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1793 commits

Author SHA1 Message Date
SusiJo
7742661784 Merge remote-tracking branch 'upstream/master' into cnvkit_bam 2022-06-02 10:51:43 +02:00
SusiJo
a21cfb666e changed container + add cram2bam conversion 2022-06-02 10:38:05 +02:00
SusiJo
9fc9be3e7b Merge remote-tracking branch 'origin/master' into cnvkit_bam 2022-06-01 17:35:47 +02:00
SusiJo
f6953b5147 adjust cnvkit/batch for germline mode 2022-06-01 17:35:02 +02:00
Nicolas Vannieuwkerke
8470f3cb7e linting 2022-06-01 09:20:20 +02:00
James A. Fellows Yates
5a94794793
Merge branch 'master' into r-ampir 2022-06-01 09:18:54 +02:00
Nicolas Vannieuwkerke
d4f3df4677 Updated the test 2022-06-01 09:17:05 +02:00
nvnieuwk
e4f51d6f59
Merge branch 'master' into new-module-gatk4/ComposeSTRTableFile 2022-06-01 08:59:19 +02:00
Alexander Peltzer
9ac3cf342a
Merge branch 'master' into gatk-realigntargetcreator 2022-05-31 21:12:59 +02:00
James Fellows Yates
7633d7816b Add GATK(3)/realignertargetcreator 2022-05-31 20:35:54 +02:00
James A. Fellows Yates
615cb0722f
Merge branch 'master' into fix-filtlong 2022-05-31 20:25:16 +02:00
James Fellows Yates
c1ac3fbb59 Skeleton 2022-05-31 20:13:48 +02:00
James Fellows Yates
df22cd80df Fix config for tests 2022-05-31 20:07:52 +02:00
FriederikeHanssen
19037ed8f4
Merge branch 'master' into get_tbi_files_from_gatk4_mergevcfs 2022-05-31 17:42:27 +02:00
Nicolas Vannieuwkerke
1166fb5150 prettier 2022-05-31 16:13:38 +02:00
Nicolas Vannieuwkerke
ec41ea6082 fix test.yml 2022-05-31 16:12:05 +02:00
Nicolas Vannieuwkerke
80366924fd added gatk4/composestrtablefile 2022-05-31 16:08:13 +02:00
asp8200
98bb45cf4e Updating test for gatk4/mergevcfs 2022-05-31 13:59:56 +00:00
SusiJo
84f584875e change string array 2022-05-31 15:50:31 +02:00
James A. Fellows Yates
edc9e83a7d
Merge branch 'master' into fix-filtlong 2022-05-31 15:47:39 +02:00
James Fellows Yates
3e20ca7e9a Don't hardcode forced output names 2022-05-31 15:46:28 +02:00
SusiJo
58389e550d test json array 2022-05-31 15:41:50 +02:00
SusiJo
49135415ae
Merge branch 'master' into gatk_spark 2022-05-31 15:36:55 +02:00
SusiJo
941760f75d ran prettier 2022-05-31 15:36:02 +02:00
SusiJo
35e296cd7d added brackets 2022-05-31 15:35:34 +02:00
SusiJo
37b543e3e7 changed to tab 2022-05-31 15:29:27 +02:00
SusiJo
810564deca
Merge branch 'master' into gatk_spark 2022-05-31 15:24:58 +02:00
nvnieuwk
a6c7635b73
Merge branch 'master' into add-tbi-to-bcftools-concat 2022-05-31 15:20:03 +02:00
Nicolas Vannieuwkerke
51b0a6e4f3 Added optional input of index files to bcftools/concat 2022-05-31 15:15:58 +02:00
SusiJo
9ef09e6add adjusted newlines 2022-05-31 14:54:39 +02:00
SusiJo
205576279f ran prettier again 2022-05-31 14:50:55 +02:00
James Fellows Yates
430def06fa Switch from md5sum to string due to conda flakiness 2022-05-31 14:45:41 +02:00
SusiJo
d484aa1906 adjusted tabs 2022-05-31 14:45:23 +02:00
SusiJo
e083bfafa0 ran prettier 2022-05-31 14:38:45 +02:00
SusiJo
1e396d767f Merge remote-tracking branch 'upstream/master' into gatk_spark 2022-05-31 14:36:14 +02:00
SusiJo
ea526051a4 new test.yml 2022-05-31 14:35:42 +02:00
SusiJo
3117b2973c added test for metrics 2022-05-31 14:35:29 +02:00
SusiJo
e0e8273f74 adjusted input to use queryname sorted bams 2022-05-31 14:35:18 +02:00
