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 |
|
Harshil Patel
|
bd59706d51
|
Merge pull request #118 from heuermh/dsh-bio
Added dsh-bio filter-bed as dsh_filterbed
|
2021-01-29 18:15:24 +00:00 |
|
Harshil Patel
|
0fcbc4233c
|
Merge pull request #126 from JoseEspinosa/samtools_viralrecon
Samtools viralrecon
|
2021-01-29 18:12:48 +00:00 |
|
JoseEspinosa
|
720db2bed5
|
Fixing samtools_mpileup test
|
2021-01-29 18:21:03 +01:00 |
|
JoseEspinosa
|
22dcdc692d
|
Adding samtools_mpileup module
|
2021-01-29 17:58:42 +01:00 |
|
JoseEspinosa
|
3eedca9bb4
|
Add samtools_view
|
2021-01-29 17:18:45 +01:00 |
|
kevinmenden
|
e8bd730164
|
added quast tests
|
2021-01-29 16:14:33 +01:00 |
|
kevinmenden
|
10bb80743a
|
started adding quast modules
|
2021-01-29 16:06:14 +01:00 |
|
kevinmenden
|
bacebdfb47
|
added pangolin workf
|
2021-01-29 12:53:51 +01:00 |
|
kevinmenden
|
44df90a795
|
Merge branch 'master' of https://github.com/nf-core/modules into pangolin-module
|
2021-01-29 12:50:24 +01:00 |
|
Harshil Patel
|
5da41ecb26
|
Merge pull request #122 from KevinMenden/master
Added tests and meta.yml files for Salmon
|
2021-01-29 11:49:03 +00:00 |
|
kevinmenden
|
9156becd19
|
changed 'covid' to 'sarscov2'
|
2021-01-29 12:45:21 +01:00 |
|
kevinmenden
|
14ade8060f
|
added preliminary pangolin test
|
2021-01-29 11:12:22 +01:00 |
|
kevinmenden
|
d91cd73e52
|
added test workflow
|
2021-01-29 09:41:24 +01:00 |
|
kevinmenden
|
0780155dc4
|
added cutadapt module and tests
|
2021-01-29 09:33:45 +01:00 |
|
kevinmenden
|
3390f7621d
|
removed should_exist tag
|
2021-01-27 16:32:04 +01:00 |
|
kevinmenden
|
48c570d6ac
|
added file exist to test.yml
|
2021-01-27 08:56:25 +01:00 |
|
kevinmenden
|
431a2eb73b
|
added quant test workflow
|
2021-01-26 15:58:22 +01:00 |
|
kevinmenden
|
915e0574a2
|
added salmon index test workflow
|
2021-01-26 15:44:22 +01:00 |
|
kevinmenden
|
81bcf0da82
|
added test.yml and md5sums
|
2021-01-26 15:38:56 +01:00 |
|
kevinmenden
|
8d4b71355e
|
added test data and salmon tests
|
2021-01-26 15:24:06 +01:00 |
|
kevinmenden
|
5be1598b29
|
remove log.progress.out from test
|
2021-01-25 15:21:48 +01:00 |
|
kevinmenden
|
a1e1e27f67
|
updated test md5sums
|
2021-01-25 15:00:18 +01:00 |
|
kevinmenden
|
71e0de733c
|
adapdted star for mutliple output BAMs
|
2021-01-25 14:09:03 +01:00 |
|
kevinmenden
|
6444af7b36
|
star module tests
|
2021-01-25 09:02:03 +01:00 |
|
Edmund Miller
|
cff3ac7e5f
|
ci: Make an edit to test pipeline trigger
Plus this got clean up in 0c9f29e0a2
|
2021-01-24 10:37:29 -06:00 |
|
kevinmenden
|
f58c1c1e9e
|
added star genomegenerate test
|
2021-01-22 14:01:59 +01:00 |
|
Michael L Heuer
|
23f9284aae
|
Added dsh-bio split-bed as dsh_splitbed
|
2021-01-21 16:34:49 -06:00 |
|
Michael L Heuer
|
eb6408f3dc
|
Added dsh-bio filter-bed as dsh_filterbed
|
2021-01-21 15:16:20 -06:00 |
|
Edmund Miller
|
daa25b9329
|
Merge branch 'preseq_test'
|
2021-01-15 17:41:13 -06:00 |
|
Edmund Miller
|
86850dc8a4
|
style: Remove old comment
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2021-01-15 10:32:20 -06:00 |
|
sruthipsuresh
|
7729fee5a9
|
Added gffread and gff3 file for testing
|
2021-01-15 10:32:20 -06:00 |
|
Edmund Miller
|
d7a78fa127
|
style: Fix indent
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2021-01-15 10:28:11 -06:00 |
|
sruthipsuresh
|
b95bd37780
|
Added ucsc module
|
2021-01-15 10:28:11 -06:00 |
|
Harshil Patel
|
27dbe8b52a
|
Merge pull request #115 from Functional-Genomics-Lab/stringtie_test
Added testing for Stringtie
|
2021-01-15 16:09:39 +00:00 |
|
Edmund Miller
|
53830e05c7
|
test: Fix typo
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2021-01-15 10:07:44 -06:00 |
|
Edmund Miller
|
fe39c7822f
|
style: Fix indentation
|
2021-01-15 10:01:02 -06:00 |
|
Edmund Miller
|
b9e8f959b3
|
style: Standardize process names
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2021-01-15 10:00:40 -06:00 |
|