| GDAC_CreateMergeDataFilesSDRF1 samplestamp | file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.HNSC.2012_10_24__11_21_08.samplestamp.txt |
| GDAC_CreateMergeDataFilesSDRF1 annotationids | cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg |
| GDAC_CreateMergeDataFilesSDRF1 datapathsfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/HNSC-Normal/2093670/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv |
| GDAC_MergeDataFiles2 inputfilelist filename | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/HNSC-Normal/2093670/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv |
| GDAC_MergeDataFiles2 output filename | HNSC-Normal |
| GDAC_MergeDataFiles2 row_column | row |
| GDAC_MergeDataFiles2 num_headers | 1 |
| GDAC_MergeDataFiles2 filetype | cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg.seg |
| Execution Times: | |
| Submitted: | 14:19:31 04-12-12 |
| Completed: | |
| Elapsed: | 04 hrs 38 mins 55 secs |
step 1. GDAC_CreateMergeDataFilesSDRF [id: 241362] 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:00467:12
| samplestamp | file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.HNSC.2012_10_24__11_21_08.samplestamp.txt |
| annotationids | cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg |
| sdrfName | |
| doNotCreateManifest | |
| datapathsfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/HNSC-Normal/2093670/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv |
| Output Files: | |
| HNSC.merger.sdrf.txt | |
| dcc_archive.properties | |
| .lsf.out | |
| dcc_archive_manifest.tsv | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 14:27:37 04-12-12 |
| Completed: | 14:47:29 04-12-12 |
| Elapsed: | 00 hrs 19 mins 52 secs |
step 2. GDAC_MergeDataFiles [id: 241363] 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/HNSC-Normal/2093670/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv |
| output filename | HNSC-Normal |
| row_column | row |
| num_headers | 1 |
| filetype | cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg.seg |
| Output Files: | |
| HNSC-Normal.cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg.seg.txt | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 14:27:37 04-12-12 |
| Completed: | 18:58:25 04-12-12 |
| Elapsed: | 04 hrs 30 mins 48 secs |