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Author SHA1 Message Date
Thomas A. Christensen II
6f1aab2667
Spelling corrections in README 2021-04-28 19:30:02 -06:00
Thomas A. Christensen II
affa7796ac
Sanitize redacted name 2021-04-28 19:27:56 -06:00
Thomas A. Christensen II
471bf4314d
Create ONT renaming script 2021-04-22 12:39:45 -06:00
Thomas A. Christensen II
42d3d542b9
Cleanup find command 2021-04-22 11:07:07 -06:00
Thomas A. Christensen II
c7545ae55d
Match ONT's nomenclature for fastqs more closely 2021-04-22 11:03:21 -06:00
Thomas A. Christensen II
ac5be401c1
Remove verbose skip logging 2021-04-20 14:35:20 -06:00
Thomas A. Christensen II
2340aa974b
Force overwrite of destination fastq.gz 2021-04-20 14:34:26 -06:00
Thomas A. Christensen II
798e7693bf
Make copying script combine fastqs 2021-04-20 12:58:48 -06:00
Thomas A. Christensen II
adce9225b2
Cleanup READMEs 2021-04-20 12:57:26 -06:00
Thomas A. Christensen II
9f715bf5cd
Cleanup main README 2021-04-13 13:58:00 -06:00
Thomas A. Christensen II
f4c8b4da97
Cleanup ONT README 2021-04-13 13:56:10 -06:00
Thomas A. Christensen II
ab3f468564
Cleanup limsdatapull README 2021-04-13 13:55:29 -06:00
Thomas A. Christensen II
4cbe3aa529
Cleanup Clearlabs README 2021-04-13 13:54:07 -06:00
Thomas A. Christensen II
8bc8362a62
Add sorting scripts to Illumina README 2021-04-13 13:52:23 -06:00
Thomas A. Christensen II
54b8fddca8
Cleanup ONT README 2021-04-13 13:17:45 -06:00
Thomas A. Christensen II
352604237e
Move src directory to correct location 2021-04-13 12:50:44 -06:00
Thomas A. Christensen II
2865b19abc Merge branch 'master' of https://github.com/MillironX/wphl-bioinformatics 2021-04-13 12:50:23 -06:00
Thomas A. Christensen II
befca3557e
Correct and cleanup Illumina README 2021-04-13 12:50:14 -06:00
Thomas A. Christensen II
8f8241761d
Create illumina.jl 2021-04-13 11:03:08 -06:00
Thomas A. Christensen II
a2a86ae788
Add script to sort NextSeq runs 2021-04-13 10:06:32 -06:00
Thomas A. Christensen II
d8e1048893
Rename rename-fastqs.jl to sort-miseq.jl 2021-04-13 10:05:59 -06:00
Thomas A. Christensen II
4565960330
Allow two digit numbers 2021-04-08 08:37:18 -06:00
Thomas A. Christensen II
33cce553f5
Create fastq sorting script 2021-04-07 15:04:47 -06:00
Thomas A. Christensen II
5683bbf83c
Update README.md 2021-04-01 10:23:31 -06:00
Thomas A. Christensen II
4b6b243257
Create README.md 2021-04-01 10:12:14 -06:00
Thomas A. Christensen II
3e8f97f71f
Create README.md 2021-04-01 09:59:35 -06:00
Thomas A. Christensen II
95a6eacc2e
Update README.md 2021-04-01 09:23:42 -06:00
Thomas A. Christensen II
ee4a45249b
Update README.md 2021-03-31 11:21:41 -06:00
Thomas A. Christensen II
70c226d0a2
Create README.md 2021-03-31 11:12:39 -06:00
Thomas A. Christensen II
39d4380c3d
Create README.md 2021-03-30 09:15:31 -06:00
Thomas A. Christensen II
254751899d
Fix hardcoded task number to unzip fastqs 2021-03-30 08:52:23 -06:00
Thomas A. Christensen II
25625085d3
Add auto-updating sample database 2021-03-26 14:25:22 -06:00
Thomas A. Christensen II
58eb8743dc
Add secret test file 2021-03-26 14:19:24 -06:00
Thomas A. Christensen II
d3af14dc57 Add 1 git-crypt collaborator 
New collaborators:

	3B9A1EA2 Wyoming Public Health Lab NGS <wphl.ngs@wyo.gov>
 2021-03-26 14:17:05 -06:00
Thomas A. Christensen II
0898acb8ac Add 1 git-crypt collaborator 
New collaborators:

	4802BC5D Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
 2021-03-26 14:13:13 -06:00
Thomas A. Christensen II
2bb31740bc
Add ONT consolidation script 2021-03-26 14:08:34 -06:00
Thomas A. Christensen II
adf52e1e71 Merge branch 'master' of https://github.com/MillironX/wphl-bioinformatics 2021-03-26 14:05:08 -06:00
Thomas A. Christensen II
4f36be2cf4
Add Illumina Basespace FASTQ downloader script 2021-03-26 14:04:50 -06:00
Thomas A. Christensen II
ce927edc81
Make ont-transfer work on actual GridION 2021-03-26 13:02:38 -06:00
Thomas A. Christensen II
21ea3896ba
Rename ont-transfer.sh to ont-transfer 2021-03-26 12:50:45 -06:00
Thomas A. Christensen II
261e1e01d6
Test if USB drive is inserted 2021-03-23 14:00:18 -06:00
Thomas A. Christensen II
7c316ff08b
Fix sequence generation 2021-03-23 12:25:57 -06:00
Thomas A. Christensen II
79c2ae7882
Correct typo in fast5 logic 2021-03-23 12:23:52 -06:00
Thomas A. Christensen II
1a560be81a
Fix fast5 detection 2021-03-23 12:21:38 -06:00
Thomas A. Christensen II
03934e8144
Add USB drive transfer script for ONT GridION 2021-03-23 11:20:58 -06:00
Thomas A. Christensen II
9735382ac5
Reorganize folder structure 2021-03-23 11:20:19 -06:00
Thomas A. Christensen II
9f940778e4
Make fasta tarball conversion work on Cygwin 2021-03-19 09:44:42 -06:00
Thomas A. Christensen II
7065e22ab3
Convert a ClearLabs fasta tarball on Linux 2021-03-17 21:54:38 -06:00
Thomas A. Christensen II
09c08c9de1
Initial commit 2021-03-17 21:51:44 -06:00