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142 commits

Author SHA1 Message Date
Edmund Miller
72b4fb35aa
test: Fix profile logic order 2021-02-02 17:32:21 -06:00
Edmund Miller
67deb0d47a
ci: Add singularity tmp dir 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-02 17:25:58 -06:00
Edmund Miller
6b675eef6d
ci: Set pull docker container to false 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-02 17:00:40 -06:00
Edmund Miller
688cc05fe8
tests: Remove -profile in tests 
See ddbca7b467 for more info
 2021-02-02 15:30:59 -06:00
Edmund Miller
ddbca7b467
test: Use profile ENV variable hack 
The user will now set the env variable and pass it to pytest. You also
can't set the env variable ahead of time, it has to be run with pytest.
Example:
PROFILE=conda pytest --tag fastqc --symlink --kwd
 2021-02-02 12:44:30 -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
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
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