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refresh with CWL upgrader #28

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refresh with CWL upgrader #28

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98 changes: 31 additions & 67 deletions cwl_awsem_v1/add-hic-normvector-to-mcool.cwl
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Original file line number Diff line number Diff line change
@@ -1,67 +1,31 @@
{
"cwlVersion": "v1.0",
"class": "CommandLineTool",
"inputs": [
{
"type": [
"null",
"File"
],
"id": "#input_hic",
"inputBinding": {
"separate": true,
"position": 1
}
},
{
"type": [
"null",
"File"
],
"id": "#input_mcool",
"inputBinding": {
"separate": true,
"position": 2
}
},
{
"type": [
"null",
"string"
],
"id": "#outdir",
"inputBinding": {
"separate": true,
"position": 3
},
"default": "."
}
],
"requirements": [
{
"class": "InlineJavascriptRequirement"
}
],
"hints": [
{
"class": "DockerRequirement",
"dockerPull": "duplexa/4dn-hic:v42.1"
}
],
"arguments": [],
"outputs": [
{
"type": [
"null",
"File"
],
"outputBinding": {
"glob": "$(inputs.outdir + '/' + '*.mcool')"
},
"id": "#mcool_with_hicnorm"
}
],
"baseCommand": [
"run-add-hicnormvector-to-mcool.sh"
]
}
cwlVersion: v1.0
class: CommandLineTool
requirements:
InlineJavascriptRequirement: {}
hints:
DockerRequirement:
dockerPull: duplexa/4dn-hic:v42.1
inputs:
input_hic:
type: File?
inputBinding:
position: 1
separate: true
input_mcool:
type: File?
inputBinding:
position: 2
separate: true
outdir:
type: string?
default: .
inputBinding:
position: 3
separate: true
baseCommand: run-add-hicnormvector-to-mcool.sh
outputs:
mcool_with_hicnorm:
type: File?
outputBinding:
glob: $(inputs.outdir + '/' + '*.mcool')

122 changes: 40 additions & 82 deletions cwl_awsem_v1/addfragtopairs.cwl
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Original file line number Diff line number Diff line change
@@ -1,82 +1,40 @@
{
"inputs": [
{
"inputBinding": {
"separate": true,
"position": 1
},
"id": "#input_pairs",
"type": [
"null",
"File"
]
},
{
"inputBinding": {
"separate": true,
"position": 2
},
"id": "#restriction_file",
"type": [
"null",
"File"
]
},
{
"inputBinding": {
"separate": true,
"position": 3
},
"id": "#outprefix",
"type": [
"null",
"string"
],
"default": "out"
},
{
"inputBinding": {
"separate": true,
"position": 0,
"prefix": "-0"
},
"id": "#donothing",
"type": [
"boolean"
],
"default": false
}
],
"hints": [
{
"class": "DockerRequirement",
"dockerPull": "duplexa/4dn-hic:v42.1"
}
],
"cwlVersion": "v1.0",
"outputs": [
{
"outputBinding": {
"glob": "$(inputs.outprefix + '.ff.pairs.gz')"
},
"type": [
"null",
"File"
],
"secondaryFiles": [
".px2"
],
"id": "#pairs_with_frags"
}
],
"class": "CommandLineTool",
"arguments": [],
"requirements": [
{
"class": "InlineJavascriptRequirement"
}
],
"baseCommand": [
"run-addfrag2pairs.sh"
]
}
cwlVersion: v1.0
class: CommandLineTool
requirements:
InlineJavascriptRequirement: {}
hints:
DockerRequirement:
dockerPull: duplexa/4dn-hic:v42.1
inputs:
input_pairs:
type: File?
inputBinding:
position: 1
separate: true
restriction_file:
type: File?
inputBinding:
position: 2
separate: true
outprefix:
type: string?
default: out
inputBinding:
position: 3
separate: true
donothing:
type: boolean
default: false
inputBinding:
position: 0
prefix: '-0'
separate: true
baseCommand: run-addfrag2pairs.sh
outputs:
pairs_with_frags:
type: File?
secondaryFiles:
- .px2
outputBinding:
glob: $(inputs.outprefix + '.ff.pairs.gz')

