Commit graph

562 commits

Author SHA1 Message Date
Harshil Patel
ff0fe1a910
Merge pull request #70 from drpatelh/versions
Update existing modules with new options and container syntax
2020-10-15 11:28:13 +01:00
drpatelh
29f9b05433 Update docs 2020-10-15 11:13:54 +01:00
drpatelh
7e2c7b1b41 Update README 2020-10-15 11:02:04 +01:00
drpatelh
530789ba85 Get tests passing 2020-10-15 10:47:15 +01:00
drpatelh
c32fcb39fc Remove git update script 2020-10-15 10:22:40 +01:00
drpatelh
1d30e2c21a Update tools not in rnaseq pipeline too 2020-10-14 18:59:25 +01:00
drpatelh
14525ed50d Remove functions file 2020-10-14 18:29:50 +01:00
Harshil Patel
a6aab020df
Merge pull request #69 from drpatelh/versions
Revert RSeQC version
2020-10-12 18:03:21 +01:00
drpatelh
e9e81e8691 Revert RSeQC version 2020-10-12 17:47:13 +01:00
Harshil Patel
d8f202c563
Merge pull request #68 from drpatelh/versions
Update tool versions
2020-10-12 16:22:31 +01:00
drpatelh
6bb3d5caea Update container 2020-10-12 16:20:35 +01:00
drpatelh
64377d4035 Bug fixes 2020-10-12 16:20:22 +01:00
drpatelh
a1b705d412 Update RSeQC version 2020-10-12 16:04:04 +01:00
drpatelh
436a1f983c Update trimgalore version 2020-10-12 15:59:46 +01:00
drpatelh
d19a8c702d Update picard version 2020-10-12 15:58:09 +01:00
drpatelh
74f27803b4 Update stringtie version 2020-10-12 15:55:07 +01:00
drpatelh
f4f96ff792 Update gffread version 2020-10-12 15:52:05 +01:00
Harshil Patel
0e11679748
Update main.nf 2020-09-18 10:39:41 +01:00
Harshil Patel
fb44f36f66
Update main.nf 2020-09-16 19:08:24 +01:00
Harshil Patel
436e37bcd0
Merge pull request #67 from drpatelh/master
Add rnaseq DSL2 modules
2020-09-10 16:49:26 +01:00
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