| GDAC_CreateMergeDataFilesSDRF1 samplestamp | file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.SKCM.2012_12_21__11_18_10.samplestamp.txt |
| GDAC_CreateMergeDataFilesSDRF1 annotationids | snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg |
| GDAC_CreateMergeDataFilesSDRF1 datapathsfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/SKCM/2172025/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv |
| GDAC_MergeDataFiles2 inputfilelist filename | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/SKCM/2172025/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv |
| GDAC_MergeDataFiles2 output filename | SKCM |
| GDAC_MergeDataFiles2 row_column | row |
| GDAC_MergeDataFiles2 num_headers | 1 |
| GDAC_MergeDataFiles2 filetype | snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg.seg |
| Execution Times: | |
| Submitted: | 22:35:23 21-12-12 |
| Completed: | |
| Elapsed: | 01 hrs 30 mins 16 secs |
step 1. GDAC_CreateMergeDataFilesSDRF [id: 275288] 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.SKCM.2012_12_21__11_18_10.samplestamp.txt |
| annotationids | snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg |
| sdrfName | |
| doNotCreateManifest | |
| datapathsfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/SKCM/2172025/GDAC_CreateMergeDataFilesSDRF1.datapathsfile.input.tsv |
| Output Files: | |
| dcc_archive.properties | |
| SKCM.merger.sdrf.txt | |
| .lsf.out | |
| dcc_archive_manifest.tsv | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 22:35:26 21-12-12 |
| Completed: | 23:21:54 21-12-12 |
| Elapsed: | 00 hrs 46 mins 27 secs |
step 2. GDAC_MergeDataFiles [id: 275289] 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/SKCM/2172025/GDAC_MergeDataFiles2.inputfilelist.filename.input.tsv |
| output filename | SKCM |
| row_column | row |
| num_headers | 1 |
| filetype | snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg.seg |
| Output Files: | |
| SKCM.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg.seg.txt | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 22:35:26 21-12-12 |
| Completed: | 00:05:37 22-12-12 |
| Elapsed: | 01 hrs 30 mins 10 secs |