This project implements analyses from the OSCA book on hematopoetic stem cell (HSC) single-cell RNA sequencing (scRNAseq) datasets. The main purpose of the project is to illustrate how Scikick projects are configured and typically used in a realistic setting. A walkthrough documents how Scikick was used throughout the project to execute and manage the state of the workflow.
All pages in this project (except this one) were obtained directly from the source code of the OSCA book (https://github.com/Bioconductor/OrchestratingSingleCellAnalysis/, revision d56676f9d) released under a CC BY 4.0 license and created by: Robert Amezquita, Aaron Lun, Stephanie Hicks, and Raphael Gottardo.
Changes to the original source code are as follows:
The “Project Map” automatically generated by Scikick below (and at the bottom of all pages) can aid in navigating and visualizing the project. Each node is a page that can be clicked to navigate to it. Pages can also be navigated with the standard bootstrap navigation at the top of each page.
Project History
List of Contributors
| Author | Number of Commits |
|---|---|
| Matthew Carlucci | 78 |
| Tadas Bareikis | 45 |
| tadasbar | 6 |
Full List of Project Changes
| Author | Message | Date | SHA |
|---|---|---|---|
| Matthew Carlucci | Merge branch 'master' of github.com:matthewcarlucci/scikick |
2023-02-17 21:37:09 GMT | a64b817b |
| Matthew Carlucci | Update docs with real simulated changes instead of touch |
2023-02-17 21:37:01 GMT | f59eb45d |
| Matthew Carlucci | Version 0.2.1 |
2023-02-17 19:41:36 GMT | f88741e7 |
| Matthew Carlucci | Always include a benchmark directory to satisfy snakemake wildcard rules |
2023-02-17 19:28:08 GMT | 332a0bf8 |
| Matthew Carlucci | Update touch tests which snakemake no longer responds to |
2023-02-17 19:18:10 GMT | e8864634 |
| Matthew Carlucci | Update tests to run with pytest and unittest to replace broken nose |
2023-02-14 18:13:53 GMT | 84ff23b7 |
| Matthew Carlucci | Bug fix for failing custom reportdir usage |
2022-01-12 21:26:10 GMT | 5e23effe |
| Matthew Carlucci | Add ignored header HTML content |
2021-03-30 16:55:20 GMT | 72dc022e |
| Matthew Carlucci | Version 0.2.0 |
2021-03-30 14:29:55 GMT | fbb1f63e |
| Matthew Carlucci | Make error logging robust to missing log file |
2021-03-29 20:38:54 GMT | ec432abb |
| Matthew Carlucci | Add graphviz dependency for project maps |
2021-03-29 20:38:02 GMT | ca7a8367 |
| Matthew Carlucci | Update documentation with more details on robust archival of scRNAseq |
2021-03-29 20:37:10 GMT | 46825577 |
| Matthew Carlucci | Fix change to site generation to re-allow homepage-only sites |
2021-03-22 22:28:17 GMT | d5fd890a |
| Matthew Carlucci | Finish fixes to layout subdir usage |
2021-03-19 15:32:43 GMT | 6b003b2f |
| Matthew Carlucci | Use default retina settings for knitr to allow fig.cap usage, docs/figure update... |
2021-03-18 19:00:55 GMT | 4b850a05 |
| Matthew Carlucci | Middle of refactoring sk layout to fix bugs |
2021-03-17 18:46:49 GMT | a30d711a |
| Matthew Carlucci | Fix interactive plot handling |
2021-03-16 21:28:56 GMT | c080c26b |
| Matthew Carlucci | Fixes to project map subgraph assignments |
2021-03-16 21:13:51 GMT | 24de163c |
| Matthew Carlucci | New docs homepage and related README/setup changes |
2021-03-16 21:11:14 GMT | ab51effe |
| Matthew Carlucci | Addition of tutorial and documentation content with some minor code adjustments ... |
2021-03-07 14:53:57 GMT | b30e1fb0 |
| Matthew Carlucci | Remove or reformat references |
2021-03-03 14:50:26 GMT | 1d751129 |
| Matthew Carlucci | Add I/O commands to make project fully executable |
2021-03-01 15:42:03 GMT | 98d53616 |
| Matthew Carlucci | Split analysis into multiple notebooks (original notebooks are from revision d56... |
2021-02-25 22:39:15 GMT | c9bbf31b |