175 changes: 55 additions & 120 deletions cwl_awsem_v1/bam2hdf5.cwl
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Original file line number Diff line number Diff line change
@@ -1,120 +1,55 @@
{
"requirements": [
{
"class": "InlineJavascriptRequirement"
}
],
"hints": [
{
"class": "DockerRequirement",
"dockerPull": "duplexa/hictool-bam2hdf5:v2"
}
],
"inputs": [
{
"type": [
"File"
],
"inputBinding": {
"separate": false,
"position": 1
},
"id": "#input_bam1"
},
{
"type": [
"File"
],
"inputBinding": {
"separate": false,
"position": 2
},
"id": "#input_bam2"
},
{
"type": [
"null",
"string"
],
"inputBinding": {
"position": 4,
"valueFrom": {
"script": "$job.inputs.output_dir || '.'",
"engine": "#cwl-js-engine",
"class": "Expression"
},
"separate": false
},
"id": "#output_dir"
},
{
"type": [
"null",
"File"
],
"inputBinding": {
"separate": false,
"position": 3
},
"id": "#RE_bed"
}
],
"baseCommand": [
"run.sh"
],
"outputs": [
{
"type": [
"null",
"File"
],
"outputBinding": {
"glob": "$(inputs.output_dir + '/fend_object.hdf5')"
},
"id": "#fend_object_hdf5"
},
{
"type": [
"null",
"File"
],
"outputBinding": {
"glob": "$(inputs.output_dir + '/HiC_data_object.hdf5')"
},
"id": "#HiC_data_object_hdf5"
},
{
"type": [
"null",
"File"
],
"outputBinding": {
"glob": "$(inputs.output_dir + '/HiC_distance_function.hdf5')"
},
"id": "#HiC_distance_function_hdf5"
},
{
"type": [
"null",
"File"
],
"outputBinding": {
"glob": "$(inputs.output_dir + '/HiC_norm_binning.hdf5')"
},
"id": "#HiC_norm_binning_hdf5"
},
{
"type": [
"null",
"File"
],
"outputBinding": {
"glob": "$(inputs.output_dir + '/HiC_project_object.hdf5' )"
},
"id": "#HiC_project_object_hdf5"
}
],
"arguments": [],
"class": "CommandLineTool",
"cwlVersion": "v1.0"
}
cwlVersion: v1.0
class: CommandLineTool
requirements:
InlineJavascriptRequirement: {}
hints:
DockerRequirement:
dockerPull: duplexa/hictool-bam2hdf5:v2
inputs:
input_bam1:
type: File
inputBinding:
position: 1
separate: false
input_bam2:
type: File
inputBinding:
position: 2
separate: false
output_dir:
type: string?
inputBinding:
position: 4
valueFrom:
engine: '#cwl-js-engine'
class: Expression
script: $job.inputs.output_dir || '.'
separate: false
RE_bed:
type: File?
inputBinding:
position: 3
separate: false
baseCommand: run.sh
outputs:
fend_object_hdf5:
type: File?
outputBinding:
glob: $(inputs.output_dir + '/fend_object.hdf5')
HiC_data_object_hdf5:
type: File?
outputBinding:
glob: $(inputs.output_dir + '/HiC_data_object.hdf5')
HiC_distance_function_hdf5:
type: File?
outputBinding:
glob: $(inputs.output_dir + '/HiC_distance_function.hdf5')
HiC_norm_binning_hdf5:
type: File?
outputBinding:
glob: $(inputs.output_dir + '/HiC_norm_binning.hdf5')
HiC_project_object_hdf5:
type: File?
outputBinding:
glob: $(inputs.output_dir + '/HiC_project_object.hdf5' )

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