| ae8d3b3 | Stephen Piccolo | 27 August 2021, 16:31:27 UTC | Added show/hide example links | 27 August 2021, 16:31:27 UTC |
| a2bb701 | Stephen Piccolo | 15 June 2021, 15:43:06 UTC | Create LICENSE | 15 June 2021, 15:43:06 UTC |
| 510933a | Stephen Piccolo | 25 May 2021, 19:24:32 UTC | Added link to the preprint. | 25 May 2021, 19:24:32 UTC |
| 8cad63c | Stephen Piccolo | 25 May 2021, 19:17:56 UTC | Added link to our preprint and cleaned up wording | 25 May 2021, 19:17:56 UTC |
| 0baa371 | Stephen Piccolo | 25 May 2021, 19:13:33 UTC | Added ability to edit steps. | 25 May 2021, 19:13:33 UTC |
| 2b104db | Stephen Piccolo | 19 April 2021, 16:21:35 UTC | Making sure secondary files line up for workflow inputs or steps to be matching with each other. | 19 April 2021, 16:21:35 UTC |
| 2b0828e | Stephen Piccolo | 15 April 2021, 17:51:24 UTC | Added more secondary files for fasta_file so they will be compatible with align_fastq.cwl | 15 April 2021, 17:51:24 UTC |
| 3196da1 | Stephen Piccolo | 15 April 2021, 17:17:05 UTC | Making sure secondary files are compatible when matching workflow inputs | 15 April 2021, 17:17:05 UTC |
| f20fb26 | Stephen Piccolo | 13 April 2021, 21:06:33 UTC | Updated title | 13 April 2021, 21:06:33 UTC |
| 173b35f | Stephen Piccolo | 13 April 2021, 21:06:02 UTC | Updated title | 13 April 2021, 21:06:02 UTC |
| 565a79f | Stephen Piccolo | 13 April 2021, 17:25:13 UTC | Migrated to production version of VueJS | 13 April 2021, 17:25:13 UTC |
| d9627fe | Stephen Piccolo | 13 April 2021, 17:19:49 UTC | Added secondary files for VCF recalibration | 13 April 2021, 17:19:49 UTC |
| a80eb1f | Stephen Piccolo | 13 April 2021, 17:05:38 UTC | Reorganized directories | 13 April 2021, 17:05:38 UTC |
| fec5d1e | Stephen Piccolo | 13 April 2021, 17:03:07 UTC | Renamed directory | 13 April 2021, 17:03:07 UTC |
| df77364 | Stephen Piccolo | 13 April 2021, 17:00:11 UTC | Fixed issue where output file format was not specified correctly. | 13 April 2021, 17:00:11 UTC |
| b9d6a2e | Stephen Piccolo | 12 April 2021, 15:38:15 UTC | Added .idx secondary file for VCF inputs | 12 April 2021, 15:38:15 UTC |
| e8a9e3a | Stephen Piccolo | 10 April 2021, 03:19:29 UTC | Added .dict as a secondary file. | 10 April 2021, 03:19:29 UTC |
| 357cf65 | Stephen Piccolo | 09 April 2021, 14:13:35 UTC | Archived old version of somatic variant calling example | 09 April 2021, 14:13:35 UTC |
| 9009635 | Stephen Piccolo | 08 April 2021, 23:25:29 UTC | Updating somatic variants example. | 08 April 2021, 23:25:29 UTC |
| 9c726cc | Stephen Piccolo | 08 April 2021, 23:03:52 UTC | Added ability to specify name of temporary file. | 08 April 2021, 23:03:52 UTC |
| 7a8674f | Stephen Piccolo | 06 April 2021, 16:37:55 UTC | Removed support for directories as a way to simplify the logic. | 06 April 2021, 16:37:55 UTC |
| f7821a3 | Stephen Piccolo | 06 April 2021, 16:29:30 UTC | Added error checking to avoid workflow input identifiers with special characters. | 06 April 2021, 16:29:30 UTC |
| 3e68d2e | Stephen Piccolo | 05 April 2021, 22:03:45 UTC | Only surround data values with quotes if they are not numeric. | 05 April 2021, 22:03:45 UTC |
| 99270b7 | Stephen Piccolo | 05 April 2021, 21:53:42 UTC | Fixed issue with special characters in object values by surrounding them with quotation marks. | 05 April 2021, 21:53:42 UTC |
| f3a2193 | Stephen Piccolo | 05 April 2021, 21:44:15 UTC | Updated run script | 05 April 2021, 21:44:15 UTC |
| 4b95b3a | Stephen Piccolo | 05 April 2021, 21:34:58 UTC | Minor tweaks to improve user experience. Updated somatic variants workflow example. | 05 April 2021, 21:34:58 UTC |
| 7e5658d | Stephen Piccolo | 31 March 2021, 18:44:13 UTC | Modified examples based on latest version | 31 March 2021, 18:44:13 UTC |