| Matthew Carlucci | Import select content from https://github.com/Bioconductor/OrchestratingSingleCe... |
2021-02-25 20:33:33 GMT | d39f3b42 |
| Matthew Carlucci | Add two tests for ipynb |
2021-02-19 17:19:21 GMT | b8aa240b |
| Matthew Carlucci | Add sk run --quiet and other minor fixes |
2021-02-19 17:16:39 GMT | da422971 |
| Matthew Carlucci | Refactor to have snakemake workflows in a more conventional format |
2021-02-17 16:32:56 GMT | 27731059 |
| Matthew Carlucci | Changes and fixes to messaging |
2021-02-09 15:06:38 GMT | 28d8f8b1 |
| Matthew Carlucci | Add an intermediate post markdown step to insert a project map to each page |
2021-01-29 19:55:58 GMT | 7cabf903 |
| Matthew Carlucci | Allow md files to depend on other steps |
2021-01-26 16:46:44 GMT | 4688ed4f |
| Matthew Carlucci | Fix issue determining site.yml files for an index only directory |
2021-01-26 16:43:48 GMT | dcea9dfe |
| Matthew Carlucci | Bug fixes in logging and sk mv |
2021-01-12 21:42:10 GMT | 3a6cb532 |
| Matthew Carlucci | Documentation and minor bug fixes for next release |
2021-01-07 18:35:06 GMT | a37b1a1f |
| Matthew Carlucci | Include system index file (homepage) in sk status |
2021-01-06 16:33:01 GMT | 5203f613 |
| Matthew Carlucci | Simplify code execution stack for R and Rmd by keeping log files and using snake... |
2021-01-06 16:19:10 GMT | c186c213 |
| Matthew Carlucci | Migrate layout setting code to own module |
2021-01-04 18:19:26 GMT | ab7ccdfc |
| Matthew Carlucci | Minor changes to init code |
2021-01-04 18:15:07 GMT | 5dd90e7b |
| Matthew Carlucci | Aggregate workflow properties and conveniece methods into ScikickConfig |
2021-01-04 16:10:58 GMT | a4486415 |
| Matthew Carlucci | Split status parsing by job type and directly use marker priroritization |
2021-01-04 15:57:27 GMT | 44f635fe |
| Matthew Carlucci | Minimized render site complexity and allow for custom outputs |
2020-12-29 17:22:09 GMT | 56ead137 |
| Matthew Carlucci | Further modularize Snakemake workflow and related scripts |
2020-12-29 17:21:00 GMT | c86afb77 |
| Matthew Carlucci | More modular and robust snakemake config setup |
2020-12-17 22:21:57 GMT | 74824108 |
| Matthew Carlucci | Minor modification to demo and template contents |
2020-12-14 20:04:54 GMT | 0dbdc007 |
| Matthew Carlucci | Misc other related to recent changes |
2020-12-11 14:56:31 GMT | 0c9599bc |
| Matthew Carlucci | sk status: fix test and rewrite snake status |
2020-12-10 22:14:07 GMT | a9cafb15 |
| Matthew Carlucci | Modify added page content, more robustness to commit special characters, include... |
2020-12-10 22:03:19 GMT | 7dad100d |
| Matthew Carlucci | Rewrite sk config |
2020-12-10 21:57:01 GMT | 540036e0 |
| Matthew Carlucci | Internal: rely on skconfig more during sk run and sk config |
2020-12-10 21:49:19 GMT | 9e15b60a |
| Matthew Carlucci | Misc refactor and commenting |
2020-12-07 20:30:20 GMT | 397c95a6 |
| Matthew Carlucci | Remove body width CSS |
2020-12-03 16:34:22 GMT | 07d736ec |
| Matthew Carlucci | Allow spaces in project path |
2020-12-01 22:31:56 GMT | 32b1ef1e |
| Matthew Carlucci | README update with demo gif |
2020-12-01 14:33:14 GMT | 8665b5a5 |
| Matthew Carlucci | New sk init template setting analysis as empty dict |
2020-11-27 17:03:45 GMT | 3cfbe5c6 |
| Matthew Carlucci | Update sk del with new -d usage for issue #2 (multiple -d) |
2020-11-27 17:02:12 GMT | a98f5411 |
| Matthew Carlucci | Updating parsers to use script instead of rmd |
2020-11-27 17:00:47 GMT | 9232007c |
| Matthew Carlucci | Modify demo for new sk add usage and add a demo test |
2020-11-27 16:55:17 GMT | c3422bd7 |
| Matthew Carlucci | Modifications to sk add to address part of issue #2 (multiple -d) |
2020-11-27 16:53:41 GMT | 93007d06 |
