From 5189f83a03a0b40e35dfd838c195fbcd8f77d767 Mon Sep 17 00:00:00 2001
From: aknecht2 <aknecht2@unl.edu>
Date: Tue, 30 May 2017 16:52:48 -0500
Subject: [PATCH] Updated all workflow job yaml files for peak calling jobs.
---
.../jobs/params/cat_awk_sort_peaks.yaml | 9 ++--
chipathlon/jobs/params/ccat_callpeak.yaml | 41 +++++++------------
chipathlon/jobs/params/ccat_format_bed.yaml | 9 ++--
chipathlon/jobs/params/cp.yaml | 12 +++---
chipathlon/jobs/params/gem_callpeak.yaml | 39 +++++++-----------
chipathlon/jobs/params/macs2_broad.yaml | 25 +++++------
chipathlon/jobs/params/macs2_narrow.yaml | 25 +++++------
chipathlon/jobs/params/music_broad.yaml | 38 ++++++-----------
chipathlon/jobs/params/music_narrow.yaml | 26 ++++--------
chipathlon/jobs/params/music_punctate.yaml | 41 +++++++------------
.../jobs/params/peakranger_callpeak.yaml | 32 ++++++---------
.../jobs/params/peakranger_format_bed.yaml | 8 ++--
.../jobs/params/sort_awk_sort_peaks.yaml | 9 ++--
chipathlon/jobs/params/spp_nodups_broad.yaml | 24 +++++------
chipathlon/jobs/params/spp_nodups_narrow.yaml | 24 +++++------
.../jobs/params/zcat_awk_sort_peaks.yaml | 9 ++--
16 files changed, 145 insertions(+), 226 deletions(-)
diff --git a/chipathlon/jobs/params/cat_awk_sort_peaks.yaml b/chipathlon/jobs/params/cat_awk_sort_peaks.yaml
index b619349..cb56f0c 100644
--- a/chipathlon/jobs/params/cat_awk_sort_peaks.yaml
+++ b/chipathlon/jobs/params/cat_awk_sort_peaks.yaml
@@ -1,21 +1,20 @@
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
diff --git a/chipathlon/jobs/params/ccat_callpeak.yaml b/chipathlon/jobs/params/ccat_callpeak.yaml
index 6bb20b4..259732b 100644
--- a/chipathlon/jobs/params/ccat_callpeak.yaml
+++ b/chipathlon/jobs/params/ccat_callpeak.yaml
@@ -1,58 +1,47 @@
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
diff --git a/chipathlon/jobs/params/ccat_format_bed.yaml b/chipathlon/jobs/params/ccat_format_bed.yaml
index 7a461c3..a9a63da 100644
--- a/chipathlon/jobs/params/ccat_format_bed.yaml
+++ b/chipathlon/jobs/params/ccat_format_bed.yaml
@@ -1,11 +1,10 @@
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: $sorted_peaks
walltime: 60
memory: 8000
cores: 1
diff --git a/chipathlon/jobs/params/cp.yaml b/chipathlon/jobs/params/cp.yaml
index 3b50d68..ded9305 100644
--- a/chipathlon/jobs/params/cp.yaml
+++ b/chipathlon/jobs/params/cp.yaml
@@ -1,21 +1,21 @@
cp:
inputs:
- - name: peak_result
+ input_file:
type: file
- file_type: bed
+ file_type: any
additional_inputs: null
outputs:
- - name: tag_align_result
+ output_file:
type: file
- file_type: bed
+ file_type: any
command: cp
arguments:
- - "$inputs.0":
+ - "$input_file":
type: file
changeable: false
required: true
has_value: false
- - "$outputs.0":
+ - "$output_file":
type: file
changeable: false
required: true
diff --git a/chipathlon/jobs/params/gem_callpeak.yaml b/chipathlon/jobs/params/gem_callpeak.yaml
index ef52ca8..d2c9b05 100644
--- a/chipathlon/jobs/params/gem_callpeak.yaml
+++ b/chipathlon/jobs/params/gem_callpeak.yaml
@@ -1,35 +1,26 @@
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
diff --git a/chipathlon/jobs/params/macs2_broad.yaml b/chipathlon/jobs/params/macs2_broad.yaml
