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Author SHA1 Message Date
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
ebf3a4529f
ci(picard): Update markduplicates 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
dfc8528df9
ci: Remove docker workflow 
This only applies to deprecated software
 2020-11-24 18:58:02 -06:00
Edmund Miller
691df9d469
style(actions): Create seperate software dir 
For future subworkflows
 2020-11-24 18:57:53 -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
Edmund Miller
b96f2d6a5e test(config): One config to rule them all 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-11-24 20:26:04 +00:00
Edmund Miller
2e56022e31 test(fastqc): Remove input symlinks 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-11-24 20:26:04 +00:00
Edmund Miller
1fd97e8804 test(fastqc): Fix md5sums 2020-11-24 20:26:04 +00:00
Edmund Miller
ba681c6f27 refactor(pytest-workflow): Move fastqc tests to tests/ 2020-11-24 20:26:04 +00:00
Edmund Miller
f235732a58
ci(fastqc): Use both threads in GitHub runner 2020-11-16 13:45:00 -06:00
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
Edmund Miller
29937fe198
test(fastqc): Add expected files and md5sums 
The md5 sums change for the zip files every run so it's difficult to hit
a moving target.
 2020-11-16 10:20:29 -06:00
Edmund Miller
6d857a2584
ci(fastqc): Run pytest-workflow instead of workflow 
This will check for the actual output files and their contents not just
whether the module runs or not.
 2020-11-16 09:37:45 -06:00
Edmund Miller
07017f401e
test(fastqc): Add initial pytest-workflow 2020-11-16 09:35:01 -06:00
Harshil Patel
751204ef33
Merge pull request #76 from drpatelh/versions 
Remove Singularity image path
 2020-11-12 15:27:06 +00:00
drpatelh
082c582258 Remove EClint for now 2020-11-12 15:22:15 +00:00
drpatelh
a3f46865ff Remove Singularity image path 2020-11-12 14:55:16 +00:00
Harshil Patel
65ba3128ee
Merge pull request #72 from drpatelh/versions 
Update badges in README
 2020-10-20 11:09:50 +01:00
drpatelh
99f5d49d37 Update README 2020-10-20 11:04:12 +01:00
drpatelh
5eb735f561 Update README 2020-10-20 11:02:46 +01:00
Harshil Patel
86dca6bfc2
Merge pull request #71 from drpatelh/versions 
Update picard version command and default container
 2020-10-20 10:24:02 +01:00
drpatelh
47d390772c Update picard version command and default container 2020-10-19 15:17:19 +01:00
Harshil Patel
ff0fe1a910
Merge pull request #70 from drpatelh/versions 
Update existing modules with new options and container syntax
 2020-10-15 11:28:13 +01:00
drpatelh
29f9b05433 Update docs 2020-10-15 11:13:54 +01:00
drpatelh
7e2c7b1b41 Update README 2020-10-15 11:02:04 +01:00
drpatelh
530789ba85 Get tests passing 2020-10-15 10:47:15 +01:00
drpatelh
c32fcb39fc Remove git update script 2020-10-15 10:22:40 +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
Harshil Patel
a6aab020df
Merge pull request #69 from drpatelh/versions 
Revert RSeQC version
 2020-10-12 18:03:21 +01:00
drpatelh
e9e81e8691 Revert RSeQC version 2020-10-12 17:47:13 +01:00
Harshil Patel
d8f202c563
Merge pull request #68 from drpatelh/versions 
Update tool versions
 2020-10-12 16:22:31 +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