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NGS_workflow_Sankemake_ABC_Final_empty.txt
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NGS_workflow_Sankemake_ABC_Final_empty.txt
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# Armadillo workflow
# Note: Saved on 2017-12-03 22:43:57
# Created on :2017-12-03 22:43:57
# Modified on:2017-12-03 22:44:23
# This file created on :2017-12-03 22:44:23
Object
#
#Sun Dec 03 22:44:23 EST 2017
ClassName=programs.loadFiles2
Connector0Output=True
Connector1Conditional=True
Description=Internal application to load a list of files into Armadillo.
EditorClassName=editors.loadFiles2Editor
HelpSupplementary=
InputAncestor=True
InputFile=Connector2
InternalArmadilloApplication=true
Keyword0=Load, Text File, Files,
Name=Load Genome
NoThread=true
Object=
ObjectID=Load Genome_311104337
ObjectType=Program
OutputFastaFile=Connector0
OutputFastqFile=Connector0
OutputGenomeFile=Connector0
OutputOutgroup=Connector0
OutputResults=Connector0
OutputSOLIDFile=Connector0
OutputText=Connector0
OutputTextFile=Connector0
Publication=NA
SampleWorkflow=LoadAllFile.properties.db
Similar0=LoadAllFile.properties
Similar1=LoadBlastDB.properties
Similar2=LoadSequence.properties
Similar3=LoadTree.properties
Tooltip=Load File(s)
Type=SYS\: Input
VerifyExitValue=false
WebServices=true
Website=NA
colorMode=BLUE
debug=false
defaultColor=BLUE
filename=/home/truc/test/armadillo2/data/properties/LoadFiles2.properties
nbInput=0
properties_id=1
x=16.0
y=59.0
Object
#
#Sun Dec 03 22:44:23 EST 2017
ClassName=programs.loadFiles2
Connector0Output=True
Connector1Conditional=True
Description=Internal application to load a list of files into Armadillo.
EditorClassName=editors.loadFiles2Editor
HelpSupplementary=
InputAncestor=True
InputFile=Connector2
InternalArmadilloApplication=true
Keyword0=Load, Text File, Files,
Name=Load Sample A
NoThread=true
Object=
ObjectID=Load Sample A_311104338
ObjectType=Program
OutputFastaFile=Connector0
OutputFastqFile=Connector0
OutputGenomeFile=Connector0
OutputOutgroup=Connector0
OutputResults=Connector0
OutputSOLIDFile=Connector0
OutputText=Connector0
OutputTextFile=Connector0
Publication=NA
SampleWorkflow=LoadAllFile.properties.db
Similar0=LoadAllFile.properties
Similar1=LoadBlastDB.properties
Similar2=LoadSequence.properties
Similar3=LoadTree.properties
Tooltip=Load File(s)
Type=SYS\: Input
VerifyExitValue=false
WebServices=true
Website=NA
colorMode=BLUE
debug=false
defaultColor=BLUE
filename=/home/truc/test/armadillo2/data/properties/LoadFiles2.properties
nbInput=0
properties_id=2
x=17.0
y=169.0
Object
#
#Sun Dec 03 22:44:23 EST 2017
ClassName=programs.loadFiles2
Connector0Output=True
Connector1Conditional=True
Description=Internal application to load a list of files into Armadillo.
EditorClassName=editors.loadFiles2Editor
HelpSupplementary=
InputAncestor=True
InputFile=Connector2
InternalArmadilloApplication=true
Keyword0=Load, Text File, Files,
Name=Load Sample B
NoThread=true
Object=
ObjectID=Load Sample B_311104339
ObjectType=Program
OutputFastaFile=Connector0
OutputFastqFile=Connector0
OutputGenomeFile=Connector0
OutputOutgroup=Connector0
OutputResults=Connector0
OutputSOLIDFile=Connector0
OutputText=Connector0
OutputTextFile=Connector0
Publication=NA
SampleWorkflow=LoadAllFile.properties.db
Similar0=LoadAllFile.properties
Similar1=LoadBlastDB.properties
Similar2=LoadSequence.properties
Similar3=LoadTree.properties
Tooltip=Load File(s)
Type=SYS\: Input
VerifyExitValue=false
WebServices=true
Website=NA
colorMode=BLUE
debug=false
defaultColor=BLUE
filename=/home/truc/test/armadillo2/data/properties/LoadFiles2.properties
nbInput=0
properties_id=3
x=14.0
y=283.0
Object
#
#Sun Dec 03 22:44:23 EST 2017
ClassName=programs.loadFiles2
Connector0Output=True
Connector1Conditional=True
Description=Internal application to load a list of files into Armadillo.