| 50ecdf2 | Stephen Piccolo | 30 March 2021, 16:09:56 UTC | Cleaned up examples to be consistent with workflow.html behavior | 30 March 2021, 16:09:56 UTC |
| 3bc0b97 | Stephen Piccolo | 30 March 2021, 15:57:59 UTC | Modified secondary file example to have two steps | 30 March 2021, 15:57:59 UTC |
| 01e0f90 | Stephen Piccolo | 26 March 2021, 22:25:57 UTC | Standardized terminology in example files. Added ability to specify name of new workflow inputs. | 26 March 2021, 22:25:57 UTC |
| df917ae | Stephen Piccolo | 26 March 2021, 22:25:31 UTC | Standardized terminology in example files. Added ability to specify name of new workflow inputs. | 26 March 2021, 22:25:31 UTC |
| bcc5e72 | Stephen Piccolo | 02 March 2021, 20:34:13 UTC | Added output for reference genome files. | 02 March 2021, 20:34:13 UTC |
| 24c3cce | Stephen Piccolo | 02 March 2021, 16:46:21 UTC | Created a separate workflow for preparing reference files. Made download tool specific to FASTQ. | 02 March 2021, 16:46:21 UTC |
| 272e659 | Stephen Piccolo | 02 March 2021, 16:45:50 UTC | Created a separate workflow for preparing reference files. Made download tool specific to FASTQ. | 02 March 2021, 16:45:50 UTC |
| 03f2614 | Stephen Piccolo | 02 March 2021, 16:43:54 UTC | Created a separate workflow for preparing reference files. Made download tool specific to FASTQ. | 02 March 2021, 16:43:54 UTC |
| 020cffd | Stephen Piccolo | 02 March 2021, 16:43:14 UTC | Created a separate workflow for preparing reference files. Made download tool specific to FASTQ. | 02 March 2021, 16:43:14 UTC |
| 887f4c9 | Stephen Piccolo | 02 March 2021, 16:41:44 UTC | Created a separate workflow for preparing reference files. Made download tool specific to FASTQ. | 02 March 2021, 16:41:44 UTC |
| a973a09 | Stephen Piccolo | 01 March 2021, 19:10:24 UTC | Revised wording about using random file name. | 01 March 2021, 19:10:24 UTC |
| 6b3de2e | Stephen Piccolo | 26 February 2021, 15:55:31 UTC | Fixed issues with example files. Changed one tool to be easier to work with workflows. Output_File supports secondary files. Matching previous steps is filtered by file format. | 26 February 2021, 15:55:31 UTC |
| 2a67b88 | Stephen Piccolo | 24 February 2021, 15:50:35 UTC | Fixed bug where step outputs weren't specified properly when there were multiple outputs. | 24 February 2021, 15:50:35 UTC |
| 5944294 | Stephen Piccolo | 24 February 2021, 15:50:15 UTC | Fixed bug where step outputs weren't specified properly when there were multiple outputs. | 24 February 2021, 15:50:15 UTC |
| 9d2bc20 | Stephen Piccolo | 23 February 2021, 16:58:00 UTC | Changed ID for consistency. | 23 February 2021, 16:58:00 UTC |
| 192bd1c | Stephen Piccolo | 23 February 2021, 16:56:55 UTC | Changed ID for consistency. | 23 February 2021, 16:56:55 UTC |
| f271ea7 | Stephen Piccolo | 23 February 2021, 16:54:41 UTC | Moved files to new directories for clarity | 23 February 2021, 16:54:41 UTC |
| 7dce962 | Stephen Piccolo | 23 February 2021, 16:53:59 UTC | Fixed bug where outputs were not being handled properly. | 23 February 2021, 16:53:59 UTC |
| 0ffe5b0 | Stephen Piccolo | 19 February 2021, 21:27:45 UTC | Added logic to generate random file name rather than specifying input for the file name. This will be used mostly for intermediate output files. Also updated examples accordingly. | 19 February 2021, 21:27:45 UTC |
| 79acc07 | Stephen Piccolo | 17 February 2021, 17:35:13 UTC | Show description next to the outputs in workflow.html. | 17 February 2021, 17:35:13 UTC |
| 333681f | Stephen Piccolo | 12 February 2021, 18:25:50 UTC | Tweaked the way output files are named and updated examples accordingly. | 12 February 2021, 18:25:50 UTC |