index e2961b8..786128a 100644
--- a/chipathlon/jobs/params/macs2_broad.yaml
+++ b/chipathlon/jobs/params/macs2_broad.yaml
@@ -1,26 +1,21 @@
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
diff --git a/chipathlon/jobs/params/macs2_narrow.yaml b/chipathlon/jobs/params/macs2_narrow.yaml
index 9a04a88..5bbb8ba 100644
--- a/chipathlon/jobs/params/macs2_narrow.yaml
+++ b/chipathlon/jobs/params/macs2_narrow.yaml
@@ -1,26 +1,21 @@
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: $prefix
- "-g":
type: string
changeable: true
diff --git a/chipathlon/jobs/params/music_broad.yaml b/chipathlon/jobs/params/music_broad.yaml
index 9d04186..fe8f3cf 100644
--- a/chipathlon/jobs/params/music_broad.yaml
+++ b/chipathlon/jobs/params/music_broad.yaml
@@ -1,45 +1,33 @@
music_broad:
inputs:
- - name: prefix
+ prefix:
type: string
-
- - name: control.bed
+ control.bed:
type: file
file_type: bed
-
- - name: signal.bed
+ signal.bed:
type: file
file_type: bed
- additional_inputs:
- - name: mapp_inputs
- type: list
- file_type: bin
outputs:
- - name: scale_1459.bed
+ scale_1459.bed:
type: file
file_type: bed
-
- - name: scale_2189.bed
+ scale_2189.bed:
type: file
file_type: bed
-
- - name: scale_3284.bed
+ scale_3284.bed:
type: file
file_type: bed
-
- - name: scale_4926.bed
+ scale_4926.bed:
type: file
file_type: bed
-
- - name: scale_7389.bed
+ scale_7389.bed:
type: file
file_type: bed
-
- - name: scale_11084.bed
+ scale_11084.bed:
type: file
file_type: bed
-
- - name: scale_16626.bed
+ scale_16626.bed:
type: file
file_type: bed
command: chip-job-music
@@ -49,7 +37,7 @@ music_broad:
changeable: false
required: true
has_value: true
- default: "$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: "$signal.bed"
- "--mapp":
type: rawfolder
changeable: true
diff --git a/chipathlon/jobs/params/music_narrow.yaml b/chipathlon/jobs/params/music_narrow.yaml
index e61122f..4675200 100644
--- a/chipathlon/jobs/params/music_narrow.yaml
+++ b/chipathlon/jobs/params/music_narrow.yaml
@@ -1,29 +1,21 @@
music_narrow:
inputs:
- - name: prefix
+ prefix:
type: string
-
- - name: control.bed
+ control.bed:
type: file
file_type: bed
-
- - name: signal.bed
+ signal.bed:
type: file
file_type: bed
- additional_inputs:
- - name: mapp_inputs
- type: list
- file_type: bin
outputs:
- - name: scale_129.bed
+ scale_129.bed:
type: file
file_type: bed
-
- - name: scale_194.bed
+ scale_194.bed:
type: file
file_type: bed
-
- - name: scale_291.bed
+ scale_291.bed:
type: file
file_type: bed
command: chip-job-music
@@ -33,7 +25,7 @@ music_narrow:
changeable: false
required: true
has_value: true
- default: "$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: "$signal.bed"
- "--mapp":
type: rawfolder
changeable: true
diff --git a/chipathlon/jobs/params/music_punctate.yaml b/chipathlon/jobs/params/music_punctate.yaml
index 7930802..0d346d6 100644
--- a/chipathlon/jobs/params/music_punctate.yaml
+++ b/chipathlon/jobs/params/music_punctate.yaml
@@ -1,49 +1,36 @@
music_punctate:
inputs:
- - name: prefix
+ prefix:
type: string
-
- - name: control.bed
+ control.bed:
type: file
file_type: bed
-
- - name: signal.bed
+ signal.bed:
type: file
file_type: bed
- additional_inputs:
- - name: mapp_inputs
- type: list
- file_type: bin
outputs:
- - name: scale_129.bed
+ scale_129.bed:
type: file
file_type: bed
-
- - name: scale_194.bed
+ scale_194.bed:
type: file
file_type: bed
-
- - name: scale_291.bed
+ scale_291.bed:
type: file
file_type: bed
-
- - name: scale_437.bed
+ scale_437.bed:
type: file
file_type: bed
-
- - name: scale_656.bed
+ scale_656.bed:
type: file
file_type: bed
-
- - name: scale_985.bed
+ scale_985.bed:
type: file
file_type: bed
-
- - name: scale_1477.bed
+ scale_1477.bed:
type: file
file_type: bed
-
- - name: scale_2216.bed
+ scale_2216.bed:
type: file
file_type: bed
command: MUSIC
@@ -53,7 +40,7 @@ music_punctate:
changeable: false
required: true
has_value: true
- default: "$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
diff --git a/chipathlon/jobs/params/peakranger_callpeak.yaml b/chipathlon/jobs/params/peakranger_callpeak.yaml
index 6eec39f..7b1c9a9 100644
--- a/chipathlon/jobs/params/peakranger_callpeak.yaml
+++ b/chipathlon/jobs/params/peakranger_callpeak.yaml
@@ -1,32 +1,26 @@
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
-
- - name: summit_bed
+ details:
type: file
file_type: bed
-
- - name: log
+ log:
type: stdout
- file_type: log
+ file_type: bed
command: peakranger
arguments:
- "ranger":
@@ -50,19 +44,19 @@ peakranger_callpeak:
changeable: false
required: true
has_value: true
- default: $inputs.0
+ default: $prefix
- "-c":
type: file
changeable: false
required: true
has_value: true
- default: $inputs.1
+ default: $control.bed
- "-o":
type: string
changeable: false
required: true
has_value: true
- default: $inputs.2
+ default: $signal.bed
- "-p":
type: numeric
changeable: true
diff --git a/chipathlon/jobs/params/peakranger_format_bed.yaml b/chipathlon/jobs/params/peakranger_format_bed.yaml
index 2c78772..8d48917 100644
--- a/chipathlon/jobs/params/peakranger_format_bed.yaml
+++ b/chipathlon/jobs/params/peakranger_format_bed.yaml
@@ -1,11 +1,11 @@
peakranger_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-peakranger-format
@@ -15,13 +15,13 @@ peakranger_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: $sorted_peaks
walltime: 60
memory: 4000
cores: 1
diff --git a/chipathlon/jobs/params/sort_awk_sort_peaks.yaml b/chipathlon/jobs/params/sort_awk_sort_peaks.yaml
index 10f7120..510f3f0 100644
--- a/chipathlon/jobs/params/sort_awk_sort_peaks.yaml
+++ b/chipathlon/jobs/params/sort_awk_sort_peaks.yaml
@@ -1,21 +1,20 @@
sort_awk_sort_peaks:
inputs:
- - name: peak_result
+ peak_results:
type: file
file_type: bed
- additional_inputs: null
outputs:
- - name: sorted_peaks
+ sorted_peaks:
type: file
file_type: bed
command: chip-job-sort-peak
arguments:
- - "$inputs.0":
+ - "$peak_results":
type: file
changeable: false
required: true
has_value: false
- - "$outputs.0":
+ - "$sorted_peaks":
type: file
changeable: false
required: true
diff --git a/chipathlon/jobs/params/spp_nodups_broad.yaml b/chipathlon/jobs/params/spp_nodups_broad.yaml
index b31b1c2..6a9c1d5 100644
--- a/chipathlon/jobs/params/spp_nodups_broad.yaml
+++ b/chipathlon/jobs/params/spp_nodups_broad.yaml
@@ -1,23 +1,19 @@
spp_nodups_broad:
inputs:
- - name: signal_tag_align
+ signal.tagAlign:
