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275 commits

Author SHA1 Message Date
Anders Goncalves da Silva
487ec7b793
Fix test.yml 2021-02-12 14:42:42 -08:00
Anders Goncalves da Silva
24b212318b Merge branch 'master' into ivar-consensus 2021-02-12 11:51:24 -08:00
Anders Goncalves da Silva
8b3c16a518
Add ref FASTA to test main.nf 2021-02-12 11:29:16 -08:00
JoseEspinosa
fafe068192 Fixing test tags 2021-02-12 18:49:57 +01:00
JoseEspinosa
0688230863 Revert since fixes to test were not working 
This reverts commit d7a219e88d.
 2021-02-12 18:02:32 +01:00
JoseEspinosa
8e23e1839d Trying to fix tests 2021-02-12 17:56:51 +01:00
JoseEspinosa
d7a219e88d Fix test.yml 2021-02-12 17:37:49 +01:00
JoseEspinosa
6e8b63fc26 Add cat fastq module 2021-02-12 17:22:07 +01:00
MaxUlysse
9c98194d3c chores: remove fasta file from bwamem2 mem process 2021-02-12 16:00:59 +01:00
MaxUlysse
0afddf6ca4 fix: CI is working 2021-02-12 15:24:09 +01:00
Maxime Garcia
27be87ac72
Merge pull request #135 from drpatelh/bwa 
Update indices syntax for BWA index and mem modules
 2021-02-12 12:45:38 +01:00
Anders Goncalves da Silva
df9125b46a
Fix test name 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-10 12:05:01 -08:00
Anders Goncalves da Silva
40bbf94ef9
Update filename for outputted mpileup file in test 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-10 12:04:46 -08:00
Anders Goncalves da Silva
68de6fef0d
Fix indentation 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-10 12:04:15 -08:00
Anders Goncalves da Silva
ffa9cf85b1
Clean up header params 
I used these for testing and forgot to remove them

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-10 12:03:50 -08:00
Anders Goncalves da Silva
1f6419f8f5
Fix indentation 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-10 10:55:24 -08:00
drpatelh
1d00a4a11c Update md5sum 2021-02-09 23:31:39 +00:00
drpatelh
79d730f2c3 Change output name 2021-02-09 23:27:08 +00:00
drpatelh
7f629bca45 OCDness 2021-02-09 23:26:55 +00:00
Harshil Patel
28866f3dc7
Update tests/software/bedtools/maskfasta/main.nf 2021-02-09 21:36:38 +00:00
Harshil Patel
aaa088dba8
Update tests/software/bedtools/getfasta/main.nf 2021-02-09 21:34:29 +00:00
Anders Goncalves da Silva
8f546a1f95 Add ivar consensus 2021-02-09 10:26:35 -08:00
JoseEspinosa
68b85d9191 Merge remote-tracking branch 'upstream/master' into bedtools_getfasta 2021-02-09 18:23:24 +01:00
JoseEspinosa
e118bc049a Add bedtools getfasta module 2021-02-09 17:56:51 +01:00
JoseEspinosa
7536b386a5 Correct channel declaration on bedtools_maskfasta 2021-02-09 17:56:01 +01:00
JoseEspinosa
12ae7b0bff Adding blast blastn module 2021-02-09 16:58:36 +01:00
JoseEspinosa
c23b355b35 Add blast makeblastdb module 2021-02-09 15:44:34 +01:00
JoseEspinosa
c93e96101a Add untar module 2021-02-09 11:50:32 +01:00
JoseEspinosa
9b65961828 Fix file output path on test 2021-02-09 10:22:50 +01:00
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 Add bedtools maskfasta module 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 2021-02-08 21:41:24 +00:00
JoseEspinosa
f8882de456 Renaming test ymls just to: software tool 2021-02-08 21:56:53 +01:00
JoseEspinosa
f4e322f88d Merging upstream changes 
# Conflicts:
#	.github/filters.yml
 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 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
17dd0415f2
Merge pull request #146 from heuermh/bandage 
Add bandage image module
 2021-02-05 08:00:44 +01:00
Michael L Heuer
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
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
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