| 4615417 | Stephen Piccolo | 09 February 2021, 16:46:27 UTC | Removed comment characters | 09 February 2021, 16:46:27 UTC |
| 597b78c | Stephen Piccolo | 09 February 2021, 16:29:34 UTC | Changed directory name | 09 February 2021, 16:29:34 UTC |
| eb42574 | Stephen Piccolo | 09 February 2021, 16:28:07 UTC | Added note about YouTube video | 09 February 2021, 16:28:07 UTC |
| 928a08d | Stephen Piccolo | 09 February 2021, 16:23:09 UTC | Merge branch 'master' of github.com:srp33/ToolJig | 09 February 2021, 16:23:09 UTC |
| 771bf3d | Stephen Piccolo | 09 February 2021, 16:23:03 UTC | Minor tweak after re-testing somatic scripts | 09 February 2021, 16:23:03 UTC |
| e94ac46 | Stephen Piccolo | 08 February 2021, 15:59:40 UTC | Showing tool description for inputs when creating step. | 08 February 2021, 15:59:40 UTC |
| 3c41fac | Stephen Piccolo | 05 February 2021, 20:42:52 UTC | Removed temporary comments | 05 February 2021, 20:42:52 UTC |
| 5441478 | Stephen Piccolo | 05 February 2021, 20:41:13 UTC | Updated instructions for running example commands. | 05 February 2021, 20:41:13 UTC |
| aaf50e1 | Stephen Piccolo | 05 February 2021, 20:23:43 UTC | Made examples consistent for Python version | 05 February 2021, 20:23:43 UTC |
| f923c9f | Stephen Piccolo | 04 February 2021, 21:05:01 UTC | Tweak descriptions for consistency | 04 February 2021, 21:05:01 UTC |
| 02421a4 | Stephen Piccolo | 04 February 2021, 20:59:05 UTC | Modify all *job.yml to *objects.yml to be consistent with the apps. | 04 February 2021, 20:59:05 UTC |
| 231af9f | Stephen Piccolo | 04 February 2021, 20:30:19 UTC | Formatting workflow outputs the same as inputs (using id). | 04 February 2021, 20:30:19 UTC |
| 4f9e0b4 | Stephen Piccolo | 03 February 2021, 20:53:58 UTC | Now using secondary files in output as well. | 03 February 2021, 20:53:58 UTC |
| 38c1a65 | Stephen Piccolo | 03 February 2021, 19:50:22 UTC | Added ability to create input-objects file in workflow. Standardized some things. | 03 February 2021, 19:50:22 UTC |
| e7c543f | Stephen Piccolo | 01 February 2021, 17:05:16 UTC | Better validation of secondary files. Sort inputs, outputs, etc. in the user interface. | 01 February 2021, 17:05:16 UTC |
| 405e9c4 | Stephen Piccolo | 29 January 2021, 20:30:53 UTC | Updated workflow examples. Updated workflow.html to support secondary files. | 29 January 2021, 20:30:53 UTC |
| 0f1bafd | Stephen Piccolo | 26 January 2021, 23:12:32 UTC | Fixed some bugs | 26 January 2021, 23:12:32 UTC |
| 1119287 | Stephen Piccolo | 19 January 2021, 22:07:53 UTC | Improved logic to check CWL version. Added ability to upload existing workflow file. | 19 January 2021, 22:07:53 UTC |
| 61ccaa7 | Stephen Piccolo | 13 January 2021, 19:09:24 UTC | Changed to a square root example | 13 January 2021, 19:09:24 UTC |
| 207026b | Stephen Piccolo | 29 December 2020, 18:03:24 UTC | Fixed bugs in workflow.html and standardized functionality between tool.html and workflow.html | 29 December 2020, 18:03:24 UTC |
| 771d66a | Stephen Piccolo | 03 December 2020, 14:07:29 UTC | Added some error checking. | 03 December 2020, 14:07:29 UTC |
| 0e2a5f0 | Stephen Piccolo | 01 October 2020, 04:02:40 UTC | Updated version to 1.2. Make sure tool CWL files uploaded to workflow.html are tools and not workflows. | 01 October 2020, 04:02:40 UTC |
| be27d76 | Stephen Piccolo | 28 September 2020, 21:26:00 UTC | Improving workflow logic and examples | 28 September 2020, 21:26:00 UTC |
| 65186ea | Stephen Piccolo | 04 August 2020, 22:05:26 UTC | Merge branch 'master' of https://github.com/srp33/ToolJig | 04 August 2020, 22:05:26 UTC |
| 00cd379 | Stephen Piccolo | 04 August 2020, 22:05:18 UTC | Saving latest versions as a checkpoint | 04 August 2020, 22:05:18 UTC |