type: file
file_type: bed
-
- - name: control_tag_align
+ control.tagAlign:
type: file
file_type: bed
- additional_inputs: null
outputs:
- - name: peak_result
+ peak_results:
type: file
file_type: bed
-
- - name: plots_pdf
+ plots_pdf:
type: file
file_type: pdf
-
- - name: score
+ score:
type: file
file_type: ccscore
command: run_spp_nodups
@@ -27,13 +23,13 @@ spp_nodups_broad:
changeable: false
required: true
has_value: true
- default: $inputs.0
+ default: $signal.tagAlign
- "-i=":
type: file
changeable: false
required: true
has_value: true
- default: $inputs.1
+ default: $control.tagAlign
- "-npeak=":
type: numeric
changeable: true
@@ -57,19 +53,19 @@ spp_nodups_broad:
changeable: false
required: true
has_value: true
- default: $outputs.0
+ default: $peak_results
- "-savp=":
type: file
changeable: false
required: true
has_value: true
- default: $outputs.1
+ default: $plots_pdf
- "-out=":
type: file
changeable: false
required: true
has_value: true
- default: $outputs.2
+ default: $score
- "-fdr=":
type: numeric
changeable: true
diff --git a/chipathlon/jobs/params/spp_nodups_narrow.yaml b/chipathlon/jobs/params/spp_nodups_narrow.yaml
index 6808e5c..a220a25 100644
--- a/chipathlon/jobs/params/spp_nodups_narrow.yaml
+++ b/chipathlon/jobs/params/spp_nodups_narrow.yaml
@@ -1,23 +1,19 @@
spp_nodups_narrow:
inputs:
- - name: signal_tag_align
+ signal.tagAlign:
type: file
file_type: bed
-
- - name: control_tag_align
+ control.tagAlign:
type: file
file_type: bed
- additional_inputs: null
outputs:
- - name: peak_result
+ peak_results:
type: file
file_type: bed
-
- - name: plots_pdf
+ plots_pdf:
type: file
file_type: pdf
-
- - name: score
+ score:
type: file
file_type: ccscore
command: run_spp_nodups
@@ -27,13 +23,13 @@ spp_nodups_narrow:
changeable: false
required: true
has_value: true
- default: $inputs.0
+ default: $signal.tagAlign
- "-i=":
type: file
changeable: false
required: true
has_value: true
- default: $inputs.1
+ default: $control.tagAlign
- "-npeak=":
type: numeric
changeable: true
@@ -57,19 +53,19 @@ spp_nodups_narrow:
changeable: false
required: true
has_value: true
- default: $outputs.0
+ default: $peak_results
- "-savp=":
type: file
changeable: false
required: true
has_value: true
- default: $outputs.1
+ default: $plots_pdf
- "-out=":
type: file
changeable: false
required: true
has_value: true
- default: $outputs.2
+ default: $score
- "-fdr=":
type: numeric
changeable: true
diff --git a/chipathlon/jobs/params/zcat_awk_sort_peaks.yaml b/chipathlon/jobs/params/zcat_awk_sort_peaks.yaml
index 11d7786..6570258 100644
--- a/chipathlon/jobs/params/zcat_awk_sort_peaks.yaml
+++ b/chipathlon/jobs/params/zcat_awk_sort_peaks.yaml
@@ -1,21 +1,20 @@
zcat_awk_sort_peaks:
inputs:
- - name: result_peaks
+ result_peaks:
type: file
file_type: bed
- additional_inputs: null
outputs:
- - name: sorted_peaks
+ sorted_peaks:
type: file
file_type: bed
command: chip-job-zcat-peak
arguments:
- - "$inputs.0":
+ - "$result_peaks":
type: file
changeable: false
required: true
has_value: false
- - "$outputs.0":
+ - "$sorted_peaks":
type: file
changeable: false
required: true
--
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