EditorClassName=editors.loadFiles2Editor
HelpSupplementary=
InputAncestor=True
InputFile=Connector2
InternalArmadilloApplication=true
Keyword0=Load, Text File, Files,
Name=Load Sample C
NoThread=true
Object=
ObjectID=Load Sample C_311104340
ObjectType=Program
OutputFastaFile=Connector0
OutputFastqFile=Connector0
OutputGenomeFile=Connector0
OutputOutgroup=Connector0
OutputResults=Connector0
OutputSOLIDFile=Connector0
OutputText=Connector0
OutputTextFile=Connector0
Publication=NA
SampleWorkflow=LoadAllFile.properties.db
Similar0=LoadAllFile.properties
Similar1=LoadBlastDB.properties
Similar2=LoadSequence.properties
Similar3=LoadTree.properties
Tooltip=Load File(s)
Type=SYS\: Input
VerifyExitValue=false
WebServices=true
Website=NA
colorMode=BLUE
debug=false
defaultColor=BLUE
filename=/home/truc/test/armadillo2/data/properties/LoadFiles2.properties
nbInput=0
properties_id=4
x=13.0
y=404.0
Object
#
#Sun Dec 03 22:44:23 EST 2017
Connector1Output=True
Name=FastqFile
Object=
ObjectID=FastqFile_311104341
ObjectType=Output
OutputFastqFile=True
colorMode=GREEN
defaultColor=GREEN
editorClass=editors.OutputEditor
outputType=FastqFile
output_fastqfile_id=0
properties_id=5
x=120.0
y=453.0
Object
#
#Sun Dec 03 22:44:23 EST 2017
Connector1Output=True
Name=FastqFile
Object=
ObjectID=FastqFile_311104342
ObjectType=Output
OutputFastqFile=True
colorMode=GREEN
defaultColor=GREEN
editorClass=editors.OutputEditor
outputType=FastqFile
output_fastqfile_id=0
properties_id=6
x=123.0
y=334.0
Object
#
#Sun Dec 03 22:44:23 EST 2017
Connector1Output=True
Name=FastqFile
Object=
ObjectID=FastqFile_311104343
ObjectType=Output
OutputFastqFile=True
colorMode=GREEN
defaultColor=GREEN
editorClass=editors.OutputEditor
outputType=FastqFile
output_fastqfile_id=0
properties_id=7
x=118.0
y=218.0
Object
#
#Sun Dec 03 22:44:23 EST 2017
Connector1Output=True
Name=FastaFile
Object=
ObjectID=FastaFile_311104344
ObjectType=Output
OutputFastaFile=True
colorMode=GREEN
defaultColor=GREEN
editorClass=editors.OutputEditor
outputType=FastaFile
output_fastafile_id=0
properties_id=8
x=120.0
y=116.0
Object
#
#Sun Dec 03 22:44:23 EST 2017
ClassName=programs.bwa_mem
ClusterProgramName=bwa
Connector0Output=True
Connector2=Fastq Pair-end
Connector3=Fastq
Connector4=Genome Ref, (Fasta)
Description=
DockerImage=jego/bwa
DockerInputs=/data/inputs/
DockerOutputs=/data/outputs/
EditorClassName=editors.bwa_memEditors
Executable=.srcprogramdocker
ExecutableCluster=bwa mem
ExecutableDocker=bwa mem
ExecutableLinux=./src/program/docker
ExecutableMacOSX=./src/program/docker
HelpSupplementary=BWA-MEM is an algorithms of BWA. BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.