James Fellows Yates
723852bf3d Fixes running without shortreads, and also ensures all tests produce non-empty fastq.gz files 2022-05-31 13:38:18 +02:00
James Fellows Yates
7ffe98ac8b Add gatk/indelrealigner 2022-05-30 21:12:21 +02:00
jtangrot
6ae405c5da prettier 2022-05-30 13:35:12 +02:00
jtangrot
6aac5c2c40 Update test 2022-05-30 13:30:27 +02:00
jtangrot
c67c15f243 Make input tuple 2022-05-30 13:01:06 +02:00
jtangrot
01d86439f5 Add idcutoff as input 2022-05-30 08:50:27 +02:00
jtangrot
589ce2d73a Add options for output file type 2022-05-30 08:50:27 +02:00
jtangrot
1c99ffd876 Add vserach usearch_global 2022-05-30 08:50:27 +02:00
Harshil Patel
ad578cafcc Fix tests 2022-05-27 12:14:10 +01:00
Sateesh Peri
ead3679829
Merge branch 'master' into rp3-add-snippy 2022-05-26 03:04:19 -04:00
Harshil Patel
241a1de035
Update main.nf 2022-05-25 19:38:12 +01:00
Matthias De Smet
bc7002b0c9
Merge branch 'master' into update/mosdepth 2022-05-25 19:20:45 +02:00
Matthias De Smet
72ff2732e3 add all remaining outputs to mosdepth 2022-05-25 19:19:39 +02:00
Mahesh Binzer-Panchal
3d532405a5
Merge branch 'master' into mash_screen_patch 2022-05-25 16:51:42 +02:00
SusiJo
1400f2e683 fixed tests - mixed chr21 + chr22 2022-05-25 16:38:30 +02:00
SusiJo
dd6d838cd7 override userEmulation 2022-05-25 16:37:44 +02:00
Mahesh Binzer-Panchal
c452f56289 Patch mash screen 2022-05-25 12:29:14 +00:00
jasmezz
77b5986463 Create ampir module 2022-05-25 13:27:10 +02:00
Jill V. Hagey, PhD
b1dd1d8a52
Merge branch 'nf-core:master' into gamma-update 2022-05-24 19:28:06 -04:00
jvhagey
127665d27b fixed test.yml 2022-05-24 19:27:09 -04:00
jvhagey
bb999395aa fixed pytest_modules.yml 2022-05-24 19:19:38 -04:00
Mahesh Binzer-Panchal
3d51956b88
Merge branch 'master' into kat_hist 2022-05-24 23:10:13 +02:00
jvhagey
b8aaea7429 updating paths in test.yml 2022-05-24 16:27:00 -04:00
jvhagey
f1fc7fc38e adding upzip 2022-05-24 15:15:07 -04:00
Ramprasad Neethiraj
c91947f8a1
Merge branch 'master' into rhocall 2022-05-24 16:07:55 +02:00
Mahesh Binzer-Panchal
9a5d6a815b
Merge branch 'master' into kat_hist 2022-05-24 15:46:12 +02:00
SusiJo
3077e4d34c
Merge branch 'master' into cnvkit/reference 2022-05-24 15:00:29 +02:00
SusiJo
8208140d21 missing meta.id changed 2022-05-24 14:59:52 +02:00
Matthias De Smet
8381a5e5dd add window test 2022-05-24 14:43:40 +02:00
Matthias De Smet
5bc2d419a9 fix fail test 2022-05-24 13:23:00 +02:00
Thiseas C. Lamnidis
6d04395c3c
Merge branch 'master' into sexdeterrmine 2022-05-24 13:17:37 +02:00
Mahesh Binzer-Panchal
afb5f226e6
Merge branch 'master' into kat_hist 2022-05-24 13:06:31 +02:00
Matthias De Smet
858cbe80c6 add must fail test 2022-05-24 12:43:49 +02:00
Matthias De Smet
01fb8851c3 mosdept: cram compatiblility 2022-05-24 11:47:58 +02:00
Harshil Patel
ec141dba08
Merge branch 'master' into umitools 2022-05-24 09:23:20 +01:00
Ramprasad Neethiraj
b4982ff6e3
Merge branch 'master' into rhocall 2022-05-24 09:41:30 +02:00
SusiJo
0f0d555f96
Merge branch 'master' into cnvkit_reference 2022-05-24 08:03:44 +02:00
SusiJo
0708f343de
Merge branch 'master' into cnvkit_bam 2022-05-24 07:49:51 +02:00
SusiJo
50128b0c86
Merge branch 'master' into cnvkit_reference 2022-05-24 07:49:44 +02:00
SusiJo
1451d62be4 rm md5sums for empty files 2022-05-24 07:38:53 +02:00
SusiJo
