Pipeline Input Name	Archive Result File REF	Comment [TCGA Archive Name]	Protocol REF	Data Transformation Name	Derived Data File	Comment [TCGA Data Type]	Comment [TCGA Data Level]	Comment [TCGA File Type]	Comment [TCGA Archive Name]	Comment [TCGA Include for Analysis]
clusterFilesTar	clusterFiles.tar	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00362:21	ParadigmWithCopyNumber_2012122100	inferredPathwayLevels.tab	Pathways-Mutations_CopyNumber_Methylation_Expression	Level_4	text	gdac.broadinstitute.org_BRCA-TP.ParadigmWithCopyNumber.Level_4.2012122100.0.0	yes
clusterFilesTar	clusterFiles.tar	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00362:21	ParadigmWithCopyNumber_2012122100	finalParams.txt	Pathways-Mutations_CopyNumber_Methylation_Expression	Level_4	text	gdac.broadinstitute.org_BRCA-TP.ParadigmWithCopyNumber.Level_4.2012122100.0.0	yes
configEM	configEM.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00362:21	ParadigmWithCopyNumber_2012122100	inferredPathwayLevels.tab	Pathways-Mutations_CopyNumber_Methylation_Expression	Level_4	text	gdac.broadinstitute.org_BRCA-TP.ParadigmWithCopyNumber.Level_4.2012122100.0.0	yes
configEM	configEM.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00362:21	ParadigmWithCopyNumber_2012122100	finalParams.txt	Pathways-Mutations_CopyNumber_Methylation_Expression	Level_4	text	gdac.broadinstitute.org_BRCA-TP.ParadigmWithCopyNumber.Level_4.2012122100.0.0	yes
templateEMScript	templateEM.sh	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00362:21	ParadigmWithCopyNumber_2012122100	inferredPathwayLevels.tab	Pathways-Mutations_CopyNumber_Methylation_Expression	Level_4	text	gdac.broadinstitute.org_BRCA-TP.ParadigmWithCopyNumber.Level_4.2012122100.0.0	yes
templateEMScript	templateEM.sh	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00362:21	ParadigmWithCopyNumber_2012122100	finalParams.txt	Pathways-Mutations_CopyNumber_Methylation_Expression	Level_4	text	gdac.broadinstitute.org_BRCA-TP.ParadigmWithCopyNumber.Level_4.2012122100.0.0	yes
config	config.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00362:21	ParadigmWithCopyNumber_2012122100	inferredPathwayLevels.tab	Pathways-Mutations_CopyNumber_Methylation_Expression	Level_4	text	gdac.broadinstitute.org_BRCA-TP.ParadigmWithCopyNumber.Level_4.2012122100.0.0	yes
config	config.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00362:21	ParadigmWithCopyNumber_2012122100	finalParams.txt	Pathways-Mutations_CopyNumber_Methylation_Expression	Level_4	text	gdac.broadinstitute.org_BRCA-TP.ParadigmWithCopyNumber.Level_4.2012122100.0.0	yes
jobsScript	jobs.sh	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00362:21	ParadigmWithCopyNumber_2012122100	inferredPathwayLevels.tab	Pathways-Mutations_CopyNumber_Methylation_Expression	Level_4	text	gdac.broadinstitute.org_BRCA-TP.ParadigmWithCopyNumber.Level_4.2012122100.0.0	yes
jobsScript	jobs.sh	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00362:21	ParadigmWithCopyNumber_2012122100	finalParams.txt	Pathways-Mutations_CopyNumber_Methylation_Expression	Level_4	text	gdac.broadinstitute.org_BRCA-TP.ParadigmWithCopyNumber.Level_4.2012122100.0.0	yes
paramsFile	params0.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00362:21	ParadigmWithCopyNumber_2012122100	inferredPathwayLevels.tab	Pathways-Mutations_CopyNumber_Methylation_Expression	Level_4	text	gdac.broadinstitute.org_BRCA-TP.ParadigmWithCopyNumber.Level_4.2012122100.0.0	yes
paramsFile	params0.txt	N/A	urn:lsid:broadinstitute.org:cancer.genome.analysis:00362:21	ParadigmWithCopyNumber_2012122100	finalParams.txt	Pathways-Mutations_CopyNumber_Methylation_Expression	Level_4	text	gdac.broadinstitute.org_BRCA-TP.ParadigmWithCopyNumber.Level_4.2012122100.0.0	yes
