JoseEspinosa
|
f7f06dd6e8
|
Add gunzip module
|
2021-02-09 10:05:55 +01:00 |
|
Harshil Patel
|
46e5df2cf7
|
Merge pull request #151 from drpatelh/bedtools
Follow up fixes for bedtools modules added in #79
|
2021-02-09 01:54:31 +00:00 |
|
Harshil Patel
|
84cf5ea2ef
|
Merge pull request #153 from JoseEspinosa/bedtools_maskfasta
Add bedtools maskfasta module
|
2021-02-08 23:11:00 +00:00 |
|
JoseEspinosa
|
1b3e5e0283
|
Fixing module name in test.yml
|
2021-02-08 23:45:01 +01:00 |
|
JoseEspinosa
|
02d10c25a3
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Add bedtools maskfasta module
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2021-02-08 23:41:10 +01:00 |
|
drpatelh
|
0b9e32e32d
|
Remove complement suffix from tests
|
2021-02-08 22:25:13 +00:00 |
|
Harshil Patel
|
0f6830f7cc
|
Update tests/software/bcftools/consensus/main.nf
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2021-02-08 21:41:24 +00:00 |
|
JoseEspinosa
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f8882de456
|
Renaming test ymls just to: software tool
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2021-02-08 21:56:53 +01:00 |
|
JoseEspinosa
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f4e322f88d
|
Merging upstream changes
# Conflicts:
# .github/filters.yml
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2021-02-08 18:09:41 +01:00 |
|
JoseEspinosa
|
4fa38ebb7a
|
Separate test data to break dependencies between bcftools modules tests
|
2021-02-08 16:51:21 +01:00 |
|
JoseEspinosa
|
83cc25860d
|
Rearranging tests to test each module separately
|
2021-02-08 15:16:51 +01:00 |
|
JoseEspinosa
|
5071bf5914
|
Merge remote-tracking branch 'upstream/master' into bcftools_viralrecon
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2021-02-08 10:45:57 +01:00 |
|
drpatelh
|
83a50d8ae0
|
Rename SOFTWARE_TOOL to TOOL_SUBTOOL
|
2021-02-07 23:20:53 +00:00 |
|
drpatelh
|
5779b180da
|
Fix bedtools sort module
|
2021-02-07 21:32:43 +00:00 |
|
drpatelh
|
f3b5af4ed5
|
Fix bedtools slip module
|
2021-02-07 21:32:20 +00:00 |
|
drpatelh
|
38964ecfc0
|
Fix bedtools intersect module
|
2021-02-07 21:32:01 +00:00 |
|
drpatelh
|
a37b116186
|
Fix bedtools merge module
|
2021-02-07 21:31:39 +00:00 |
|
drpatelh
|
4564ef0e54
|
Fix bedtools genomecov module
|
2021-02-07 21:31:21 +00:00 |
|
drpatelh
|
a0c08e0c06
|
Fix bedtools complement module
|
2021-02-07 21:31:02 +00:00 |
|
Harshil Patel
|
0393d39105
|
Update tests/software/bedtools/complement/main.nf
|
2021-02-07 20:35:51 +00:00 |
|
Harshil Patel
|
5269c1ec60
|
Update tests/software/bedtools/intersect/main.nf
|
2021-02-07 20:35:12 +00:00 |
|
Harshil Patel
|
8841af1267
|
Update tests/software/bedtools/merge/main.nf
|
2021-02-07 20:34:30 +00:00 |
|
Harshil Patel
|
b068f2fc53
|
Update tests/software/bedtools/sort/main.nf
|
2021-02-07 20:33:02 +00:00 |
|
drpatelh
|
137d00b523
|
Fix tests
|
2021-02-05 10:44:08 +00:00 |
|
drpatelh
|
81ae0089bc
|
Fix merge conflicts
|
2021-02-05 10:06:39 +00:00 |
|
Kevin Menden
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17dd0415f2
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Merge pull request #146 from heuermh/bandage
Add bandage image module
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2021-02-05 08:00:44 +01:00 |
|
Michael L Heuer
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37a9f6f456
|
Address review comments
|
2021-02-04 12:10:54 -06:00 |
|
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 |
|
Edmund Miller
|
431c699727
|
Revert "ci: Test bowtie-build instead of _"
This reverts commit 9b454416d2 .