63c038ad68
Merge branch 'nf-core:master' into cnvkit_bam 2022-05-24 07:37:24 +02:00
SusiJo
b3e2f70651
Merge branch 'master' into cnvkit/antitarget 2022-05-24 07:36:07 +02:00
SusiJo
33a72367c6
Merge branch 'nf-core:master' into cnvkit_reference 2022-05-24 07:30:29 +02:00
Harshil Patel
a3e70777ad Fix Conda tests 2022-05-23 22:39:12 +01:00
Harshil Patel
84f02a08a5 Update umitools/dedup module to make --output-stats optional 2022-05-23 22:31:09 +01:00
Sateesh Peri
da0ead705e
Merge branch 'master' into update/picard 2022-05-23 13:38:18 -04:00
SusiJo
8fec7ae321 added new testdata path 2022-05-23 19:01:46 +02:00
SusiJo
bbee9e3c3b add new module cnvkit/reference 2022-05-23 18:35:50 +02:00
Thiseas Christos Lamnidis
37c6fb8fed Merge remote-tracking branch 'upstream/master' into sexdeterrmine 2022-05-23 17:30:21 +02:00
Thiseas Christos Lamnidis
96260ced83 Add test data to config 2022-05-23 17:15:57 +02:00
Thiseas Christos Lamnidis
9011fc7212 Corrected test-datasets input 2022-05-23 17:08:40 +02:00
SusiJo
5d5eacee63
Merge branch 'nf-core:master' into cnvkit/antitarget 2022-05-23 16:52:33 +02:00
SusiJo
4f9d672e55 added new module cnvkit/antitarget 2022-05-23 16:52:06 +02:00
FriederikeHanssen
754afa9ff3
Merge branch 'master' into gatk_filter 2022-05-23 15:37:44 +02:00
Thiseas Christos Lamnidis
070dee0f5b Use newly added test bam 2022-05-23 15:22:22 +02:00
Rike
e34dcdd8bc add brackets to contains 2022-05-23 13:19:42 +02:00
Rike
dc6ad1bff6 add brackets to contains 2022-05-23 13:07:08 +02:00
Ramprasad Neethiraj
9fb327fec7 Merge branch 'master' of https://github.com/nf-core/modules into rhocall 2022-05-23 13:06:00 +02:00
Rike
093e3aafdd contains 2022-05-23 13:04:49 +02:00
Ramprasad Neethiraj
06a3bff201 fix lint error 2022-05-23 12:59:48 +02:00
Rike
a8de9fd085 test path update 2022-05-23 12:53:36 +02:00
Rike
3af61cfbbc fix input cardinality for index 2022-05-23 12:26:12 +02:00
Rike
a8dac59c50 md5sum not consistent 2022-05-23 12:10:50 +02:00
Rike
2f36a44f61 nf-core create-test-yml 2022-05-23 12:00:31 +02:00
SusiJo
fd31f64266
Merge branch 'master' into cnvkit_bam 2022-05-23 11:31:56 +02:00
Mahesh Binzer-Panchal
e06fb752c3
Merge branch 'master' into kat_hist 2022-05-23 08:52:13 +02:00
Mahesh Binzer-Panchal
d7c1fe1477
Update tests/modules/kat/hist/test.yml 
Co-authored-by: Sateesh Peri <105730406+sateeshblue@users.noreply.github.com>
 2022-05-23 08:51:49 +02:00
Mahesh Binzer-Panchal
b40b147004
Update tests/modules/kat/hist/test.yml 
Co-authored-by: Sateesh Peri <105730406+sateeshblue@users.noreply.github.com>
 2022-05-23 08:51:29 +02:00
Rike
cd60b4c6eb add in testdata paths 2022-05-22 13:35:35 +02:00
Rike
520dd06ca3 add new testdata 2022-05-22 13:25:39 +02:00
Matthias De Smet
e13fbf423e fix tests (again) 2022-05-22 06:54:09 +02:00
Matthias De Smet
cbceee9621 fix tests 2022-05-22 06:51:27 +02:00
Matthias De Smet
3a2de0cf6f update test for wgsmetrics 2022-05-22 06:49:31 +02:00
Matthias De Smet
4da143ce62 add tests 2022-05-22 06:44:17 +02:00
Ramprasad Neethiraj
995bf88327 add stub 2022-05-20 17:10:09 +02:00
Ramprasad Neethiraj
635edc0022 fix typo 2022-05-20 17:07:42 +02:00
Ramprasad Neethiraj
2542c9d176 add tests 2022-05-20 16:46:19 +02:00
Mahesh Binzer-Panchal
2926ec0abb Add mash screen 2022-05-20 13:23:11 +00:00
Ramprasad Neethiraj
