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NGS_workflow_Sankemake_AB_Final_empty.txt
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NGS_workflow_Sankemake_AB_Final_empty.txt
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# Armadillo workflow
# Note: Saved on 2017-12-03 22:44:32
# Created on :2017-12-03 22:43:57
# Modified on:2017-12-03 22:44:49
# This file created on :2017-12-03 22:44:49
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#Sun Dec 03 22:44:49 EST 2017
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#Sun Dec 03 22:44:49 EST 2017
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#Sun Dec 03 22:44:49 EST 2017
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Similar2=LoadSequence.properties
Similar3=LoadTree.properties
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Type=SYS\: Input
VerifyExitValue=false
WebServices=true
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colorMode=BLUE
debug=false
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#
#Sun Dec 03 22:44:49 EST 2017
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#Sun Dec 03 22:44:49 EST 2017
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#Sun Dec 03 22:44:49 EST 2017
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Object
#
#Sun Dec 03 22:44:49 EST 2017
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DockerOutputs=/data/outputs/
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ExecutableMacOSX=./src/program/docker
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ObjectType=Program
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OutputOutputText=Connector0
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OutputSamFile=Connector0
Publication=
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debug=false
defaultColor=ORANGE
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input_fastafile_id40=0
input_fastqfile_id30=0
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properties_id=7
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Object
#
#Sun Dec 03 22:44:49 EST 2017
ClassName=programs.bwa_mem
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ExecutableMacOSX=./src/program/docker
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Object=
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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
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#Sun Dec 03 22:44:49 EST 2017
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#
#Sun Dec 03 22:44:49 EST 2017
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VerifyExitValue=false
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colorMode=ORANGE
debug=false
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#
#Sun Dec 03 22:44:49 EST 2017
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#Sun Dec 03 22:44:49 EST 2017
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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).
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InputCramFile=Connector2
InputSamFile=Connector2
Name=samtools view
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Object=
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ObjectType=Program
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OutputSamFile=Connector0
Publication=
Type=NGS\: SAMTOOLS
VerifyExitValue=false
Version=1.3.2
WebServices=
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colorMode=ORANGE
debug=false
defaultColor=ORANGE
defaultPgrmValues=Default_Options<>true<>
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#Sun Dec 03 22:44:49 EST 2017
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#Sun Dec 03 22:44:49 EST 2017
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#Sun Dec 03 22:44:49 EST 2017
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#
#Sun Dec 03 22:44:49 EST 2017
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#Sun Dec 03 22:44:49 EST 2017
AO_CVCO__multiallelicHYPHENSYMBOLcaller_box=true
AO_FFO__outputHYPHENSYMBOLtype_JComboBoxValue=v
AO_FFO__outputHYPHENSYMBOLtype_box=v
AO_IOO__variantsHYPHENSYMBOLonly_box=true
Advanced_Options=true
ClassName=programs.bcftools_call
ClusterProgramName=bcftools
Connector0Output=True
Connector2=VCF, BCF
Description=
DockerImage=jego/samtools
DockerInputs=/data/inputs/
DockerOutputs=/data/outputs/
EditorClassName=editors.bcftools_callEditors
Executable=.srcprogramdocker
ExecutableCluster=bcftools call
ExecutableDocker=bcftools call
ExecutableLinux=./src/program/docker
ExecutableMacOSX=./src/program/docker
HelpSupplementary=
InputBCFFile=Connector2
InputVCFFile=Connector2
Name=bcftools call
NoThread=false
NormalExitValue=0
Object=
ObjectID=bcftools call_311104358
ObjectType=Program
OneConnectorOnlyFor=2
OutputBCFFile=Connector0
OutputOutputText=Connector0
OutputResults=Connector0
OutputVCFFile=Connector0
Publication=
SolelyConnectors=2
Type=NGS\: BCFTOOLS
VerifyExitValue=false
Version=1.3.1
WebServices=
Website=
colorMode=ORANGE
debug=false
defaultColor=ORANGE
defaultPgrmValues=Default_Options<>true<>AO_FFO__outputHYPHENSYMBOLtype_JComboBoxValue<>u<>
filename=/home/truc/Dropbox/UQAM/0_MaitriseUQAM/Memoire/github/armadillo2-master/data/properties/bcftools_call.properties
input_bcffile_id20=0
nbInput=1
properties_id=17
x=1098.0
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Object
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#Sun Dec 03 22:44:49 EST 2017
Connector1Output=True
Name=VCFFile
Object=
ObjectID=VCFFile_311104359
ObjectType=Output
OutputVCFFile=True
ParentID=bcftools call_1810114858
colorMode=GREEN
defaultColor=GREEN
editorClass=editors.OutputEditor
outputType=VCFFile
output_vcffile_id=0
properties_id=18
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Object
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#Sun Dec 03 22:44:49 EST 2017
AO_AO1_O_JComboBoxValue=bam
AO_AO1_O_box=bam
AO_AO1_T_JTextFieldValue=PREFIX
Advanced_Options=true
ClassName=programs.samtools_sort
ClusterProgramName=samtools
Connector0Output=True
Connector2=Sam, Bam, Cram File
Description=
DockerImage=jego/samtools
DockerInputs=/data/inputs/
DockerOutputs=/data/outputs/
EditorClassName=editors.samtools_sortEditors
Executable=.srcprogramdocker
ExecutableCluster=samtools sort
ExecutableDocker=samtools sort
ExecutableLinux=./src/program/docker
ExecutableMacOSX=./src/program/docker
HelpSupplementary=Sort alignments by leftmost coordinates, or by read name when -n is used. An appropriate @HD-SO sort order header tag will be added or an existing one updated if necessary.
