Permalink
| --- | |
| # Example file for specifying run information to bcbio_nextgen.py | |
| # In a fully Galaxy automated setup this information can be retrieved | |
| # from the Galaxy server based on user inputs. This YAML files allows you to | |
| # run the automated pipeline separately or from other external programs | |
| # If your folder naming is not standard Illumina style | |
| # (110729_SN728_0036_A81UJUABXX) you can optionally specify a date and a unique name | |
| # to use for naming the output files and project directories. | |
| fc_date: '110812' | |
| fc_name: unique_name | |
| # Directory to upload final results to. Also supports Galaxy and S3 upload. | |
| upload: | |
| dir: ../final | |
| details: | |
| # For each flowcell, you specify either the lane if the files follow standard | |
| # naming conventions (1_110729_A81UJUABXX) or the names of the files if they | |
| # are differently named. Can specify either one file for single end or two for | |
| # paired. | |
| - files: [/path/to/1_1-fastq.txt, /path/to/1_2-fastq.txt] | |
| description: 'Sample 1' | |
| genome_build: GRCh37 | |
| analysis: variant2 | |
| algorithm: | |
| aligner: novoalign | |
| variantcaller: gatk |