c70b169f61 create modules 2022-05-20 13:34:54 +02:00
SusiJo
00077c36c8 removed unnecessary fasta for tumor_only_bam 2022-05-20 13:06:16 +02:00
SusiJo
dd2f48810a
Merge branch 'nf-core:master' into cnvkit_bam 2022-05-20 09:14:21 +02:00
SusiJo
3d57caa683 added test & corrected cram input 2022-05-20 09:13:27 +02:00
Rike
bb3e64647b Merge remote-tracking branch 'origin/master' into gatk_filter 2022-05-18 15:52:47 +02:00
FriederikeHanssen
44e9cf56fa
Merge branch 'master' into gatk_cnnscore 2022-05-18 15:32:36 +02:00
Rike
e8221cf98e Merge remote-tracking branch 'origin' into gatk_cnnscore 2022-05-18 14:27:25 +02:00
James A. Fellows Yates
965fabdd54
Merge branch 'master' into motus_profile 2022-05-18 11:25:48 +01:00
Rike
5ae757121f Add indices and meta 2022-05-17 23:38:26 +02:00
Rike
15fba1dd7c add filter variant tranches 2022-05-17 23:01:24 +02:00
Rike
afa0f2a995 update test 2022-05-17 22:53:41 +02:00
Rike
265fd882ca update test 2022-05-17 19:44:48 +02:00
Rike
5f63904a50 update test 2022-05-17 19:37:18 +02:00
Rike
05611cf27c update pytest 2022-05-17 19:11:05 +02:00
Rike
e0fcbb428d Add CNNScoreVariants 2022-05-17 19:09:46 +02:00
Jose Espinosa-Carrasco
3614c19206
Merge branch 'master' into biobambam/bammerge 2022-05-17 15:07:37 +02:00
Nicolas Vannieuwkerke
6342f5b099 added bedtools split 2022-05-17 14:24:32 +02:00
Matthias De Smet
c5627e0274 fix config 2022-05-17 09:09:19 +02:00
Matthias De Smet
743e95c61b fix config 2022-05-17 09:01:02 +02:00
Matthias De Smet
d3ddc2221a
Merge branch 'master' into biobambam/bammerge 2022-05-17 08:26:28 +02:00
Matthias De Smet
6be91ce82d fix optional output detection 2022-05-17 08:20:47 +02:00
Subazini TK
79c2c529fc
Merge branch 'master' into hmtnote 2022-05-17 08:05:47 +02:00
JIANHONG OU
671bacb6df
Merge branch 'master' into motus_profile 2022-05-16 17:34:49 -04:00
Matthias De Smet
d0db186e84
Merge branch 'master' into biobambam/bammerge 2022-05-16 20:52:48 +02:00
Matthias De Smet
a79b9adeee address review comments 2022-05-16 20:51:39 +02:00
Subazini TK
252fcb17c4 Update main.nf 2022-05-16 15:20:15 +00:00
Subazini TK
cb21fa0c96 Update main.nf 2022-05-16 15:20:15 +00:00
Subazini TK
cbae48d06d Update nextflow.config 2022-05-16 15:20:15 +00:00
Subazini TK
541f403963 Update main.nf 2022-05-16 15:20:15 +00:00
Subazini TK
69243db3d7 Update test.yml 2022-05-16 15:20:15 +00:00
Subazini TK
c8c6fdd2e3 Update main.nf 2022-05-16 15:20:15 +00:00
Subazini TK
fb66e8ba97 Update test.yml 2022-05-16 15:20:15 +00:00
Subazini TK
f0713f4723 Update test.yml 2022-05-16 15:20:15 +00:00
Subazini TK
060d33f2c3 Update test.yml 2022-05-16 15:20:15 +00:00
Subazini TK
df8f1eae69 Update test.yml 2022-05-16 15:20:15 +00:00
sysbiocoder
31fc8b560f hmtnote 2022-05-16 15:20:15 +00:00
sysbiocoder
fe009b738a modified: tests/config/pytest_modules.yml 2022-05-16 15:20:15 +00:00
Matthias De Smet
af69ea749d add module: biobambam/bammerge 2022-05-16 14:39:58 +02:00
Veit Schwämmle
74a1c1400e
Merge branch 'master' into maxquant 2022-05-16 13:26:35 +02:00
Jasmin F
982c9183fa
Merge branch 'master' into antismashlite 2022-05-16 11:42:44 +02:00
Jasmin F
adcfae6cd4
Merge branch 'master' into antismashlite 2022-05-16 10:38:01 +02:00
Rike
eb841d4ea0 revert markduplciatespark changes 2022-05-16 10:33:01 +02:00
FriederikeHanssen
8b4d021189