InputBamFile=Connector2
InputCramFile=Connector2
InputSamFile=Connector2
Name=samtools sort
NoThread=false
NormalExitValue=0
Object=
ObjectID=samtools sort_311104361
ObjectType=Program
OneConnectorOnlyFor=2
OutputBamFile=Connector0
OutputCramFile=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<>AO_AO1_T_JTextFieldValue<>PREFIX<>AO_AO1_O_JComboBoxValue<>bam<>
filename=/home/truc/Dropbox/UQAM/0_MaitriseUQAM/Memoire/github/armadillo2-master/data/properties/samtools_sort.properties
input_bamfile_id20=0
nbInput=1
properties_id=19
x=672.0
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Object
#
#Sun Dec 03 22:44:49 EST 2017
Connector1Output=True
Name=BamFile
Object=
ObjectID=BamFile_311104362
ObjectType=Output
OutputBamFile=True
colorMode=GREEN
defaultColor=GREEN
editorClass=editors.OutputEditor
outputType=BamFile
output_bamfile_id=0
properties_id=20
x=780.0
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Object
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#Sun Dec 03 22:44:49 EST 2017
AO_OO__BCF_box=true
Advanced_Options=true
ClassName=programs.samtools_mpileup
ClusterProgramName=samtools
Connector0Output=True
Connector2=Bam, (Bai)
Connector3=faidx-indexed reference
Connector4=Bed or position list,
Description=Alignment records are grouped by sample (SM) identifiers in @RG header lines. If sample identifiers are absent, each input file is regarded as one sample. In the pileup format (without -u or -g), each line represents a genomic position, consisting of chromosome name, 1-based coordinate, reference base, the number of reads covering the site, read bases, base qualities and alignment mapping qualities. Information on match, mismatch, indel, strand, mapping quality and start and end of a read are all encoded at the read base column. At this column, a dot stands for a match to the reference base on the forward strand, a comma for a match on the reverse strand, a '>' or '<' for a reference skip, `ACGTN' for a mismatch on the forward strand and `acgtn' for a mismatch on the reverse strand. A pattern `\\+[0-9]+[ACGTNacgtn]+' indicates there is an insertion between this reference position and the next reference position. The length of the insertion is given by the integer in the pattern, followed by the inserted sequence. Similarly, a pattern `-[0-9]+[ACGTNacgtn]+' represents a deletion from the reference. The deleted bases will be presented as `*' in the following lines. Also at the read base column, a symbol `^' marks the start of a read. The ASCII of the character following `^' minus 33 gives the mapping quality. A symbol `$' marks the end of a read segment. Note that there are two orthogonal ways to specify locations in the input file; via -r region and -l file. The former uses (and requires) an index to do random access while the latter streams through the file contents filtering out the specified regions, requiring no index. The two may be used in conjunction. For example a BED file containing locations of genes in chromosome 20 could be specified using -r 20 -l chr20.bed, meaning that the index is used to find chromosome 20 and then it is filtered for the regions listed in the bed file.
DockerImage=jego/samtools
DockerInputs=/data/inputs/
DockerOutputs=/data/outputs/
EditorClassName=editors.samtools_mpileupEditors
Executable=.srcprogramdocker
ExecutableCluster=samtools mpileup
ExecutableDocker=samtools mpileup
ExecutableLinux=./src/program/docker
ExecutableMacOSX=./src/program/docker
HelpSupplementary=samtools mpileup [-EBugp] [-C capQcoef] [-r reg] [-f in.fa] [-l list] [-Q minBaseQ] [-q minMapQ] in.bam [in2.bam [...]] Generate VCF, BCF or pileup for one or multiple BAM files.
