sizes
- name: signal_bed
control.bed:
type: file
file_type: bed
- name: control_bed
signal.bed:
type: file
file_type: bed
- name: prefix
type: string
- name: genome
genome:
type: string
additional_inputs:
- name: read_distribution
type: file
file_type: read_dist
- name: chr_fasta
type: list
chr_fasta:
type: file_list
file_type: chr_fasta
outputs:
- name: gem_peak_result
gem_peak_result:
type: file
file_type: bed
- name: gps_peak_result
gps_peak_result:
type: file
file_type: bed
command: gem
......@@ -47,31 +38,31 @@ gem_callpeak:
changeable: false
required: true
has_value: true
default: $inputs.0
default: $chrom.sizes
- "--expt":
type: file
changeable: false
required: true
has_value: true
default: $inputs.1
default: $exp.bed
- "--ctrl":
type: file
changeable: false
required: true
has_value: true
default: $inputs.2
default: $control.bed
- "--out":
type: argument
changeable: false
required: true
has_value: true
default: $inputs.3
default: $prefix
- "--genome":
type: string
changeable: false
required: true
has_value: true
default: "$inputs.4"
default: "$genome"
- "--k_min":
type: numeric
changeable: true
......
macs2_broad:
inputs:
- name: signal_bed
prefix:
type: string
control.bed:
type: file
file_type: bed
- name: control_bed
signal.bed:
type: file
file_type: bed
- name: prefix
type: string
additional_inputs: null
outputs:
- name: result_peak
result_peaks:
type: file
file_type: bed
- name: excel_result
excel_result:
type: file
file_type: xls
- name: result_summit
result_summit:
type: file
file_type: bed
command: macs2
......@@ -35,13 +30,13 @@ macs2_broad:
changeable: false
required: true
has_value: true
default: $inputs.0
default: $signal.bed
- "-c":
type: file
changeable: false
required: true
has_value: true
default: $inputs.1
default: $control.bed
- "-f":
type: string
changeable: false
......@@ -53,7 +48,7 @@ macs2_broad:
changeable: false
required: true
has_value: true
default: $inputs.2
default: $prefix
- "-g":
type: string
changeable: true
......
macs2_narrow:
inputs:
- name: signal_bed
prefix:
type: string
control.bed:
type: file
file_type: bed
- name: control_bed
signal.bed:
type: file
file_type: bed
- name: prefix
type: string
additional_inputs: null
outputs:
- name: result_peak
result_peaks:
type: file
file_type: bed
- name: excel_result
excel_result:
type: file
file_type: xls
- name: result_summit
result_summit:
type: file
file_type: bed
command: macs2
......@@ -35,13 +30,13 @@ macs2_narrow:
changeable: false
required: true
has_value: true
default: $inputs.0
default: $signal.bed
- "-c":
type: file
changeable: false
required: true
has_value: true
default: $inputs.1
default: $control.bed
- "-f":
type: string
changeable: false
......@@ -53,7 +48,7 @@ macs2_narrow:
changeable: false
required: true
has_value: true
default: $inputs.2
default: $prefix
- "-g":
type: string
changeable: true
......
music_broad:
inputs:
- name: prefix
prefix:
type: string
- name: control.bed
control.bed:
type: file
file_type: bed
- name: signal.bed
signal.bed:
type: file
file_type: bed
additional_inputs:
- name: mapp_inputs
type: list
file_type: bin
outputs:
- name: scale_1459.bed
scale_1459.bed:
type: file
file_type: bed
- name: scale_2189.bed
scale_2189.bed:
type: file
file_type: bed
- name: scale_3284.bed
scale_3284.bed:
type: file
file_type: bed
- name: scale_4926.bed
scale_4926.bed:
type: file
file_type: bed
- name: scale_7389.bed
scale_7389.bed:
type: file
file_type: bed
- name: scale_11084.bed
scale_11084.bed:
type: file
file_type: bed
- name: scale_16626.bed
scale_16626.bed:
type: file
file_type: bed
command: chip-job-music
......@@ -49,7 +37,7 @@ music_broad:
changeable: false
required: true
has_value: true
default: "$inputs.0"
default: "$prefix"
- "--peak_type":
type: string
changeable: false
......@@ -61,13 +49,13 @@ music_broad:
changeable: false
required: true
has_value: true
default: "$inputs.1"
default: "$control.bed"
- "--signals":
type: file
changeable: false
required: true
has_value: true
default: "$inputs.2"
default: "$signal.bed"
- "--mapp":
type: rawfolder
changeable: true
......
music_narrow:
inputs:
- name: prefix
prefix:
type: string
- name: control.bed
control.bed:
type: file
file_type: bed
- name: signal.bed
signal.bed:
type: file
file_type: bed
additional_inputs:
- name: mapp_inputs
type: list
file_type: bin
outputs:
- name: scale_129.bed
scale_129.bed:
type: file
file_type: bed
- name: scale_194.bed
scale_194.bed:
type: file
file_type: bed
- name: scale_291.bed
scale_291.bed:
type: file
file_type: bed
command: chip-job-music
......@@ -33,7 +25,7 @@ music_narrow:
changeable: false
required: true
has_value: true
default: "$inputs.0"
default: "$prefix"
- "--peak_type":
type: string
changeable: false
......@@ -45,13 +37,13 @@ music_narrow:
changeable: false
required: true
has_value: true
default: "$inputs.1"
default: "$control.bed"
- "--signals":
type: file
changeable: false
required: true
has_value: true
default: "$inputs.2"
default: "$signal.bed"
- "--mapp":
type: rawfolder
changeable: true
......
music_punctate:
inputs:
- name: prefix
prefix:
type: string
- name: control.bed
control.bed:
type: file
file_type: bed
- name: signal.bed
signal.bed:
type: file
file_type: bed
additional_inputs:
- name: mapp_inputs
type: list
file_type: bin
outputs:
- name: scale_129.bed
scale_129.bed:
type: file
file_type: bed
- name: scale_194.bed
scale_194.bed:
type: file
file_type: bed
- name: scale_291.bed
scale_291.bed:
type: file
file_type: bed
- name: scale_437.bed
scale_437.bed:
type: file
file_type: bed
- name: scale_656.bed
scale_656.bed:
type: file
file_type: bed
- name: scale_985.bed
scale_985.bed:
type: file
file_type: bed
- name: scale_1477.bed
scale_1477.bed:
type: file
file_type: bed
- name: scale_2216.bed
scale_2216.bed:
type: file
file_type: bed
command: MUSIC
......@@ -53,7 +40,7 @@ music_punctate:
changeable: false
required: true
has_value: true
default: "$inputs.0"
default: "$prefix"
- "--peak_type":
type: string
changeable: false
......@@ -65,13 +52,13 @@ music_punctate:
changeable: false
required: true
has_value: true
default: "$inputs.1"
default: "$control.bed"
- "--signals":
type: file
changeable: false
required: true
has_value: true
default: "$inputs.2"
default: "$signal.bed"
- "--mapp":
type: rawfolder
changeable: true
......
peakranger_callpeak:
inputs:
- name: signal_bed
prefix:
type: string
control.bed:
type: file
file_type: bed
- name: control_bed
signal.bed:
type: file
file_type: bed
- name: prefix
type: string
additional_inputs: null
outputs:
- name: details
region_bed:
type: file
file_type: any
- name: region_bed
file_type: bed
summit_bed:
type: file
file_type: bed