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Table of contents

Component summary

Name Version Inputs Outputs Description
Array2Folder 1.1 array, template folder Transforms an array into binary folder.
ArrayCombiner 1.1 array1, ..., array20 array Combines multiple arrays into one using set operations on array keys.
ArrayConstructor 1.0 file1, ..., file99 array Constructs an array from atomic elements.
ArrayExtractor 1.0 array file1, ..., file9 Extracts elements from an array.
AssignFileDset 1.0 destDirs, files, restrictions fileDests Assigns destination paths in local file system for files to be downloaded from CGHub and other sources so that space requirements are met.
CGHubXMLCSV2Map 1.1 csv map Transforms the CSV table transformed by XML2CSV from an XML obtained by CGQuery into the sequence file map table.
Folder2Array 1.2 folder1, ..., folder9 array Constructs an array from folder contents.
Func2SeqRefTable 1.1 fileReference, manifest SeqFileMap Transforms fileReference table by GetFromTcga into the Sequence Files Map table understood by SelectSeqFromTcga.
GetFromTcga 1.6.11 archivesQuery, aliquotsQuery, aliquots, connection dataFiles, aliquotReference, fileReference, report, array, readme, readme_dcc, description TCGA data importer.
INPUT   in Imports an external input file or directory to the pipeline.
JSelectTCGAPhenFiles 1.0 selection, authFile, keyFile includeArchives, excludeArchives, parentFolders Transforms a query to TCGA download web/ftp site or to its mirror into the table of annotated phenotype TCGA data archives (either tar.gz or txt files or folders).
OUTPUT   out out Exports a result file or directory to an output directory.
Pause   Halts pipeline execution.
StringInput   in Turns a string into a file usable in the pipeline.
TCGAClinStorScanner 1.0.1 tables, keyDiseaseMapping aliquot, analyte, drug, patient, portion, radiation, sample, slide Reads array of tables with the TCGA Clinical data, chooses the latest data out of them and generates tables for: patients, samples, portions, analytes, aliquots, drugs, radiation, slides.
TCGASeqStorMap 1.0 dirs, authFile, keyFile fileReference Scans directories with the TCGA sequence data downloaded from DbGaP NCBI NIH site and builds the map of annotated sequence files.
URLGet 1.2 authFile, keyFile, downList files Gets array of remote files.
URLInput   in Imports an external input file to a workflow script from a URL source.
URLTCGABrowse 1.2 authFile, keyFile files Gets the listing of a remote directory.

Function summary

Name Version Inputs Outputs Description
CGDownload 1.1 content_specifier, credential_file Downloads BAM files from CGHub basing on an XML specification file obtained by CGQuery.
CGHubQueryMap 1.1 queryTable content_specifier, content_specifiers, seq_files_map Searches for the sequence data at CGHub and builds up the reference map table of selected map files.
CGHubSeqStorScanner 1.1 dirs, authFile, keyFile fileReference Reads directories with BAM files downloaded from CGHub and generates the reference map likewise TCGASeqStorMap.
CGHubXML2Map 1.1 xml seq_files_map Transforms a response from CGHub from XML format into file reference map CSV table.
CGQuery 1.0 queryTable content_specifier, content_specifiers Searches for the sequence data at CGHub.
SelectSeqFromTcga 1.3 connect, label2path, selection, authFile, keyFile rawFiles, alignedFiles, auxFiles, bamIndexFiles, bamHeaderFiles, bamXMLFiles, rawFilesTable, alignedFilesTable Imports TCGA sequence files organized either in dbgap ncbi or in the tcga-data nci site manners.
SRA2FASTQ 1.1 Transforms a Sequence Read Archive (SRA) file (presented by the National Center for Biotechnology Information) into BAM files.
SyncTCGAPhenMirror 1.1 selection, authFile, keyFile new, updated, unchanged, localFiles, download Synchronizes TCGA phenotype mirror directory with the original source.
SyncTCGASeqMirror 1.1.1 destDirs, credential_file, fileReference, queryTable, restrictions fileReference Synchronizes TCGA sequence mirror directory with the original source (CGHub portal): first checks for any updates in CGHub for the files currently stored in the mirror, then verifies if any new downloads for the selection criteria in queryTable are available at CGHub, then downloads what necessary.

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