InputBamBaiFile=Connector2
InputBamFile=Connector2
InputBedFile=Connector4
InputFastaFile=Connector3
Name=samtools mpileup
NoThread=false
NormalExitValue=0
Object=
ObjectID=samtools mpileup_311104469
ObjectType=Program
OneConnectorOnlyFor=4,3
OutputBCFFile=Connector0
OutputBamFile=Connector0
OutputOutputText=Connector0
OutputResults=Connector0
OutputVCFFile=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_mpileup.properties
input_bamfile_id20=0
input_bamfile_id21=0
input_fastafile_id30=0
nbInput=3
properties_id=21
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Object
#
#Sun Dec 03 22:44:49 EST 2017
Connector1Output=True
Name=BCFFile
Object=
ObjectID=BCFFile_311104470
ObjectType=Output
OutputBCFFile=True
colorMode=GREEN
defaultColor=GREEN
editorClass=editors.OutputEditor
outputType=BCFFile
output_bcffile_id=0
properties_id=22
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Connector
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#Sun Dec 03 22:44:49 EST 2017
Name=connector_-14606047
dest_properties_id=4
destination=0
displayEdge=false
notDeletabled=true
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source_properties_id=3
Connector
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#Sun Dec 03 22:44:49 EST 2017
Name=connector_-14540254
dest_properties_id=5
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displayEdge=false
notDeletabled=true
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source_properties_id=2
Connector
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#Sun Dec 03 22:44:49 EST 2017
Name=connector_-14474461
dest_properties_id=6
destination=0
displayEdge=false
notDeletabled=true
source=0
source_properties_id=1
Connector
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#Sun Dec 03 22:44:49 EST 2017
Name=connector_-14408668
dest_properties_id=7
destination=4
displayEdge=false
notDeletabled=false
source=1
source_properties_id=6
Connector
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#Sun Dec 03 22:44:49 EST 2017
Name=connector_-14342875
dest_properties_id=8
destination=4
displayEdge=false
notDeletabled=false
source=1
source_properties_id=6
Connector
#
#Sun Dec 03 22:44:49 EST 2017
Name=connector_-14211289
dest_properties_id=7
destination=3
displayEdge=false
notDeletabled=false
source=1
source_properties_id=5
Connector
#
#Sun Dec 03 22:44:49 EST 2017
Name=connector_-14145496
dest_properties_id=8
destination=3
displayEdge=false
notDeletabled=false
source=1
source_properties_id=4
Connector
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#Sun Dec 03 22:44:49 EST 2017
Name=connector_-14013910
dest_properties_id=9
destination=0
displayEdge=false
notDeletabled=true
source=0
source_properties_id=7
Connector
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#Sun Dec 03 22:44:49 EST 2017
Name=connector_-13948117
dest_properties_id=10
destination=2
displayEdge=false
notDeletabled=false
source=1
source_properties_id=9
Connector
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#Sun Dec 03 22:44:49 EST 2017
Name=connector_-13882324
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destination=0
displayEdge=false
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Connector
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#Sun Dec 03 22:44:49 EST 2017
Name=connector_-13816531
dest_properties_id=12
destination=2
displayEdge=false
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source=1
source_properties_id=11
Connector
#
#Sun Dec 03 22:44:49 EST 2017
Name=connector_-13619152
dest_properties_id=13
destination=0
displayEdge=false
notDeletabled=true
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Connector
#
#Sun Dec 03 22:44:49 EST 2017
Name=connector_-13553359
dest_properties_id=15
destination=2
displayEdge=false
notDeletabled=false
source=1
source_properties_id=13
Connector
#
#Sun Dec 03 22:44:49 EST 2017
Name=connector_-13487566
dest_properties_id=14
destination=0
displayEdge=false
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source=0
source_properties_id=12
Connector
#
#Sun Dec 03 22:44:49 EST 2017
Name=connector_-13421773
dest_properties_id=19
destination=2
displayEdge=false
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source=1
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Connector
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#Sun Dec 03 22:44:49 EST 2017
Name=connector_-13224394
dest_properties_id=21
destination=3
displayEdge=false
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source=1
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Connector
#
#Sun Dec 03 22:44:49 EST 2017
Name=connector_-13158601
dest_properties_id=16
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displayEdge=false
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Connector
#
#Sun Dec 03 22:44:49 EST 2017
Name=connector_-13092808
dest_properties_id=21
destination=2
displayEdge=false
notDeletabled=false
source=1
source_properties_id=16
Connector
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#Sun Dec 03 22:44:49 EST 2017
Name=connector_-13027015
dest_properties_id=20
destination=0
displayEdge=false
notDeletabled=true
source=0
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Connector
#
#Sun Dec 03 22:44:49 EST 2017
Name=connector_-12961222
dest_properties_id=21
destination=2
displayEdge=false
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source=1
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Connector
#
#Sun Dec 03 22:44:49 EST 2017
Name=connector_-12763843
dest_properties_id=22
destination=0
displayEdge=false
notDeletabled=true
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source_properties_id=21
Connector
#