millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-11-14 13:43:09 +00:00
Code Issues Releases Packages Activity
792 commits 30 branches 0 tags 142 MiB
Commit graph

792 commits

This branch
This branch
All branches
Author SHA1 Message Date
sruthipsuresh
fefbdb9893 Created test file for checking code. 
Still need to add parameters map and chrom sizes path.
 2021-01-29 23:17:44 -06:00
Sruthi Suresh
185ca19930 Added module for slopRefseq, including meta.yml, functions and main 2021-01-29 23:17:44 -06:00
Sruthi Suresh
352a48741f updated test file and main.nf file 2021-01-29 23:17:44 -06:00
Sruthi Suresh
5a997c5ac6 Updated module, need to fix cardinality of tuple 2021-01-29 23:17:44 -06:00
Sruthi Suresh
022b0bfe54 Updated test directory with input files, corrected main.nf and config. Additionally, main.nf for the process was updated. 2021-01-29 23:17:44 -06:00
sruthipsuresh
74f1a62fa4 Corrected errors in naming. 2021-01-29 23:17:44 -06:00
sruthipsuresh
ec6ebe086f Updated test.mainnf file. 
Added the necessary chrom sizes input and changed test file to directory (as specified in nfcore).
 2021-01-29 23:17:44 -06:00
sruthipsuresh
898c0775c6 Main.nf for bedtools module added. 2021-01-29 23:17:44 -06:00
sruthipsuresh
a654c0f5fa Created fixbedcoordinates functions.nf file 2021-01-29 23:17:44 -06:00
sruthipsuresh
c8f30720a1 Created meta file for the fixbedcoordinates module. 2021-01-29 23:17:44 -06:00
sruthipsuresh
8d6d48f067 Created test file for checking code. 
Still need to add parameters map and chrom sizes path.
 2021-01-29 23:17:44 -06:00
sruthipsuresh
5f705f69e1 Fixed version error in bedtools. 2021-01-29 23:17:44 -06:00
sruthipsuresh
fe2e27c793 Update main.nf 
Updated bedtools module with updated container version and upstream/downstream values.
 2021-01-29 23:17:44 -06:00
Sruthi Suresh
69f9f1cc89 Updated with removegenes folder (with meta, main and generic function file). 2021-01-29 23:17:44 -06:00
Sruthi Suresh
cfe8a490d8 Added module for slopRefseq, including meta.yml, functions and main 2021-01-29 23:17:44 -06:00
Harshil Patel
b260192942
Merge pull request #149 from heuermh/minimap2 
Add minimap2 align module
 2021-02-07 16:37:26 +00:00
Michael L Heuer
35ed09b06e Fix CI test failure 2021-02-05 11:41:36 -06:00
Michael L Heuer
6b873d7d33 Remove single_end if/else 2021-02-05 11:35:11 -06:00
Harshil Patel
31520fce97
Update software/minimap2/align/main.nf 2021-02-05 10:45:34 +00:00
Kevin Menden
17dd0415f2
Merge pull request #146 from heuermh/bandage 
Add bandage image module
 2021-02-05 08:00:44 +01:00
Michael L Heuer
50bebac136 Remove pairwise test 2021-02-04 15:22:12 -06:00
Michael L Heuer
061b13bf25 Fix md5 --> md5sum 2021-02-04 13:48:56 -06:00
Michael L Heuer
bbc8c725a2 Fix lint errors 2021-02-04 13:45:39 -06:00
Michael L Heuer
d5f2f5e32d Add minimap2 align module 2021-02-04 13:42:08 -06:00
Michael L Heuer
37a9f6f456 Address review comments 2021-02-04 12:10:54 -06:00
Kevin Menden
089af956fb
Merge pull request #148 from nf-core/fix-artifact-path 
ci: Fix artifact path
 2021-02-04 15:48:52 +01:00
Edmund Miller
05c09429a3
ci: Fix artifact path 
Had to change it for singularity
 2021-02-04 08:45:34 -06:00
Harshil Patel
08d8443510
Merge pull request #143 from nf-core/ci-fixes 
Get Singularity CI tests working
 2021-02-04 11:28:49 +00:00
Harshil Patel
5aa920eb53
Update tests/software/bowtie/align/test.yml 2021-02-04 10:19:28 +00:00
Harshil Patel
68f9a0b711
Update tests/software/bowtie/build/test.yml 2021-02-04 10:08:01 +00:00
Harshil Patel
eb45368a35
Update tests/software/bowtie2/build/test.yml 2021-02-04 10:07:44 +00:00
Kevin Menden
f298c594fe
Update meta.yml 
Just a small edit, we want to keep this consistent for linting
 2021-02-04 07:34:08 +01:00
Edmund Miller
d48e865401
ci: Use bowtie filter 
This will cause a bit of duplication, but it appears to work. Still the
same logic, because any changes to bowtie*/build will run the align
modules also. So the bowtie_align tags may not even be necessary, since
we can't seem to get the bowtie*_build tags to kick off on their own
anyways. Thank you for coming to my TED talk.
 2021-02-03 20:15:56 -06:00
Edmund Miller
6fe7b48b5b
Revert "Run alllll the testsgit add .github/workflows/pytest-workflow.yml" 
This reverts commit ffc218e51b.
 2021-02-03 20:08:11 -06:00
Edmund Miller
431c699727
Revert "ci: Test bowtie-build instead of _" 
This reverts commit 9b454416d2.
 2021-02-03 20:06:05 -06:00
drpatelh
ffc218e51b
Run alllll the testsgit add .github/workflows/pytest-workflow.yml 2021-02-03 20:03:45 -06:00
drpatelh
fe3cb87f6d
Direct download Singularity containers 2021-02-03 20:03:45 -06:00
drpatelh
0c88ff7458
Upgrade Singularity and change TMPDIR for pytest output 2021-02-03 20:03:43 -06:00
Michael L Heuer
05d257e8f5 Fix lint errors 2021-02-03 19:34:25 -06:00
Michael L Heuer
c466255f6f Add bandage image module 2021-02-03 19:31:58 -06:00
Edmund Miller
9b454416d2
ci: Test bowtie-build instead of _ 2021-02-03 13:17:14 -06:00
Edmund Miller
7dbac4bdef
ci: Test adding another work to test name 2021-02-03 13:17:14 -06:00
Edmund Miller
b058da5856
ci: Test buil to see if build is special 2021-02-03 12:43:18 -06:00
Edmund Miller
4d58a037f6
test(bowtie_align): Fix md5sum 2021-02-03 12:37:19 -06:00
Edmund Miller
6901c7e830
ci: Fix bowtie_build names with "" 2021-02-03 12:37:14 -06:00
Harshil Patel
5f810beaa4
Merge pull request #142 from drpatelh/split_tests 
Split tests
 2021-02-03 18:09:30 +00:00
drpatelh
e71b3eaaa5 Rename workflows 2021-02-03 17:48:17 +00:00
drpatelh
ff6f0642d2 Fix multiqc tests 2021-02-03 17:43:14 +00:00
drpatelh
0683efc679 Fix salmon quant tests 2021-02-03 17:36:06 +00:00
drpatelh
550494cbd1 Fix picard mergesamfiles test 2021-02-03 17:31:41 +00:00