|
2021-02-03 20:06:05 -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
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ci: Test buil to see if build is special
|
2021-02-03 12:43:18 -06:00 |
|
Edmund Miller
|
4d58a037f6
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test(bowtie_align): Fix md5sum
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2021-02-03 12:37:19 -06:00 |
|
Edmund Miller
|
6901c7e830
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ci: Fix bowtie_build names with ""
|
2021-02-03 12:37:14 -06:00 |
|
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 |
|
drpatelh
|
f079ce9d1f
|
Fix preseq tests
|
2021-02-03 17:28:44 +00:00 |
|
drpatelh
|
f37fb66f40
|
Fix bwa mem tests
|
2021-02-03 17:26:43 +00:00 |
|
drpatelh
|
8a15852756
|
Fix salmon index tests
|
2021-02-03 17:13:47 +00:00 |
|
drpatelh
|
058d7b397c
|
Fix fastqc test
|
2021-02-03 17:03:30 +00:00 |
|
drpatelh
|
39b8600dbb
|
Fix trimgalore test
|
2021-02-03 17:02:52 +00:00 |
|
drpatelh
|
305d47fc87
|
Change path to tests
|
2021-02-03 16:44:56 +00:00 |
|
drpatelh
|
a87d584c48
|
Change path to bowtie tests
|
2021-02-03 16:39:00 +00:00 |
|
drpatelh
|
9b153f296d
|
Add check to see if bowtie bam files exists
|
2021-02-03 16:26:10 +00:00 |
|
drpatelh
|
239cbe17ad
|
Fix relative paths
|
2021-02-03 16:20:02 +00:00 |
|
drpatelh
|
38c3ecfac6
|
Merge branch 'master' of https://github.com/nf-core/modules into split_tests
|
2021-02-03 16:05:06 +00:00 |
|
drpatelh
|
743ba37d4b
|
Update filters paths
|
2021-02-03 16:04:43 +00:00 |
|
drpatelh
|
ff23473e82
|
Restructure tests to run individually for each module
|
2021-02-03 16:02:58 +00:00 |
|
drpatelh
|
8be5e05111
|
Remove bam md5sum check for bowtie
|
2021-02-03 13:46:44 +00:00 |
|
drpatelh
|
1512c9af74
|
Unable to test BAM due to command
|
2021-02-03 12:26:10 +00:00 |
|
Edmund Miller
|
688cc05fe8
|
tests: Remove -profile in tests
See ddbca7b467 for more info
|
2021-02-02 15:30:59 -06:00 |
|
Harshil Patel
|
e7b1241449
|
Merge pull request #120 from nf-core/composite-runs
Universal CI job
|
2021-02-02 18:26:02 +00:00 |
|
drpatelh
|
6ac252e407
|
Change singularity to docker again
|
2021-02-02 13:38:34 +00:00 |
|
drpatelh
|
838defa350
|
Update md5sums
|
2021-02-02 13:37:40 +00:00 |
|
drpatelh
|
05b15df17e
|
Remove file extension
|
2021-02-02 12:46:34 +00:00 |
|
drpatelh
|
d63d40827e
|
Fix bwa index tests
|
2021-02-02 12:40:55 +00:00 |
|
drpatelh
|
ade6124a84
|
Change tests
|
2021-02-02 12:35:06 +00:00 |
|
JoseEspinosa
|
26829497d5
|
Fixing typo on path for md5 check
|
2021-02-02 12:19:57 +01:00 |
|
JoseEspinosa
|
e7f15feccf
|
Adding --no-version to bcftools_isec for tests md5 check
|
2021-02-02 11:00:02 +01:00 |
|
JoseEspinosa
|
3a40ec5664
|
Adding bcftools_isec taking a path with several vcfs and its tests
|
2021-02-02 10:50:45 +01:00 |
|
JoseEspinosa
|
8e4764b8ed
|
bcftools_filter adding argument to test to enable md5 check
|
2021-02-02 10:19:34 +01:00 |
|
JoseEspinosa
|
c25f8f0f6c
|
Fixing tests
|
2021-02-02 09:57:55 +01:00 |
|
JoseEspinosa
|
cee37852cd
|
Merge remote-tracking branch 'upstream/master' into bcftools_viralrecon
