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
ci: Test buil to see if build is special
2021-02-03 12:43:18 -06:00
Edmund Miller
4d58a037f6
test(bowtie_align): Fix md5sum
2021-02-03 12:37:19 -06:00
Edmund Miller
6901c7e830
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
467d1595c4
test: Use docker image with singularity
2021-02-02 18:14:39 -06:00
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