Commit graph

334 commits

Author SHA1 Message Date
kevinmenden
07f0a2476a fixed linting errors 2020-12-18 09:50:05 +01:00
Chris Cheshire
a57169a5da seacr | updated test script 2020-12-17 14:23:20 +00:00
Chris Cheshire
b24834dfce seacr | local testing implimented 2020-12-17 14:20:24 +00:00
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
kevinmenden
9d67da2b2c added module yml files 2020-12-08 13:40:32 +01:00
Abhinav Sharma
5949bfc15b Edit the location of multiqc_config file 2020-12-04 22:55:15 +05:30
Abhinav Sharma
27b4b29976 Remove the extra data files 2020-12-04 20:20:59 +05:30
Abhinav Sharma
3da7aec183 Update the signatures 2020-12-04 12:25:16 +05:30
Abhinav Sharma
a30df8a59b Iterate again on MultiQC 2020-12-04 12:11:17 +05:30
Abhinav Sharma
84c0bda00e Apply suggestions from code review by @Emiller88 2020-12-03 12:57:24 +05:30
Abhinav Sharma
5fd3ba3ce6 Update the tests for MultiQC 2020-12-02 13:09:32 +05:30
Edmund Miller
6404c3390d
ci(fastqc): Remove md5sums
These may not work across nextflow versions
2020-12-01 11:18:55 -06:00
Abhinav Sharma
b43c1f3937 Refactor the multiqc test code 2020-12-01 12:19:52 +05:30
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
d1a77b2fb2
test(picard): Add failing test for markduplicates 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
d009420a0c
test(fastqc): Fix md5sums
These must have gotten messed up at some point
83539fcdf2 is my guess
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
83539fcdf2
test(fastqc): restructure under software/fastqc
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2020-11-24 15:30:51 -06:00