1.2.0 (2024-02-21)
- added possibility to run with singularity container (9d4598e)
- option to add padding between CDS and intergenic region, closes #25 (de3f8bf)
- added .vscode (d4a15e0)
- bug in export of NTC guides when all are filtered out (bf97758)
- overhauled plotting of intergenic regions, closes #28 (da7135c)
- updated container, bumped version (cc9dcf9)
1.1.0 (2024-01-12)
- added config README and updated workflow catalog options (13649a1)
- added image with pipeline overview (69a816c)
- added option to export guide list as gff file, closes #16 (470025c)
- major and changes to support tiling based guide design (478c68f)
- more flexibility with chromosome names, updated envs, closes #15 (edd1d16)
- parsing of GFF file improved considerably by using bcbio GFF lib, #15 (80c66ff)
- smarter retrieveal of genome name and tax ID; closes #19 (afdc2e3)
- added --cores to lint command (c9fd2a5)
- added missing example pics (7a935a8)
- added option to specify GFF sources in config file; closes #21 (b02e869)
- availability of tx_list when target is empty (2e0a248)
- bumped versions and removed unnecessary dependency (2a1975a)
- extended documentation for 'usage' page on sm-workflow-catalog (bd6b4fe)
- removed 1 branch from CI test workflow (f3fe343)
- removed a comment (ac5a6e2)
- removed additional flag fields entirely (53319a0)
- restored original empty fields for flags (01ef026)
- add major module to find, score and filter guide RNAs (4f93545)
- added basic R markdown report module (3950bcd)
- added CI test dir (bdfe96c)
- added dev branch to GH actions (303de61)
- added function to exclude RNAs from guide design (63f0b0e)
- added functionality to design random control guides (a32185b)
- added functionality to handle and visualize guides with multiple targets. Closes #11 (ac4cd79)
- added log entry with number of non-targeted genes (1b1653f)
- added module to convert html report to pdf (37f30a4)
- added module to generate BSgenome object on the fly, for use with bowtie, closes #4 (c344d0d)
- added module to make bowtie2 index (cf11e73)
- added more TSS features to result table, and new viz figures (8ffa6a2)
- added option to add arbitrary linkers to guide RNA ends (d931cb7)
- added optional weights to calculate mean score (5678c38)
- added output of failed guide RNA design to report (4019861)
- added percentages to report plots (da8b5d9)
- added score for G eenrichment, closes #5 (a1b35a1)
- changed license to GPL (9ce508a)
- export table of targets where guide design failed (e377f4b)
- filter for guides that fall within TSS window and transcript region + visualization (39e9cea)
- finished module for obtaining genomes from NCBI or user (5c1fa2b)
- first draft of module to generate bsgenome object on the fly (a5f8b77)
- fixed small bugs to improve usage of custom fasta/gff files (ab76a25)
- improved prediction around TSS and added TSS dist score, closes #3 (290b675)
- included visualization of guide RNA location, and option for strand preference (d345099)
- simplified handling of result files (ddcb925)
- added missing documentation for paramter filter_multi_targets (32476e5)
- added r-base environment to conda list (e2d7cbf)
- added variable TSS windows, closes #9 (014e6ec)
- changed syntax for env defs, use dry run for test (32f5e82)
- conda env error nothing provides libgcc-ng (ffc9cec)
- fixed small syntax error for env (bd1775b)
- improvements to score correlation plot (7afc9cb)
- removed typo in dry snakemake test command (8e3e5c0)
- replaced bowtie2 with bowtie1 as a req for crisprDesign module (f8cd5fb)
- small improvements to report and docs (d24c36c)
- small update to guide RNA drawing (18eac19)
- some corrections to pipeline overview (2e519ed)