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1232 commits 30 branches 0 tags 142 MiB
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360 commits

Author SHA1 Message Date
phue
e73bda26f5 add bismark/deduplicate + tests 2021-02-23 18:02:16 +01:00
FriederikeHanssen
e67515809a try to only make paired-end test work, pass locally with conda & docker 2021-02-23 15:47:16 +01:00
FriederikeHanssen
13733b2581 Add beautiful md5sums 2021-02-23 14:57:07 +01:00
FriederikeHanssen
5e365d5eff Make all these tests pass 2021-02-23 14:09:46 +01:00
FriederikeHanssen
25a2a16f2d Try to make a single test pass 2021-02-23 13:34:50 +01:00
FriederikeHanssen
312bf85f70 use reasonable option params 2021-02-23 11:26:54 +01:00
FriederikeHanssen
9c51e05125 remove wrong md5 sums 2021-02-23 11:25:45 +01:00
FriederikeHanssen
c7d2bc8d43 Add tests for different options 2021-02-23 11:14:51 +01:00
FriederikeHanssen
ec63f335d5 Add split2 options 2021-02-22 22:43:32 +01:00
kevinmenden
3fee38ee2d added gatk4 revertsam 2021-02-22 15:21:39 +01:00
kevinmenden
efd60d94ee adding revertsam/ fix typo in mergevcfs 2021-02-22 15:10:20 +01:00
kevinmenden
69d7bb4fca reformatted input to tuple 2021-02-22 13:31:54 +01:00
kevinmenden
43446bc37e added sarscov2 fastq and bam files 2021-02-22 13:19:12 +01:00
phue
2d8baa8b75 bwameth/index: update test.yml 2021-02-20 12:55:09 +01:00
phue
c67e591caf apply suggestions from review 
thanks @drpatelh
 2021-02-20 12:51:01 +01:00
kevinmenden
bb5c0ceca5 adding SplitNCigarReads 2021-02-19 14:59:29 +01:00
Kevin Menden
0202162b17
Merge branch 'master' into gatk4-mergevcfs 2021-02-19 14:11:30 +01:00
kevinmenden
02abe106ec added optional reference dictionary as input 2021-02-19 14:09:32 +01:00
kevinmenden
3ac5c5fad6 working test 2021-02-19 13:36:42 +01:00
kevinmenden
c288e081b4 initial commit adding mergevcfs 2021-02-19 13:29:08 +01:00
Kevin Menden
5c325f2942
Merge branch 'master' into master 2021-02-19 13:08:43 +01:00
kevinmenden
908e55ee5c fixed tag 2021-02-19 12:46:59 +01:00
kevinmenden
bd8ba42a8d added gatk4 SamToFastq 2021-02-19 12:41:29 +01:00
kevinmenden
6dcaf5ffc8 add gatk4 bedtointervallist 2021-02-19 11:26:31 +01:00
phue
a963c67481 bwameth: pass genome index as directory 
instead of single files
 2021-02-18 11:51:36 +01:00
phue
0d8f5f0572 add bismark/genome_preparation + tests 2021-02-18 10:56:36 +01:00
Patrick Hüther
dba295155e
Merge pull request #219 from phue/qualimap_bamqc 
add qualimap/bamqc + test
 2021-02-18 10:09:03 +01:00
Harshil Patel
5695e4ccce
Merge pull request #222 from phue/methyldackel 
add methyldackel modules
 2021-02-17 22:17:26 +00:00
Harshil Patel
ecd26b388d
Merge pull request #221 from heuermh/seqwish 
Add module for seqwish/induce
 2021-02-17 22:14:49 +00:00
phue
52b00d4286 add methyldackel/mbias + tests 2021-02-17 19:27:57 +01:00
phue
5ad7c6bc51 add methyldackel/extract + tests + testdata 2021-02-17 19:18:55 +01:00
phue
1a414261c4 bwameth/align: update checksums 2021-02-17 18:35:39 +01:00
phue
84a5da0d91 add bwameth/align module + tests 2021-02-17 18:23:11 +01:00
Michael L Heuer
206b605666 Add module for seqwish/induce 2021-02-17 11:19:47 -06:00
phue
180b1cf36b add bwameth/index module + test 2021-02-17 18:03:48 +01:00
phue
b5b259a2d9 add qualimap/bamqc + test 2021-02-17 17:34:51 +01:00
FriederikeHanssen
5f9aa7264e Add tests 2021-02-17 17:25:41 +01:00
Patrick Hüther
0cbe0a4173
Update tests/software/samtools/faidx/main.nf 
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
 2021-02-17 17:24:50 +01:00
phue
3b1d126a0e add samtools/faidx + tests 2021-02-17 16:46:34 +01:00
Harshil Patel
ed573db194
Merge pull request #184 from MaxUlysse/master_fix_ci 
fix: update checksum or filename
 2021-02-17 10:54:38 +00:00
Harshil Patel
4d656c8f5f
Merge pull request #181 from drpatelh/fixes 
Fix tests for iVar variants
 2021-02-17 10:08:57 +00:00
MaxUlysse
28fb5e8cbd fix: update checksum or filename 2021-02-17 01:34:50 +01:00
Harshil Patel
412172cda6
Merge pull request #180 from MaxUlysse/master_tabix_bgzip 
Replace bcftools/bgzip by tabix/bgzip
 2021-02-16 23:32:23 +00:00
drpatelh
c6a0976f52 Fix tests for iVar variants 2021-02-16 23:29:15 +00:00
MaxUlysse
596bb18394 fix: rename file to input and gz, plus fix tests 2021-02-17 00:28:32 +01:00
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
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
10524e3515 chores: add modules for htslib/tabix 2021-02-16 14:47:53 +01:00
MaxUlysse
763800a0e2 fix: correct md5sum 2021-02-16 13:54:54 +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
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