| GDAC_CreateMergeDataFilesSDRF1 samplestamp | file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.BRCA.2012_10_24__11_21_08.samplestamp.txt |
| GDAC_CreateMergeDataFilesSDRF1 annotationids | rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__exon_quantification__data |
| GDAC_CreateMergeDataFilesSDRF1 datapathsfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BRCA/1971011/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv |
| GDAC_MergeDataFiles2 inputfilelist filename | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BRCA/1971011/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv |
| GDAC_MergeDataFiles2 output filename | BRCA |
| GDAC_MergeDataFiles2 row_column | column |
| GDAC_MergeDataFiles2 num_headers | 1 |
| GDAC_MergeDataFiles2 filetype | rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__exon_quantification__data.data |
| Execution Times: | |
| Submitted: | 08:19:29 04-11-12 |
| Completed: | |
| Elapsed: | 00 hrs 51 mins 06 secs |
step 1. GDAC_CreateMergeDataFilesSDRF [id: 218150] This module parses a samplestamp based on an input annotation id and creates an SDRF file as output.
urn:lsid:broadinstitute.org:cancer.genome.analysis:00467:11
| samplestamp | file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.BRCA.2012_10_24__11_21_08.samplestamp.txt |
| annotationids | rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__exon_quantification__data |
| sdrfName | |
| doNotCreateManifest | |
| datapathsfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BRCA/1971011/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv |
| Output Files: | |
| BRCA.merger.sdrf.txt | |
| dcc_archive.properties | |
| .lsf.out | |
| dcc_archive_manifest.tsv | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 08:20:19 04-11-12 |
| Completed: | 08:25:59 04-11-12 |
| Elapsed: | 00 hrs 05 mins 40 secs |
step 2. GDAC_MergeDataFiles [id: 218151] Merges row or column oriented text datatable files, validating that the headers match.
urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
| inputfilelist filename | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BRCA/1971011/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv |
| output filename | BRCA |
| row_column | column |
| num_headers | 1 |
| filetype | rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__exon_quantification__data.data |
| Output Files: | |
| BRCA.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__exon_quantification__data.data.txt | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 08:20:19 04-11-12 |
| Completed: | 09:10:29 04-11-12 |
| Elapsed: | 00 hrs 50 mins 09 secs |