Sruthi Suresh
a984c1be7c
Added all modules with basic functionality and updated meta.yml files.
2021-01-29 23:17:44 -06:00
Sruthi Suresh
89e5473b44
Updated modules with the changed container format
2021-01-29 23:17:44 -06:00
Sruthi Suresh
6677c98b11
Updated complement and completed slop module with all parameters available.
2021-01-29 23:17:44 -06:00
Sruthi Suresh
199dfc5ea3
Added complement module with necessary test dir/parameters
2021-01-29 23:17:44 -06:00
Sruthi Suresh
709970e9af
Completed slop module for modules with test directory and updated meta.yml file
2021-01-29 23:17:44 -06:00
Sruthi Suresh
5205ce286a
Added all modules using bedtools in the enhancer transcript identification section
2021-01-29 23:17:44 -06:00
Sruthi Suresh
637b545168
Removed extraneous modules and updated removegenes module
2021-01-29 23:17:44 -06:00
Sruthi Suresh
1426d89440
Completed sloprefseq and removegenes modules (main.nf, meta.yml and functiosn.nf file). Also added the test directory with input/output/main.nf files.
2021-01-29 23:17:44 -06:00
Sruthi Suresh
5b2633757e
updated test file and main.nf file
2021-01-29 23:17:44 -06:00
sruthipsuresh
521c87f999
Updated test.mainnf file.
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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
fefbdb9893
Created test file for checking code.
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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.
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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.
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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
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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
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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
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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
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ci: Fix artifact path
2021-02-04 15:48:52 +01:00
Edmund Miller
05c09429a3
ci: Fix artifact path
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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
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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
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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
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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"
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This reverts commit ffc218e51b
2021-02-03 20:08:11 -06:00
Edmund Miller
431c699727
Revert "ci: Test bowtie-build instead of _"
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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
