Edmund Miller
|
6eeb930bdb
|
chore: Remove test directory from dummy tool
|
2020-11-24 21:09:55 -06:00 |
|
Edmund Miller
|
2fc39e02e2
|
test(trimgalore): Refactor se and pe to use pytest-workflow
|
2020-11-24 21:08:34 -06:00 |
|
Edmund Miller
|
b2cd464ad3
|
test(samtools): Refactor stats to use pytest-workflow
|
2020-11-24 21:08:34 -06:00 |
|
Edmund Miller
|
36bbf6baa3
|
test(samtools): Refactor sort to use pytest-workflow
Pretty sure this is passing it a sorted bam though?
|
2020-11-24 21:08:34 -06:00 |
|
Edmund Miller
|
6448638b55
|
test(samtools): Refactor index to use pytest-workflow
|
2020-11-24 21:08:34 -06:00 |
|
Edmund Miller
|
16cb794892
|
test(samtools): Refactor idxstats to use pytest-workflow
|
2020-11-24 21:08:34 -06:00 |
|
Edmund Miller
|
34d86427a6
|
test(samtools): Refactor flagstat to use pytest-workflow
|
2020-11-24 21:08:33 -06:00 |
|
Edmund Miller
|
7848019cdb
|
test(picard): Refactor markduplicates to use pytest-workflow
|
2020-11-24 21:08:33 -06:00 |
|
Edmund Miller
|
939f5ca744
|
test(picard): Refactor collectmultiplemetrics to use pytest-workflow
|
2020-11-24 21:03:40 -06:00 |
|
Edmund Miller
|
234e85bdce
|
test(picard): Refactor mergesamfiles to use pytest-workflow
|
2020-11-24 19:01:12 -06:00 |
|
Edmund Miller
|
016d8684f3
|
test(bwa): Refactor to use pytest-workflow
|
2020-11-24 19:00:11 -06:00 |
|
Edmund Miller
|
ba681c6f27
|
refactor(pytest-workflow): Move fastqc tests to tests/
|
2020-11-24 20:26:04 +00:00 |
|
Edmund Miller
|
c264c66a49
|
test(fastqc): Use -entry to speed up tests
`--wt, --workflow-threads` is now an option and can be used to run tests
simultaneously.
|
2020-11-16 13:41:59 -06:00 |
|
Edmund Miller
|
a4544a11ad
|
chore(fastqc): Remove test output
|
2020-11-16 10:22:19 -06:00 |
|
drpatelh
|
a3f46865ff
|
Remove Singularity image path
|
2020-11-12 14:55:16 +00:00 |
|
drpatelh
|
47d390772c
|
Update picard version command and default container
|
2020-10-19 15:17:19 +01:00 |
|
drpatelh
|
29f9b05433
|
Update docs
|
2020-10-15 11:13:54 +01:00 |
|
drpatelh
|
530789ba85
|
Get tests passing
|
2020-10-15 10:47:15 +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 |
|
drpatelh
|
e9e81e8691
|
Revert RSeQC version
|
2020-10-12 17:47:13 +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 |
|
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 |
|
Jeremy1805
|
789dc4f09a
|
Changed options.publish_files definition in functions.nf/initOptions
|
2020-08-20 11:57:10 +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
|
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
|
6333786d62
|
Add test BAM files
|
2020-08-07 14:04:39 +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
|
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 |
|
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 |
|
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 |
|
drpatelh
|
a63897ee9c
|
Add input output test folders
|
