Commit graph

1392 commits

Author SHA1 Message Date
drpatelh
e438d026bd Unify syntax 2020-09-10 16:45:11 +01:00
drpatelh
cbf8329ffd Add new modules 2020-09-10 16:09:54 +01:00
drpatelh
46edf8ae4c Update featurecounts module 2020-09-10 16:07:21 +01:00
drpatelh
473f1b192f Update functions script 2020-09-10 15:59:26 +01:00
Harshil Patel
b1b0a6e3b1
Merge pull request #66 from Jeremy1805/master
Changed options.publish_files definition in functions.nf/initOptions
2020-08-20 13:20:04 +01:00
Jeremy1805
789dc4f09a Changed options.publish_files definition in functions.nf/initOptions 2020-08-20 11:57:10 +01:00
Harshil Patel
47b6dd70e4
Merge pull request #64 from drpatelh/master
Add tests and docs for picard tools
2020-08-07 16:46:59 +01:00
drpatelh
b22ec332e9 Add GitHub Actions 2020-08-07 16:42:56 +01:00
drpatelh
08723c9d61 Add tests for mergesamfiles 2020-08-07 16:39:16 +01:00
drpatelh
3547b64eab Add docs and tests for markduplicates 2020-08-07 16:30:28 +01:00
drpatelh
cb85acddf0 Add docs and tests for collectmultiplemetrics 2020-08-07 16:29:37 +01:00
drpatelh
50a628ad0a Remove deprecated tests 2020-08-07 15:55:23 +01:00
Harshil Patel
bd98988f23
Merge pull request #63 from drpatelh/master
Add docs and tests for all samtools commands
2020-08-07 15:40:03 +01:00
drpatelh
238f43789e Add tests for all samtools commands 2020-08-07 15:35:19 +01:00
drpatelh
14480affba Add flagstat test 2020-08-07 15:32:09 +01:00
drpatelh
d6f7bb055b Fix indents 2020-08-07 15:27:35 +01:00
drpatelh
e648dc335c Add samtools stats commands 2020-08-07 15:23:39 +01:00
drpatelh
d5b16db27d Add samtools sort 2020-08-07 15:21:28 +01:00
drpatelh
0287cad1f8 Add samtools index tests 2020-08-07 15:17:46 +01:00
drpatelh
17b5f5ef3b Get samtools idxstats tests passing 2020-08-07 15:14:45 +01:00
drpatelh
46e4d35ec3 Get samtools flagstat passing 2020-08-07 15:12:03 +01:00
drpatelh
cf5cb8945c Get samtools flagstat passing 2020-08-07 15:11:31 +01:00
drpatelh
736a0aa43c Update indents and syntax 2020-08-07 15:05:25 +01:00
drpatelh
29f1585068 Remove test functions folder 2020-08-07 14:05:55 +01:00
drpatelh
6333786d62 Add test BAM files 2020-08-07 14:04:39 +01:00
drpatelh
953256f967 Reformat paired-end fastqs 2020-08-07 13:46:23 +01:00
Harshil Patel
347bbcc609
Merge pull request #62 from drpatelh/master
Add docs and test data for BWA mem
2020-08-07 13:29:56 +01:00
drpatelh
0ad26e3b19 Add output files 2020-08-07 13:28:18 +01:00
drpatelh
d10878f19d Change to SE 2020-08-07 13:27:06 +01:00
drpatelh
0cbefde4b0 Add index test data for BWA 2020-08-07 13:25:02 +01:00
drpatelh
7ab1245eb5 Add test data 2020-08-07 13:24:39 +01:00
drpatelh
b5338efb7d Add tests for BWA mem 2020-08-07 13:24:24 +01:00
Harshil Patel
efce3024de
Merge pull request #61 from drpatelh/master
Add docs and tests for BWA index
2020-08-07 13:01:10 +01:00
drpatelh
cff81ef875 Add test data 2020-08-07 12:57:32 +01:00
drpatelh
7604bd27fc Add test nextflow.config 2020-08-07 12:56:52 +01:00
drpatelh
f367f9ef69 Add main test script 2020-08-07 12:56:39 +01:00
drpatelh
375af1428e Minor change 2020-08-07 12:38:10 +01:00
drpatelh
a6fc702c8b Update bwa index docs 2020-08-07 12:38:01 +01:00
Harshil Patel
ad4151703f
Merge pull request #60 from drpatelh/master
Add docs and tests for TrimGalore!
2020-08-07 12:27:43 +01:00
drpatelh
9f4192d433 Add TrimGalore GitHub Actions test 2020-08-07 12:21:47 +01:00
drpatelh
36f2544c36 Add single_end input file for testing 2020-08-07 12:19:47 +01:00
drpatelh
6522b04ee3 Remove old code 2020-08-07 12:19:28 +01:00
drpatelh
30256d8e81 Update tests 2020-08-07 12:18:53 +01:00
drpatelh
2c0f552908 Add output files 2020-08-07 12:18:43 +01:00
drpatelh
4df72f0396 Update nextflow.config 2020-08-07 12:14:12 +01:00
drpatelh
f32950d0f2 Update docs for trimgalore 2020-08-07 12:10:42 +01:00
Harshil Patel
7c900e2d17
Merge pull request #59 from drpatelh/master
Refine module TEMPLATE
2020-08-07 11:41:56 +01:00
drpatelh
a63897ee9c Add input output test folders 2020-08-07 11:40:51 +01:00
drpatelh
d63982b41e Update README 2020-08-07 11:38:48 +01:00
drpatelh
3a4fbf36ae Add test 2020-08-07 11:31:07 +01:00