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Author SHA1 Message Date
JoseEspinosa
13e9f81160 Fixing lint tests 2021-01-29 18:01:58 +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
34cfc32c29 added quast workflow 2021-01-29 16:15:45 +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
Michael L Heuer
d2723408ad
Apply suggestions from code review 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-01-29 09:01:21 -06:00
Harshil Patel
29ce4e670f
Merge pull request #124 from KevinMenden/pangolin-module 
Added pangolin module
 2021-01-29 11:58:54 +00:00
kevinmenden
d30994c6ef Merge branch 'pangolin-module' of https://github.com/KevinMenden/modules into pangolin-module 2021-01-29 12:54:38 +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
Harshil Patel
adfb38aa62
Merge pull request #123 from KevinMenden/cutadapt-module 
Added cutadapt module
 2021-01-29 11:47:21 +00:00
kevinmenden
4e48b416b9 Merge branch 'master' of https://github.com/KevinMenden/modules 2021-01-29 12:45:38 +01:00
kevinmenden
9156becd19 changed 'covid' to 'sarscov2' 2021-01-29 12:45:21 +01:00
Harshil Patel
59e3e8202b
Update software/pangolin/main.nf 2021-01-29 11:43:42 +00:00
Kevin Menden
afaef3c30d
Apply suggestions from code review 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-01-29 12:40:15 +01:00
kevinmenden
a22f430674 updated input description 2021-01-29 12:34:23 +01:00
Kevin Menden
8f2f936cd4
Apply suggestions from code review 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-01-29 12:33:37 +01:00
kevinmenden
14ade8060f added preliminary pangolin test 2021-01-29 11:12:22 +01:00
kevinmenden
69a41cadbc added pangolin module 2021-01-29 11:03:54 +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
3750bea2dd fixed typo 2021-01-26 16:18:46 +01:00
kevinmenden
a3185732ff added meta.yml files 2021-01-26 16:12:41 +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
Harshil Patel
3ef16b7cfd
Merge pull request #121 from KevinMenden/master 
Adding test for STAR
 2021-01-26 13:01:27 +00:00
kevinmenden
84355f674d added optional output files 2021-01-26 13:31:30 +01:00
Kevin Menden
8e2749beb7
Apply suggestions from code review 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-01-26 12:46:30 +01:00
kevinmenden
5be1598b29 remove log.progress.out from test 2021-01-25 15:21:48 +01:00
kevinmenden
272de7c021 Added meta.yml files for align and genomegenerate 2021-01-25 15:14:57 +01:00
kevinmenden
046444a736 added workflow files 2021-01-25 15:00:51 +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
Michael L Heuer
e6547d5b16 Update dsh-bio version to 2.0 2021-01-22 12:12:56 -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
Edmund Miller
4f0c34bbfb ci: Bump nextflow version 
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