| GDAC_CreateMergeDataFilesSDRF1 samplestamp | file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.COADREAD.2012_09_13__00_00_04.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/COADREAD/1708474/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv |
| GDAC_MergeDataFiles2 inputfilelist filename | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/COADREAD/1708474/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv |
| GDAC_MergeDataFiles2 output filename | COADREAD |
| 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: | 13:29:45 14-09-12 |
| Completed: | |
| Elapsed: | 00 hrs 01 mins 20 secs |
step 1. GDAC_CreateMergeDataFilesSDRF [id: 165261] 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.COADREAD.2012_09_13__00_00_04.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/COADREAD/1708474/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv |
| Output Files: | |
| missingFirehoseIds.txt | |
| COADREAD.merger.sdrf.txt | |
| dcc_archive.properties | |
| dcc_archive_manifest.tsv | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 13:29:46 14-09-12 |
| Completed: | 13:30:23 14-09-12 |
| Elapsed: | 00 hrs 00 mins 36 secs |
step 2. GDAC_MergeDataFiles [id: 165262] 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/COADREAD/1708474/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv |
| output filename | COADREAD |
| row_column | row |
| num_headers | 1 |
| filetype | cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg.seg |
| Output Files: | |
| COADREAD.cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg.seg.txt | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 13:29:46 14-09-12 |
| Completed: | 13:31:03 14-09-12 |
| Elapsed: | 00 hrs 01 mins 17 secs |