Commit graph

30 commits

Author SHA1 Message Date
Edmund Miller
d76638d6f8
style(#77): Fix editorconfig errors 2020-12-17 17:50:24 -06:00
drpatelh
200c946693 Add --singularity_pull_docker_container to module yml 2020-12-14 00:34:24 +00:00
drpatelh
99a2364a26 Update all other modules 2020-12-14 00:05:48 +00:00
Edmund Miller
016d8684f3
test(bwa): Refactor to use pytest-workflow 2020-11-24 19:00:11 -06:00
drpatelh
a3f46865ff Remove Singularity image path 2020-11-12 14:55:16 +00:00
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
e438d026bd Unify syntax 2020-09-10 16:45:11 +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
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
a6fc702c8b Update bwa index docs 2020-08-07 12:38:01 +01:00
drpatelh
f315a7b3c4 Hard copy files 2020-08-05 18:38:27 +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
3b1669c317 Add bwa mem 2020-08-05 17:16:08 +01:00
drpatelh
7938a60a02 Add bwa index 2020-08-05 17:15:56 +01:00
drpatelh
c08e6959a5 Reorganise everything 2020-08-05 16:09:25 +01:00
Paolo Di Tommaso
70daf8be30
Minor style improvents
This commit provides a minor refactoring with som
Nextflow code style improvments:
- Replaces `.toGiga()` with `.giga`
- Replaces `tag { foo }` with `tag "$foo"`
- Move publishDir before input declarations. Directives should be
  before the first input. Tho this is not enforced, it may be in
  future versions.
- Replaces input `file` with `path`
- Remove unnecessary parentheses
2020-07-27 12:11:42 +02:00
Phil Ewels
d3f3432451 Update test file imports 2020-07-11 14:33:12 +02:00
Phil Ewels
014fef2e92 Rename tools to software 2020-07-11 14:27:21 +02:00