| Matthew Carlucci | Add argument need pages to yaml in() for steps requiring non-empty analysis |
2020-11-27 16:47:25 GMT | 156b9179 |
| Matthew Carlucci | Dump snakemake logs after unexpected errors |
2020-11-23 19:45:47 GMT | 2a863837 |
| Matthew Carlucci | Code cleanup and commenting |
2020-11-23 16:32:01 GMT | e01f0977 |
| Matthew Carlucci | Allow sk run <doc> usage with empty yaml |
2020-10-01 16:03:34 GMT | 5ec45662 |
| Matthew Carlucci | Change analysis metadata from button to details tag |
2020-10-01 16:02:22 GMT | d898a354 |
| Matthew Carlucci | Code cleanup (few functional differences) |
2020-10-01 15:49:36 GMT | 026e863f |
| Matthew Carlucci | Internal function name changes and sk init description update |
2020-09-29 20:59:42 GMT | 52fbc636 |
| Matthew Carlucci | Modify defaults allow execution of run snakemake without arguments |
2020-09-28 19:59:20 GMT | 0c950981 |
| Matthew Carlucci | Simplify software check outputs |
2020-09-28 19:57:43 GMT | 63ac1ef5 |
| Matthew Carlucci | Clean up sk init and demo outputs |
2020-09-28 19:04:56 GMT | 5aa4446a |
| Matthew Carlucci | Include a snakemake badge |
2020-09-28 19:03:59 GMT | 81716a03 |
| Matthew Carlucci | Add pop snakefile for debugging scikick Snakefile issues |
2020-09-25 16:16:37 GMT | 42bf8e6a |
| Matthew Carlucci | Rename rules and reorganize scripts |
2020-09-25 16:14:31 GMT | c6a65140 |
| tadasbar | Merge branch 'dev' of https://github.com/matthewcarlucci/scikick into dev |
2020-09-10 13:53:51 GMT | 0dedc510 |
| tadasbar | Updated the comments in scikick/status.py |
2020-09-10 08:04:59 GMT | 729e5106 |
| Matthew Carlucci | Increment to 0.1.2 for new release |
2020-09-09 16:28:20 GMT | 1c62fbb7 |
| tadasbar | Limit the "Unrecognized scikick.yml field" message to sk (run, config, status) |
2020-09-09 12:18:32 GMT | 20b23090 |
| Tadas Bareikis | Change help string for "sk status rmd" |
2020-09-04 02:12:01 GMT | 5bf396f5 |
| Matthew Carlucci | Update changelog for nearing 0.1.2 release |
2020-09-03 21:34:47 GMT | 4402fe56 |
| Matthew Carlucci | Include more installation details with a conda install method |
2020-09-03 21:33:12 GMT | f581b8aa |
| Tadas Bareikis | Update "sk status --help"; Change "-e-", "-u-" definitions and output in "sk sta... |
2020-09-03 10:50:39 GMT | 71468f38 |
| Tadas Bareikis | Print warnings/errors only in case of error is non-verbose output of "sk run" |
2020-09-03 09:00:26 GMT | 31684b39 |
| Tadas Bareikis | Add "-u-" marker for "sk status" |
2020-09-02 04:50:54 GMT | 73d023fb |
| Tadas Bareikis | Print snakemake logfile name even in case of error; fix scikick.yml field check ... |
2020-09-02 03:04:00 GMT | d3064381 |
| Tadas Bareikis | Check for unsupported scikick.yml fields on every scikick execution |
2020-09-01 08:11:23 GMT | 8c358568 |
| Tadas Bareikis | Change "sk status" output by adding additional info to "m--" marker |
2020-09-01 06:02:41 GMT | 9e006504 |
| Tadas Bareikis | Add knitmeta test for singularity run |
2020-08-28 03:43:26 GMT | 12978314 |
| Tadas Bareikis | Add singularity (and conda) support for pageRender rule |
2020-08-28 03:27:23 GMT | a4ad452e |
| Tadas Bareikis | Modify messages for internal/external dependencies |
2020-08-27 07:36:47 GMT | f8dafa31 |
| Tadas Bareikis | Make "sk config" print all variables when no options are provided |
2020-08-27 06:34:40 GMT | a04b4d3f |
| Tadas Bareikis | Add messages for internal/external dependencies |
2020-08-27 04:36:51 GMT | e297a12d |
| Tadas Bareikis | Add warnings for unsupported formats in scikick.yml |
2020-08-27 02:49:32 GMT | e6a79c25 |
| Tadas Bareikis | Merge branch 'dev' of https://github.com/matthewcarlucci/scikick into dev |
2020-08-26 11:03:14 GMT | 201f3b29 |
| Tadas Bareikis | Fix "sk status" output for modified md files |
2020-08-26 11:02:38 GMT | e71ed31d |