2020-08-07 11:40:51 +01:00 |
|
drpatelh
|
3a4fbf36ae
|
Add test
|
2020-08-07 11:31:07 +01:00 |
|
drpatelh
|
b1381bb577
|
Add TODOs
|
2020-08-07 11:30:55 +01:00 |
|
drpatelh
|
e657363900
|
Add nextflow config to folder
|
2020-08-07 10:59:05 +01:00 |
|
drpatelh
|
bdfe187440
|
Add TODO comments
|
2020-08-07 10:58:36 +01:00 |
|
drpatelh
|
9296897009
|
Define options as input
|
2020-08-07 10:58:24 +01:00 |
|
drpatelh
|
4f76bb6b03
|
Add nextflow.config
|
2020-08-07 10:06:45 +01:00 |
|
drpatelh
|
7efd46b489
|
Add nextflow.config
|
2020-08-07 09:59:19 +01:00 |
|
drpatelh
|
fab020461b
|
Add -with-docker
|
2020-08-07 09:44:16 +01:00 |
|
drpatelh
|
111b1505fa
|
Add basedir
|
2020-08-07 09:40:02 +01:00 |
|
drpatelh
|
75e7e1573c
|
Add output files
|
2020-08-07 09:32:28 +01:00 |
|
drpatelh
|
754fad7c8e
|
Update output paths
|
2020-08-07 09:32:03 +01:00 |
|
drpatelh
|
b0abd14135
|
Update tests
|
2020-08-07 09:31:27 +01:00 |
|
drpatelh
|
0466d5249b
|
Update docs
|
2020-08-07 00:50:49 +01:00 |
|
drpatelh
|
f014e67de6
|
Remove old outputs
|
2020-08-07 00:37:13 +01:00 |
|
drpatelh
|
2c7abca088
|
Move unit tests to deprecated
|
2020-08-07 00:36:05 +01:00 |
|
drpatelh
|
16d3ad5d06
|
Adapt script for meta
|
2020-08-07 00:35:34 +01:00 |
|
drpatelh
|
c98b32dfa8
|
Add link to functions file
|
2020-08-06 16:26:57 +01:00 |
|
drpatelh
|
e2b47a6fa3
|
Add software requirements section
|
2020-08-06 15:22:32 +01:00 |
|
drpatelh
|
2c9cd2d89b
|
Update main script
|
2020-08-06 12:00:38 +01:00 |
|
drpatelh
|
530b4c1bd9
|
Add test directory
|
2020-08-06 11:32:38 +01:00 |
|
drpatelh
|
b7d0ee043e
|
Initial commit
|
2020-08-06 11:32:18 +01:00 |
|
drpatelh
|
f021ab119b
|
Initial commit
|
2020-08-06 11:32:11 +01:00 |
|
drpatelh
|
ab512be9aa
|
Initial commit
|
2020-08-06 11:31:52 +01:00 |
|
drpatelh
|
f315a7b3c4
|
Hard copy files
|
2020-08-05 18:38:27 +01:00 |
|
drpatelh
|
ab8a9025a0
|
Copy across test data and docs for trimgalore
|
2020-08-05 17:28:25 +01:00 |
|
drpatelh
|
50fce8b3cf
|
Copy across test data and docs for samtools sort
|
2020-08-05 17:28:09 +01:00 |
|
drpatelh
|
de9d33da12
|
Copy across test data and docs for samtools index
|
2020-08-05 17:27:58 +01:00 |
|
drpatelh
|
fb697eca2f
|
Copy across test data and docs for bwa mem
|
2020-08-05 17:27:42 +01:00 |
|
drpatelh
|
da4dcee934
|
Copy across test data and docs for bwa index
|
2020-08-05 17:27:28 +01:00 |
|
drpatelh
|
5d224740cd
|
Change path
|
2020-08-05 17:17:58 +01:00 |
|
drpatelh
|
137db462a7
|
Add samtools
|
2020-08-05 17:17:47 +01:00 |
|
drpatelh
|
993d0d5743
|
Add picard
|
2020-08-05 17:17:41 +01:00 |
|
drpatelh
|
9d168cf29e
|
Add deeptools
|
2020-08-05 17:17:34 +01:00 |
|
drpatelh
|
f481899049
|
Add subread
|
2020-08-05 17:17:19 +01:00 |
|
drpatelh
|
20e6d847a3
|
Add trimgalore
|
2020-08-05 17:17:12 +01:00 |
|
drpatelh
|
c5bb9c2fde
|
Add macs2
|
2020-08-05 17:17:05 +01:00 |
|
drpatelh
|
f61ad7506a
|
Add homer
|
2020-08-05 17:16:56 +01:00 |
|