| 2e9ada3 | Stephen Piccolo | 16 July 2020, 18:04:31 UTC | Set theme jekyll-theme-minimal | 16 July 2020, 18:04:31 UTC |
| b7d8bd8 | Stephen Piccolo | 16 July 2020, 18:01:05 UTC | Created simple workflow example and created stud of workflow tool. | 16 July 2020, 18:01:05 UTC |
| ff06140 | Stephen Piccolo | 15 July 2020, 23:31:03 UTC | Updated all the somatic examples so that file format is specified in input-object files. | 15 July 2020, 23:31:03 UTC |
| cd97f15 | Stephen Piccolo | 15 July 2020, 03:10:52 UTC | Minor tweaks | 15 July 2020, 03:10:52 UTC |
| fc2a96e | Stephen Piccolo | 13 July 2020, 23:51:28 UTC | Merge branch 'master' of https://github.com/srp33/ToolJig | 13 July 2020, 23:51:28 UTC |
| 5827c44 | Stephen Piccolo | 13 July 2020, 23:51:21 UTC | Fixed bug in which secondaryFiles were being listed when none were specified. Updated examples to match output from ToolJig. | 13 July 2020, 23:51:21 UTC |
| 2a14945 | Stephen Piccolo | 13 July 2020, 22:20:33 UTC | Updated examples to match ToolJig output | 13 July 2020, 22:20:33 UTC |
| 76aa035 | Stephen Piccolo | 13 July 2020, 21:52:04 UTC | Updated examples to be consistent with ToolJig output | 13 July 2020, 21:52:04 UTC |
| 225e225 | Stephen Piccolo | 13 July 2020, 21:51:20 UTC | Merge branch 'master' of https://github.com/srp33/ToolJig | 13 July 2020, 21:51:20 UTC |
| e95e55d | Stephen Piccolo | 13 July 2020, 21:51:14 UTC | Updated examples to be consistent with ToolJig output | 13 July 2020, 21:51:14 UTC |
| b6d97a2 | Stephen Piccolo | 13 July 2020, 21:43:52 UTC | Updated deseq2 to the latest version of Bioconductor | 13 July 2020, 21:43:52 UTC |
| b82ced0 | Stephen Piccolo | 13 July 2020, 21:43:11 UTC | Updated deseq2 to the latest version of Bioconductor | 13 July 2020, 21:43:11 UTC |
| 8e8e10c | Stephen Piccolo | 13 July 2020, 21:13:06 UTC | Updated examples to be consistent with ToolJig output | 13 July 2020, 21:13:06 UTC |
| 4f82e8e | Stephen Piccolo | 13 July 2020, 20:56:47 UTC | Tweaked README files | 13 July 2020, 20:56:47 UTC |
| c5f2816 | Stephen Piccolo | 13 July 2020, 20:56:16 UTC | Tweaked README files | 13 July 2020, 20:56:16 UTC |
| a3154d5 | Stephen Piccolo | 13 July 2020, 20:55:03 UTC | Tweaked README files | 13 July 2020, 20:55:03 UTC |
| 0cd28c9 | Stephen Piccolo | 13 July 2020, 20:51:55 UTC | Added support for EDAM file formats, etc. | 13 July 2020, 20:51:55 UTC |
| e4e81bd | Stephen Piccolo | 01 July 2020, 22:15:18 UTC | Merge branch 'master' of github.com:srp33/ToolJig | 01 July 2020, 22:15:18 UTC |
| 0ad97d4 | Stephen Piccolo | 01 July 2020, 22:14:50 UTC | Uncommented lines | 01 July 2020, 22:14:50 UTC |
| a07731c | Stephen Piccolo | 30 June 2020, 23:35:32 UTC | Adding support for specifying file formats | 30 June 2020, 23:35:32 UTC |
| 9b717cc | Stephen Piccolo | 30 June 2020, 23:34:43 UTC | Adding support for specifying file formats | 30 June 2020, 23:34:43 UTC |
| 7603ab1 | Stephen Piccolo | 30 June 2020, 23:31:00 UTC | Adding support for specifying file formats | 30 June 2020, 23:31:00 UTC |
| 33a91b3 | Stephen Piccolo | 25 June 2020, 17:54:05 UTC | Added ability to manage outputs and updated examples | 25 June 2020, 17:54:05 UTC |
| 787d16c | Stephen Piccolo | 27 May 2020, 23:22:11 UTC | Added support to specify names of standard output and standard error. | 27 May 2020, 23:22:11 UTC |
| d2d5b1d | Stephen Piccolo | 27 May 2020, 19:53:18 UTC | Now supporting secondaryFiles on File inputs | 27 May 2020, 19:53:18 UTC |
| 564519f | Stephen Piccolo | 27 May 2020, 17:06:15 UTC | Removed unnecessary lines | 27 May 2020, 17:06:15 UTC |
| 68783db | Stephen Piccolo | 22 May 2020, 20:30:57 UTC | Fixed spacing in Dockerfile contents | 22 May 2020, 20:30:57 UTC |
