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406 commits

Author SHA1 Message Date
Harshil Patel
a282ecd8c7
Merge pull request #172 from andersgs/ivar-variant 
Add ivar variants
 2021-02-16 23:20:30 +00:00
Harshil Patel
cf2f0762aa
Update main.nf 2021-02-16 23:06:26 +00:00
Harshil Patel
7c276d2974
Update tests/software/ivar/variants/main.nf 2021-02-16 23:01:27 +00:00
Harshil Patel
27020105aa
Update tests/software/ivar/variants/main.nf 2021-02-16 23:00:30 +00:00
Harshil Patel
de90d371dc
Update tests/software/ivar/variants/main.nf 2021-02-16 22:58:38 +00:00
Harshil Patel
23987bdad0
Update tests/software/ivar/variants/main.nf 2021-02-16 22:57:47 +00:00
Harshil Patel
b07ad23efa
Merge pull request #179 from MaxUlysse/master_htslib_tabix 
Replace bcftools/tabix by tabix/tabix
 2021-02-16 22:30:45 +00:00
Harshil Patel
4f11064ae2
Update tests/software/tabix/bgzip/main.nf 2021-02-16 22:30:06 +00:00
Harshil Patel
8dd6d1d38a
Update tests/software/tabix/bgzip/main.nf 2021-02-16 22:29:13 +00:00
Harshil Patel
d6d34a4b5b
Merge pull request #177 from MaxUlysse/master_gatk_createsequencedictionary 
Add gatk/createsequencedictionary
 2021-02-16 22:21:38 +00:00
MaxUlysse
6a147b8aaa chores: replace bcftools/bgzip by tabix/bgzip cf #179 2021-02-16 19:11:36 +01:00
MaxUlysse
5a144d6213 fix: merge bcftools/tabix and htslib/tabix tests into tabix/tabix 2021-02-16 18:35:32 +01:00
MaxUlysse
f660324508 chores: move file 2021-02-16 18:20:43 +01:00
MaxUlysse
5e71dc94d6 fix: make HTSLIB_TABIX more modular 2021-02-16 17:06:55 +01:00
MaxUlysse
fa34f806d2 chores: add bgzip files for tests 2021-02-16 17:06:09 +01:00
MaxUlysse
10524e3515 chores: add modules for htslib/tabix 2021-02-16 14:47:53 +01:00
MaxUlysse
4968458b6c chores: add cpus, memory and time requirements to limit resource consumption 2021-02-16 14:18:29 +01:00
MaxUlysse
763800a0e2 fix: correct md5sum 2021-02-16 13:54:54 +01:00
MaxUlysse
28dc9227d7 fix: remove memory requirements and simplify URI 2021-02-16 13:54:40 +01:00
MaxUlysse
053dd6ee1b add minimal cpu,memory and time requirements 2021-02-16 13:40:22 +01:00
MaxUlysse
7f35a1742d chores: add gatk/createsequencedictionary module 2021-02-16 13:40:06 +01:00
Anders Goncalves da Silva
eeedb959c9
Clean out comments 2021-02-15 21:04:17 -08:00
Anders Goncalves da Silva
b99972f3a0
Move params to nextflow invocation 2021-02-15 20:59:45 -08:00
Anders Goncalves da Silva
89f65e0875 Merge branch 'master' into ivar-variant 2021-02-15 20:50:35 -08:00
Anders Goncalves da Silva
c12a558f15
Add tests without mpileup 2021-02-15 20:49:27 -08:00
Anders Goncalves da Silva
3188b8e30e
Add explicit gff is false param 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:55:34 -08:00
Anders Goncalves da Silva
ee4c2828a0
Update gff assignment to string 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:55:12 -08:00
Anders Goncalves da Silva
39401ccd07
Add gff as input 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:54:36 -08:00
Anders Goncalves da Silva
8b6989f2d7
Add gff as input 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:54:19 -08:00
Harshil Patel
8eb3acc43f
Merge pull request #171 from JoseEspinosa/mosdepth 
Add mosdepth module
 2021-02-15 23:13:01 +00:00
Anders Goncalves da Silva
9a5aa0f145
Fix tests to work with gff param 2021-02-15 11:51:04 -08:00
Anders Goncalves da Silva
4af7414419
Add tests for ivar variants 2021-02-15 09:29:40 -08:00
JoseEspinosa
6e92a6a080 Adding mosdepth module 2021-02-15 14:33:44 +01:00
Maxime Garcia
ec0bf0145e
Merge branch 'master' into master_bwa-mem2 2021-02-15 13:08:52 +01:00
Harshil Patel
f51f8c6400
Update tests/software/ivar/trim/main.nf 2021-02-13 08:18:32 +00:00
Harshil Patel
9d6f29fc61
Update tests/software/ivar/trim/main.nf 2021-02-13 08:17:15 +00:00
Harshil Patel
cdd9be0a2d
Update tests/software/ivar/trim/main.nf 2021-02-13 08:16:44 +00:00
Anders Goncalves da Silva
47670a12ad
Fix ivar trim test.yml 2021-02-12 16:03:18 -08:00
Anders Goncalves da Silva
ed74d366bf
Clean up ivar trim main.nf 2021-02-12 16:03:07 -08:00
Anders Goncalves da Silva
6dca7799e6
Add ivar trim 2021-02-12 16:02:10 -08:00
Harshil Patel
63a20e7b5c
Merge pull request #168 from JoseEspinosa/bcftools_merge 
Add bcftools merge module
 2021-02-12 23:20:30 +00:00
JoseEspinosa
5313698705 Add bcftools merge module 2021-02-13 00:08:57 +01:00
Harshil Patel
96d3b0a18b
Update tests/software/ivar/consensus/main.nf 2021-02-12 23:02:25 +00:00
Harshil Patel
f8916060f8
Update tests/software/ivar/consensus/main.nf 2021-02-12 23:02:19 +00:00
Anders Goncalves da Silva
ffc849761d
Edit test to output mpileup and passing args to samtools 2021-02-12 14:43:19 -08:00
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
Anders Goncalves da Silva
0a6e8400ac
Add reference SC2 genome to test data 2021-02-12 11:27:12 -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
Harshil Patel
132dabbbb6
Update tests/data/bed/C.bed 2021-02-08 23:03:26 +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
drpatelh
fe3cb87f6d
Direct download Singularity containers 2021-02-03 20:03:45 -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
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
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
382ea31e7e Adding bcftools test data 2021-02-02 09:18:28 +01:00