|
2021-02-02 09:15:20 +01:00 |
|
JoseEspinosa
|
a3ce63c79c
|
Adding tests for bcftools
|
2021-02-02 09:14:00 +01:00 |
|
drpatelh
|
f84e5b59ca
|
Rename bowtie_index to bowtie_build
|
2021-02-01 17:53:31 +00:00 |
|
Harshil Patel
|
0a41130276
|
Merge pull request #131 from KevinMenden/fastp-module
Adding fastp module
|
2021-02-01 13:43:35 +00:00 |
|
Harshil Patel
|
e851da8640
|
Merge pull request #130 from KevinMenden/master
Adding a QUAST module
|
2021-02-01 13:17:57 +00:00 |
|
Kevin Menden
|
0bd8506ea1
|
Update tests/software/quast/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2021-02-01 14:04:08 +01:00 |
|
Kevin Menden
|
05370b5e16
|
Update tests/software/quast/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2021-02-01 14:03:49 +01:00 |
|
kevinmenden
|
e9e795633d
|
added fastp tests
|
2021-02-01 14:02:06 +01:00 |
|
kevinmenden
|
a342296d70
|
fixed test md5s
|
2021-02-01 13:36:25 +01:00 |
|
kevinmenden
|
b5298f94d8
|
refactored quast module
|
2021-02-01 13:13:21 +01:00 |
|
Harshil Patel
|
c74d8a1711
|
Merge pull request #128 from JoseEspinosa/bowtie2_viralrecon
Bowtie2 viralrecon 2
|
2021-02-01 09:56:11 +00:00 |
|
Harshil Patel
|
2c962f34df
|
Merge pull request #110 from luslab/master
Add SEACR module containing a single CALLPEAK process
|
2021-02-01 09:48:15 +00:00 |
|
JoseEspinosa
|
8fb6b80abd
|
Fixing some md5 hashes
|
2021-01-30 23:08:17 +01:00 |
|
Harshil Patel
|
eadbea4b83
|
Merge pull request #127 from JoseEspinosa/bowtie2_viralrecon
Bowtie2 viralrecon
|
2021-01-30 13:22:30 +00:00 |
|
sruthipsuresh
|
7a1c2a2eb5
|
Fixed slop module
|
2021-01-29 23:17:44 -06:00 |
|
sruthipsuresh
|
93e414635b
|
Fixed md5sum, fixed filters, fixed slop input
|
2021-01-29 23:17:44 -06:00 |
|
sruthipsuresh
|
78ac4435be
|
Added new tests, todo: fix md5sums
|
2021-01-29 23:17:44 -06:00 |
|
Edmund Miller
|
2b0d51ca9c
|
test(bedtools): Remove old style tests
AKA how the tests were done last week.
|
2021-01-29 23:17:44 -06:00 |
|
Edmund Miller
|
7d52907d1c
|
test(bedtools): Fix typo on yaml indentation
|
2021-01-29 23:17:44 -06:00 |
|
sruthipsuresh
|
ac7f634675
|
Added complement test
|
2021-01-29 23:17:44 -06:00 |
|
sruthipsuresh
|
e360617ac6
|
Fixed images, genomecov
|
2021-01-29 23:17:44 -06:00 |
|
sruthipsuresh
|
e3bbbb48fc
|
Fixed slop file
|
2021-01-29 23:17:44 -06:00 |
|
sruthipsuresh
|
29639c522f
|
Corrected sort
|
2021-01-29 23:17:44 -06:00 |
|
sruthipsuresh
|
a108bd407e
|
Corrected md5sum and output
|
2021-01-29 23:17:44 -06:00 |
|
sruthipsuresh
|
2f19b4279c
|
All modules corrected, TODO config
|
2021-01-29 23:17:44 -06:00 |
|
sruthipsuresh
|
32564137fd
|
Corrected workflows and ran editor config
|
2021-01-29 23:17:44 -06:00 |
|
sruthipsuresh
|
672f94f2af
|
rebased and updated all bedtools testing and modules
|
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
|
6b873d7d33
|
Remove single_end if/else
|
2021-02-05 11:35:11 -06:00 |
|
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
|
d5f2f5e32d
|
Add minimap2 align module
|
2021-02-04 13:42:08 -06:00 |
|
JoseEspinosa
|
ddbe8055c2
|
Adding tests
|
2021-01-29 19:31:33 +01:00 |
|