InputFastaFile=Connector4
InputFastqFile=Connector3
InputGenomeFile=Connector4
Name=bwa mem
NoThread=false
NormalExitValue=0
Object=
ObjectID=bwa mem_311104345
ObjectType=Program
OneConnectorOnlyFor=4,2,3
OutputOutputText=Connector0
OutputResults=Connector0
OutputSamFile=Connector0
Publication=
Type=NGS\: Mapping
VerifyExitValue=false
Version=0.7.12
WebServices=
Website=
colorMode=ORANGE
debug=false
defaultColor=ORANGE
defaultPgrmValues=Default_Options<>true<>AO_AO1_t_JSpinnerValue<>1
filename=/home/truc/Dropbox/UQAM/0_MaitriseUQAM/Memoire/github/armadillo2-master/data/properties/bwa_mem.properties
input_fastafile_id40=0
input_fastqfile_id30=0
nbInput=3
properties_id=9
x=245.0
y=162.0
Object
#
#Sun Dec 03 22:44:23 EST 2017
ClassName=programs.bwa_mem
ClusterProgramName=bwa
Connector0Output=True
Connector2=Fastq Pair-end
Connector3=Fastq
Connector4=Genome Ref, (Fasta)
Description=
DockerImage=jego/bwa
DockerInputs=/data/inputs/
DockerOutputs=/data/outputs/
EditorClassName=editors.bwa_memEditors
Executable=.srcprogramdocker
ExecutableCluster=bwa mem
ExecutableDocker=bwa mem
ExecutableLinux=./src/program/docker
ExecutableMacOSX=./src/program/docker
HelpSupplementary=BWA-MEM is an algorithms of BWA. BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.
InputFastaFile=Connector4
InputFastqFile=Connector3
InputGenomeFile=Connector4
Name=bwa mem
NoThread=false
NormalExitValue=0
Object=
ObjectID=bwa mem_311104346
ObjectType=Program
OneConnectorOnlyFor=4,2,3
OutputOutputText=Connector0
OutputResults=Connector0
OutputSamFile=Connector0
Publication=
Type=NGS\: Mapping
VerifyExitValue=false
Version=0.7.12
WebServices=
Website=
colorMode=ORANGE
debug=false
defaultColor=ORANGE
defaultPgrmValues=Default_Options<>true<>AO_AO1_t_JSpinnerValue<>1
filename=/home/truc/Dropbox/UQAM/0_MaitriseUQAM/Memoire/github/armadillo2-master/data/properties/bwa_mem.properties
input_fastafile_id40=0
input_fastqfile_id30=0
nbInput=3
properties_id=10
x=245.0
y=274.0
Object
#
#Sun Dec 03 22:44:23 EST 2017
ClassName=programs.bwa_mem
ClusterProgramName=bwa
Connector0Output=True
Connector2=Fastq Pair-end
Connector3=Fastq
Connector4=Genome Ref, (Fasta)
Description=
DockerImage=jego/bwa
DockerInputs=/data/inputs/
DockerOutputs=/data/outputs/
EditorClassName=editors.bwa_memEditors
Executable=.srcprogramdocker
ExecutableCluster=bwa mem
ExecutableDocker=bwa mem
ExecutableLinux=./src/program/docker
ExecutableMacOSX=./src/program/docker
HelpSupplementary=BWA-MEM is an algorithms of BWA. BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.
InputFastaFile=Connector4
InputFastqFile=Connector3
InputGenomeFile=Connector4
Name=bwa mem
NoThread=false
NormalExitValue=0
Object=
ObjectID=bwa mem_311104347
ObjectType=Program
OneConnectorOnlyFor=4,2,3
OutputOutputText=Connector0
OutputResults=Connector0
OutputSamFile=Connector0
Publication=
Type=NGS\: Mapping
VerifyExitValue=false
Version=0.7.12
WebServices=
Website=
colorMode=ORANGE
debug=false
defaultColor=ORANGE
defaultPgrmValues=Default_Options<>true<>AO_AO1_t_JSpinnerValue<>1
filename=/home/truc/Dropbox/UQAM/0_MaitriseUQAM/Memoire/github/armadillo2-master/data/properties/bwa_mem.properties
input_fastafile_id40=0
input_fastqfile_id30=0
nbInput=3
properties_id=11
x=244.0
y=387.0
Object
#
#Sun Dec 03 22:44:23 EST 2017
Connector1Output=True
Name=SamFile
Object=
ObjectID=SamFile_311104348
ObjectType=Output
OutputSamFile=True
colorMode=GREEN
defaultColor=GREEN
editorClass=editors.OutputEditor
outputType=SamFile
output_samfile_id=0
properties_id=12
x=360.0
y=213.0
Object
#
#Sun Dec 03 22:44:23 EST 2017
AO_AO1_S_box=true
AO_AO1_b_box=true
Advanced_Options=true
ClassName=programs.samtools_view
ClusterProgramName=samtools
Connector0Output=True
Connector2=Sam, Bam, Cram File
Description=
DockerImage=jego/samtools
DockerInputs=/data/inputs/
DockerOutputs=/data/outputs/
EditorClassName=editors.samtools_viewEditors
Executable=.srcprogramdocker
ExecutableCluster=samtools view
ExecutableDocker=samtools view
ExecutableLinux=./src/program/docker
ExecutableMacOSX=./src/program/docker
HelpSupplementary=With no options or regions specified, prints all alignments in the specified input alignment file (in SAM, BAM, or CRAM format) to standard output in SAM format (with no header).
