Merged pull requests:
- Include tests in README #107 (ssjunnebo)
- Update README #106 (ssjunnebo)
- 574328 fix travis tests #105 (ssjunnebo)
- remove version nr, autoversion instead #104 (ssjunnebo)
v0.0.1 (2018-01-25)
Merged pull requests:
- Add version number #103 (ssjunnebo)
- Fix Travis Errors #102 (ssjunnebo)
- change order of imeta query to speed things up #101 (andrewjpage)
- add run_date from mlwarehouse #100 (andrewjpage)
- Get insert size from new warehouse #99 (andrewjpage)
- add hash to check common name #98 (ssjunnebo)
- update email address #97 (ssjunnebo)
- dont import if there is no run id #96 (andrewjpage)
- filter out old pb lanes #95 (andrewjpage)
- inconsistent naming of library #94 (andrewjpage)
- populate library name and sample public name if missing #93 (andrewjpage)
- if library or sample missing fill in with placeholder data #92 (andrewjpage)
- Pacbio duplicate libraries #91 (andrewjpage)
- infgen #90 (andrewjpage)
- update from 108 to 118 #89 (andrewjpage)
- SRA fastq-dump header replacing #88 (vaofford)
- add symlink rsync #87 (vaofford)
- lookup xml directly first before using bioperl #86 (andrewjpage)
- ncbi changed to https #85 (andrewjpage)
- skip missing common name #84 (andrewjpage)
- filter out lanes without study name #83 (andrewjpage)
- pacbio should draw in results from irods #82 (andrewjpage)
- nds_change_to_dist_zilla_starter_bundle #81 (nds)
- bin directory should be set by softwarerc #80 (andrewjpage)
- remove blank header cells #79 (andrewjpage)
- Long running validate reports failing #78 (andrewjpage)
- Fix for validate GCLP warehouse #77 (andrewjpage)
- Data access group #76 (andrewjpage)
- expose threads option for spreadsheet #75 (andrewjpage)
- Run date #74 (andrewjpage)
- update warehouse 2 cname #73 (andrewjpage)
- only print sync message when verbose on #72 (andrewjpage)
- Increase stability #71 (andrewjpage)
- Reduce unnessisary lookups for warehouse fragment size #70 (andrewjpage)
- cram file type in validation #69 (andrewjpage)
- filter rows #68 (andrewjpage)
- make sure there are no duplicate filenames #67 (andrewjpage)
- Speedup md5 #66 (andrewjpage)
- least specific to most specific speeds up irods query #65 (andrewjpage)
- change target param to end of search #64 (andrewjpage)
- default to bam #63 (andrewjpage)
- add support to import cram files #62 (andrewjpage)
- pull in reference #61 (andrewjpage)
- import all QC'd bams #60 (sb10)
- fix syntax for study lookup #59 (andrewjpage)
- update lane #58 (andrewjpage)
- missing data in irods so use warehouse primarily #57 (andrewjpage)
- Pacbio err numbers #56 (andrewjpage)
- Reduce memory usage and move to dist zilla #55 (andrewjpage)
- Update ERR numbers from irods #54 (andrewjpage)
- Added AUTHORS file #53 (aslett1)
- resolve and merge vertres changes #52 (andrewjpage)
- lower default num reads #51 (andrewjpage)
- Pac bio metadata tracking #49 (andrewjpage)
- all tests now pass #48 (andrewjpage)
- added --species option to avoid NCBI database look up #47 (sb10)
- -md5 and -use_supplier_name fixes #46 (sb10)
- Changes made to vertebrate resequencing update pipeline (updated) #45 (sb10)
- Changes made to vertebrate resequencing update pipeline #43 (jm23)
- set mysql_auto_connect #42 (CraigPorter)
- added confirm completed message #41 (CraigPorter)
- pull fragment size for wells from batch requests #39 (andrewjpage)
- GPL #38 (andrewjpage)
- update tests for fastq direction #36 (andrewjpage)
- Set readlength, reads and bases when importing using spreadsheet. #35 (CraigPorter)
- If irods manual_qc not set, check warehouse #34 (andrewjpage)
- replaced listallmissing option with no_pending_lanes #33 (CraigPorter)
- added option to list missing lanes if qc pending #32 (CraigPorter)
- list missing lanes after qc complete #31 (CraigPorter)
- Lock file to prevent duplicate processes on the same host #30 (andrewjpage)
- update warehouse host #29 (andrewjpage)
- Spreadsheet changes #28 (aslett1)
- New SimpleLookup for species name and changed tags for optional parameters #27 (jm23)
- Set file types for forward and reverse fastqs #26 (CraigPorter)
- new warehouse #25 (andrewjpage)
- ichksum format changed #24 (andrewjpage)
- Md5 fastqcheck spreadsheet #23 (andrewjpage)
- create fastqcheck file and md5 #22 (andrewjpage)
- Changes for vertres tracking pipeline #21 (jm23)
- Add no moose and make meta immutable #20 (mp15)
- add a random number to hierarchy name in individual if clash #19 (andrewjpage)
- dont add common name by default #18 (andrewjpage)
- Updated spreadsheet template for remote users #17 (aslett1)
- spreadsheet tempalte #16 (andrewjpage)
- Spreadsheet import #15 (andrewjpage)
- command line option to activate read count check #14 (fy2)
- Validation has been extended #13 (fy2)
- merge changes from jm23 #12 (andrewjpage)
- update warehouse sql #10 (andrewjpage)
- warehouse two sql schema #9 (andrewjpage)
- lookup study ssid from seqscape tables first to avoid data problems with... #8 (andrewjpage)
- validate #7 (andrewjpage)
- Mean insert size #6 (andrewjpage)
- delete files when lane reset #5 (andrewjpage)
- Build vr track #4 (andrewjpage)
- reduce sensitivity #3 (andrewjpage)
- tweaks for error email #2 (andrewjpage)
- Report which flags up problematic lanes in the pipelines #1 (andrewjpage)