Commit graph

97 commits

Author SHA1 Message Date
JoseEspinosa
22dcdc692d Adding samtools_mpileup module 2021-01-29 17:58:42 +01:00
JoseEspinosa
3eedca9bb4 Add samtools_view 2021-01-29 17:18:45 +01:00
kevinmenden
5be1598b29 remove log.progress.out from test 2021-01-25 15:21:48 +01:00
kevinmenden
a1e1e27f67 updated test md5sums 2021-01-25 15:00:18 +01:00
kevinmenden
71e0de733c adapdted star for mutliple output BAMs 2021-01-25 14:09:03 +01:00
kevinmenden
6444af7b36 star module tests 2021-01-25 09:02:03 +01:00
kevinmenden
f58c1c1e9e added star genomegenerate test 2021-01-22 14:01:59 +01:00
Edmund Miller
daa25b9329
Merge branch 'preseq_test' 2021-01-15 17:41:13 -06:00
Edmund Miller
86850dc8a4 style: Remove old comment
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-15 10:32:20 -06:00
sruthipsuresh
7729fee5a9 Added gffread and gff3 file for testing 2021-01-15 10:32:20 -06:00
Edmund Miller
d7a78fa127 style: Fix indent
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-15 10:28:11 -06:00
sruthipsuresh
b95bd37780 Added ucsc module 2021-01-15 10:28:11 -06:00
Harshil Patel
27dbe8b52a
Merge pull request #115 from Functional-Genomics-Lab/stringtie_test
Added testing for Stringtie
2021-01-15 16:09:39 +00:00
Edmund Miller
53830e05c7
test: Fix typo
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-15 10:07:44 -06:00
Edmund Miller
fe39c7822f
style: Fix indentation 2021-01-15 10:01:02 -06:00
Edmund Miller
b9e8f959b3
style: Standardize process names
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-15 10:00:40 -06:00
sruthipsuresh
ec91171152 Corrected naming to ensure test checks work 2021-01-15 09:38:13 -06:00
sruthipsuresh
5a1c1f90e5 removed md5sums for pdf, rdata 2021-01-15 09:38:13 -06:00
sruthipsuresh
3f814d1e2f Workflow and md5sums added 2021-01-15 09:38:13 -06:00
sruthipsuresh
269d9888fe Corrected bash error, tested process 2021-01-15 09:38:13 -06:00
Sruthi Suresh
b7435b0159 added test file for phantompeakqualtools for testing 2021-01-15 09:38:13 -06:00
sruthipsuresh
09d56efe12 Fixed with mr file for size issues 2021-01-14 02:12:57 -06:00
sruthipsuresh
00ef1d3863
Changed input to bed files 2021-01-15 16:52:17 -06:00
sruthipsuresh
a66618be98
Delete tests/software/phantompeakqualtools directory 2021-01-13 21:23:02 -06:00
sruthipsuresh
6f3cbfcd9a Fixed test.yml 2021-01-12 18:14:28 -06:00
sruthipsuresh
b297f7aea1 Fixed test and removed phantompeak tests 2021-01-12 18:04:12 -06:00
sruthipsuresh
7c88cf4f67 Finished module with md5sums 2021-01-12 09:29:31 -06:00
sruthipsuresh
0a04c96357 Added module, TODO data 2021-01-12 09:13:37 -06:00
sruthipsuresh
3b581d1912 Updated test.yml 2021-01-12 08:56:11 -06:00
sruthipsuresh
a2faeb703f Fixed md5sums 2021-01-12 08:50:20 -06:00
sruthipsuresh
cb39fcb915 Added preseq module and workflow 2021-01-12 08:41:09 -06:00
sruthipsuresh
e1a3d1b18a Corrected naming to ensure test checks work 2020-12-21 19:53:03 -06:00
sruthipsuresh
5319eabbc5 removed md5sums for pdf, rdata 2020-12-19 06:09:04 -06:00
sruthipsuresh
522b896534 Workflow and md5sums added 2020-12-19 06:09:04 -06:00
sruthipsuresh
8c088d473b Corrected bash error, tested process 2020-12-19 06:09:04 -06:00
Sruthi Suresh
10d0058a1a added test file for phantompeakqualtools for testing 2020-12-19 06:09:04 -06:00
Harshil Patel
c98f9284a2
Merge pull request #89 from KevinMenden/master
Add bowtie module
2020-12-18 14:56:29 +00:00
kevinmenden
8f75bac67e update test.bam md5sums 2020-12-18 11:16:58 +01:00
kevinmenden
db0b631906 removed index from test output 2020-12-18 11:06:02 +01:00
kevinmenden
299a3fa07e adding .index back 2020-12-18 10:58:37 +01:00
kevinmenden
07f0a2476a fixed linting errors 2020-12-18 09:50:05 +01:00
kevinmenden
f35850bf14 bowtie bam output 2020-12-16 11:02:58 +01:00
drpatelh
141ca290b7 Change md5sum for picard Markduplicates due to version bump 2020-12-14 00:44:49 +00:00
kevinmenden
0d7c8276b7 added test yml and md5s 2020-12-09 16:54:11 +01:00
kevinmenden
42020ce5ac added tests for bowtie paired-end alignment; resolved index bug 2020-12-09 16:39:05 +01:00
Harshil Patel
79a0ce79ab
Merge pull request #82 from abhi18av/master
Add multiqc module
2020-12-09 11:31:07 +00:00
Abhinav Sharma
0c9f29e0a2 Give finishing touches after the review 2020-12-08 19:08:00 +05:30
Abhinav Sharma
b56a0322ab
Apply suggestions from code review by @drpatelh
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2020-12-08 18:57:14 +05:30
kevinmenden
fee0707af1 added bowtie_align workflow test 2020-12-08 14:19:34 +01:00
kevinmenden
6660a597a3 added tests for bowtie module 2020-12-08 13:59:14 +01:00