InputBamFile=Connector2
InputCramFile=Connector2
InputSamFile=Connector2
Name=samtools view
NoThread=false
NormalExitValue=0
Object=
ObjectID=samtools view_311104349
ObjectType=Program
OneConnectorOnlyFor=2
OutputBamFile=Connector0
OutputOutputText=Connector0
OutputResults=Connector0
OutputSamFile=Connector0
Publication=
Type=NGS\: SAMTOOLS
VerifyExitValue=false
Version=1.3.2
WebServices=
Website=
colorMode=ORANGE
debug=false
defaultColor=ORANGE
defaultPgrmValues=Default_Options<>true<>
filename=/home/truc/Dropbox/UQAM/0_MaitriseUQAM/Memoire/github/armadillo2-master/data/properties/samtools_view.properties
input_samfile_id20=0
nbInput=1
properties_id=13
x=460.0
y=159.0
Object
#
#Sun Dec 03 22:44:23 EST 2017
Connector1Output=True
Name=SamFile
Object=
ObjectID=SamFile_311104350
ObjectType=Output
OutputSamFile=True
colorMode=GREEN
defaultColor=GREEN
editorClass=editors.OutputEditor
outputType=SamFile
output_samfile_id=0
properties_id=14
x=347.0
y=327.0
Object
#
#Sun Dec 03 22:44:23 EST 2017
AO_AO1_S_box=true
AO_AO1_b_box=true
Advanced_Options=true
ClassName=programs.samtools_view
ClusterProgramName=samtools
Connector0Output=True
Connector2=Sam, Bam, Cram File
Description=
DockerImage=jego/samtools
DockerInputs=/data/inputs/
DockerOutputs=/data/outputs/
EditorClassName=editors.samtools_viewEditors
Executable=.srcprogramdocker
ExecutableCluster=samtools view
ExecutableDocker=samtools view
ExecutableLinux=./src/program/docker
ExecutableMacOSX=./src/program/docker
HelpSupplementary=With no options or regions specified, prints all alignments in the specified input alignment file (in SAM, BAM, or CRAM format) to standard output in SAM format (with no header).
InputBamFile=Connector2
InputCramFile=Connector2
InputSamFile=Connector2
Name=samtools view
NoThread=false
NormalExitValue=0
Object=
ObjectID=samtools view_311104351
ObjectType=Program
OneConnectorOnlyFor=2
OutputBamFile=Connector0
OutputOutputText=Connector0
OutputResults=Connector0
OutputSamFile=Connector0
Publication=
Type=NGS\: SAMTOOLS
VerifyExitValue=false
Version=1.3.2
WebServices=
Website=
colorMode=ORANGE
debug=false
defaultColor=ORANGE
defaultPgrmValues=Default_Options<>true<>
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#
#Sun Dec 03 22:44:23 EST 2017
Connector1Output=True
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#
#Sun Dec 03 22:44:23 EST 2017
Connector1Output=True
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Object
#
#Sun Dec 03 22:44:23 EST 2017
Connector1Output=True
Name=BamFile
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#Sun Dec 03 22:44:23 EST 2017
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AO_AO1_O_box=bam
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DockerOutputs=/data/outputs/
EditorClassName=editors.samtools_sortEditors
Executable=.srcprogramdocker
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ExecutableDocker=samtools sort
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ExecutableMacOSX=./src/program/docker
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Publication=
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colorMode=ORANGE
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#
#Sun Dec 03 22:44:23 EST 2017
Connector1Output=True
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#Sun Dec 03 22:44:23 EST 2017
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#Sun Dec 03 22:44:23 EST 2017
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#Sun Dec 03 22:44:23 EST 2017
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#
#Sun Dec 03 22:44:23 EST 2017
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#Sun Dec 03 22:44:23 EST 2017
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#Sun Dec 03 22:44:23 EST 2017
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#Sun Dec 03 22:44:23 EST 2017
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#Sun Dec 03 22:44:23 EST 2017
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#
#Sun Dec 03 22:44:23 EST 2017
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