| Tadas Bareikis | Add commit sha column to the "List of Changes" in the footer |
2020-08-26 05:51:47 GMT | 6b015c03 |
| Tadas Bareikis | Minor fix in "sk status" output for internal dependencies |
2020-08-26 04:36:54 GMT | 56467e9d |
| Matthew Carlucci | Merge branch 'dev' of github.com:matthewcarlucci/scikick into dev |
2020-08-25 14:13:28 GMT | 63e2729c |
| Matthew Carlucci | Add CHANGELOG.md |
2020-08-25 14:13:18 GMT | 1061588d |
| Matthew Carlucci | Update sk init --readme output |
2020-08-25 14:10:26 GMT | 06012c0f |
| Tadas Bareikis | Fix "sk status" output for missing htmls |
2020-08-22 12:46:47 GMT | ed2b21fb |
| Tadas Bareikis | Change the version from "0.1.1" to "0.1.1.dev0" |
2020-08-21 14:40:58 GMT | 9982e6e4 |
| Tadas Bareikis | Retain timestamp of md when correcting for moved figuredir |
2020-08-20 18:24:25 GMT | 4d426f19 |
| Tadas Bareikis | Add snakemake's "target" argument to "sk run" as "rmds" |
2020-08-20 12:24:11 GMT | 8a5dd12b |
| Tadas Bareikis | Add the option to specify an rmd for "sk status" |
2020-08-18 14:44:10 GMT | 632985cb |
| Tadas Bareikis | Ensure that mandatory fields (analysis and reportdir) are present in the yaml |
2020-08-18 11:50:48 GMT | 1497f5ac |
| Tadas Bareikis | Warn and move on after git failures in 'sk mv -g' |
2020-08-18 11:02:23 GMT | 0df47142 |
| Tadas Bareikis | Add error messages on snakemake failures in 'sk run' |
2020-08-17 17:00:03 GMT | 6d9e3cd0 |
| Tadas Bareikis | Add "--copy-deps" argument to "sk add" |
2020-08-17 14:07:25 GMT | e6976008 |
| Tadas Bareikis | Fix "Generating * html" output |
2020-08-17 11:17:34 GMT | 430584ed |
| Tadas Bareikis | Fix 'sk mv' for non-Rmd dependencies |
2020-08-16 22:02:55 GMT | 7db5e63f |
| Tadas Bareikis | Fix R package renv usage with sk run |
2020-08-14 13:46:50 GMT | a07b920b |
| Tadas Bareikis | --singularity-args can be used with the -s argument |
2020-08-13 18:11:35 GMT | d71bd937 |
| tadasbar | Remove gitpython dependency, use R's git2r instead |
2020-08-13 14:32:02 GMT | 7b910597 |
| tadasbar | Fix Git Log in footer for non-Rmd files |
2020-08-07 09:16:07 GMT | 17475d5e |
| tadasbar | Add checks for git2r version |
2020-08-06 12:57:44 GMT | df743c18 |
| Tadas Bareikis | Rewrite the tests |
2020-08-04 07:50:46 GMT | af60b461 |
| Tadas Bareikis | Merge branch 'master' into dev |
2020-08-04 02:01:58 GMT | a3b63679 |
| Tadas Bareikis | Update the setup.py file and push to pip v0.1.1 |
2020-07-28 08:56:53 GMT | d405da9e |
| Tadas Bareikis | Merge branch 'dev' of https://github.com/matthewcarlucci/scikick into dev |
2020-07-28 05:02:44 GMT | 07dfbe15 |
| Tadas Bareikis | Added sk init --demo and fixed index page usage |
2020-07-28 03:50:56 GMT | 5e6180b3 |
| Tadas Bareikis | Appending the system index.Rmd to index pages |
2020-07-27 10:59:52 GMT | b0669d7f |
| Tadas Bareikis | Index page fixes: index page at the root; no error when adding a 3rd... index pa... |
2020-07-27 08:52:53 GMT | 9e704ff5 |
| Tadas Bareikis | Removed 'plot.Rmd' from the demo |
2020-07-27 08:19:19 GMT | 225db271 |
| Tadas Bareikis | Updated the demo |
2020-07-27 02:50:41 GMT | 725db621 |
| Tadas Bareikis | Changed some wording in the demo |
2020-07-26 12:09:23 GMT | d8e6519e |
| Tadas Bareikis | Added 'sk init --demo' |
2020-07-26 11:59:30 GMT | 409d5b77 |
| Tadas Bareikis | Removed unnecessary outputs |
2020-07-26 06:01:27 GMT | 19a2cd2a |
| Tadas Bareikis | Fixes in 'sk status' for the index page |
2020-07-26 05:47:06 GMT | 77658c59 |
| Matthew Carlucci | Update README.md introduction |
2020-07-24 19:15:32 GMT | 8dc6c7b0 |
| Tadas Bareikis | Silenced git warnings, using git2r in template index.Rmd |
2020-07-24 13:30:41 GMT | 450685c9 |
| Tadas Bareikis | New user-defined index page usage |
2020-07-24 12:25:00 GMT | 0725b105 |
| Matthew Carlucci | Initial release |
2020-07-23 22:07:27 GMT | 968ff086 |