Commit 07b45be1 authored by aknecht2's avatar aknecht2
Browse files

Fixed all issues with new yaml files for peak calling.

parent ee7d99f5
......@@ -110,6 +110,7 @@ peak_call:
outputs:
region_sorted.bed:
param_name: sorted_peaks
final_result: true
- peakranger_format_bed:
inputs:
summit.bed:
......@@ -117,6 +118,7 @@ peak_call:
outputs:
summit_sorted.bed:
param_name: sorted_peaks
final_result: true
- ccat[tool]:
- broad[peak_type]:
- ccat_callpeak:
......@@ -149,13 +151,15 @@ peak_call:
outputs:
region_sorted.bed:
param_name: sorted_peaks
final_result: true
- ccat_format_bed:
inputs:
significant.peak:
param_name: result_peaks:
param_name: result_peaks
outputs:
peak_sorted.bed:
param_name: sorted_peaks
final_result: true
- gem[tool]:
- narrow[peak_type]:
- gem_callpeak:
......@@ -231,6 +235,7 @@ peak_call:
outputs:
results_sorted.bed:
param_name: sorted_peaks
final_result: true
- broad[peak_type]:
- spp_nodups_broad:
inputs:
......@@ -252,6 +257,7 @@ peak_call:
outputs:
results_sorted.bed:
param_name: sorted_peaks
final_result: true
- macs2[tool]:
- narrow[peak_type]:
- macs2_narrow:
......@@ -276,6 +282,7 @@ peak_call:
outputs:
results_sorted.bed:
param_name: sorted_peaks
final_result: true
- broad[peak_type]:
- macs2_broad:
inputs:
......@@ -299,3 +306,4 @@ peak_call:
outputs:
results_sorted.bed:
param_name: sorted_peaks
final_result: true
......@@ -10,7 +10,7 @@ ccat_callpeak:
file_type: bed
chrom.sizes:
type: file
file_type: bed
file_type: chrom_sizes
outputs:
significant_peak:
type: file
......@@ -18,7 +18,7 @@ ccat_callpeak:
significant_region:
type: file
file_type: bed
top_1000000_peak:
top_100000_peak:
type: file
file_type: bed
ccat_log:
......
......@@ -3,7 +3,6 @@ cp:
input_file:
type: file
file_type: any
additional_inputs: null
outputs:
output_file:
type: file
......
......@@ -3,7 +3,6 @@ peakranger_format_bed:
result_peaks:
type: file
file_type: bed
additional_inputs: null
outputs:
sorted_peaks:
type: file
......
samtools_remove_duplicates:
inputs:
- name: sorted_bam
sorted_bam:
type: file
file_type: bam
additional_inputs: null
file_type: bam
outputs:
- name: no_dups_bam
no_dups_bam:
type: file
file_type: bam
command: samtools
......@@ -31,8 +30,8 @@ samtools_remove_duplicates:
changeable: false
required: true
has_value: true
default: $outputs.0
- "$inputs.0":
default: $no_dups_bam
- "$sorted_bam":
type: file
changeable: false
required: true
......
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