Commit graph

125 commits

Author SHA1 Message Date
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