Merge branch 'master' into gatk_426 2022-05-16 09:50:13 +02:00
Matthias De Smet
5a2e303522 add PE sorted test 2022-05-13 19:16:50 +02:00
Taniguti
ac7fe89a78
Merge branch 'master' into haplocheck 2022-05-13 11:24:10 -03:00
Matthias De Smet
04f82d4d34 fix test name 2022-05-13 15:32:14 +02:00
JIANHONG OU
fadb83cf44
Merge branch 'master' into motus_profile 2022-05-13 09:30:20 -04:00
Matthias De Smet
cbc47767f7 add sort option to bowtie2 2022-05-13 15:26:41 +02:00
Nicolas Vannieuwkerke
a72f06dfe8 removed versions checksum 2022-05-13 14:27:59 +02:00
nvnieuwk
1d4862ba60
Merge branch 'master' into new-module-gatk4/splitintervals 2022-05-13 13:47:20 +02:00
Nicolas Vannieuwkerke
8a17b6dd0e added gatk4/splitintervals 2022-05-13 13:46:34 +02:00
Chris Cheshire
ea55129ba3 Removed version file checksums 2022-05-13 12:20:41 +01:00
Chris Cheshire
9f6a1ae4a4
Merge branch 'master' into bowtie2-test-fix 2022-05-13 12:05:48 +01:00
Chris Cheshire
d816f2bc5d Reactivated all tests 2022-05-13 12:01:16 +01:00
Taniguti
4728b2bcd2
Merge branch 'master' into haplocheck 2022-05-13 07:49:55 -03:00
Lucas Taniguti
c1ed4e21be tests: add haplocheck tests 2022-05-13 07:42:34 -03:00
Mahesh Binzer-Panchal
00826dc2e9
Merge branch 'master' into genomescope2 2022-05-13 11:28:47 +02:00
Mahesh Binzer-Panchal
5df0bcf1be
Update tests/modules/genomescope2/test.yml 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-13 11:27:42 +02:00
James A. Fellows Yates
2eebab4f35
Update tests/modules/motus/profile/test.yml 2022-05-12 20:55:54 +01:00
James A. Fellows Yates
8dd711aba2
Update tests/modules/motus/profile/main.nf 2022-05-12 20:08:37 +01:00
FriederikeHanssen
868150e1af
Merge branch 'master' into gatk_426 2022-05-12 19:33:07 +02:00
Rike
99880654bf add output default bam 2022-05-12 18:06:15 +02:00
Rike
8792d102ee fix test input 2022-05-12 17:37:06 +02:00
Rike
a694267b4b fix empty index input 2022-05-12 17:01:03 +02:00
Mahesh Binzer-Panchal
308ab8801d
Merge branch 'master' into kat_hist 2022-05-12 16:52:05 +02:00
Rike
b3bd55da76 getpileupsummaries requires intervals files 2022-05-12 16:51:17 +02:00
Rike
15fbf21b28 double tmpdir args removed, porb leftover after massive refactor where we decided to make it mandatory everywhere 2022-05-12 16:16:53 +02:00
Rike
fef5434c4c Update md5sums 2022-05-12 16:07:12 +02:00
Jasmin F
85b3c2bcf2
Apply suggestions from code review 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-12 15:28:19 +02:00
James A. Fellows Yates
3c02e6056c
Merge branch 'master' into antismashlite 2022-05-12 14:53:52 +02:00
Sateesh Peri
c5d3c90524
Merge branch 'master' into rp3-add-snippy 2022-05-12 07:48:33 -04:00
jasmezz
d2ef476321 Fix Prettier linting error 2022-05-12 12:19:50 +02:00
jasmezz
37cc6f250b Fixed test.yml 2022-05-12 12:14:19 +02:00
Chris Cheshire
90c67794bf Added extra tests but error with collection 2022-05-12 10:01:33 +01:00
jasmezz
bd4b70439b Streamlined some output channels, formatted tests main.nf 2022-05-12 10:56:48 +02:00
Robert A. Petit III
8b6e1aff38
Merge branch 'master' into rp3-add-snippy 2022-05-11 12:28:27 -06:00
Robert A. Petit III
7ced6e20de make prettier 2022-05-11 18:00:36 +00:00
Moritz E. Beber
74b11ccc44 refactor: rename and update subworkflow 2022-05-11 19:24:16 +02:00
Matthias De Smet
dcf9c07fc9
Merge branch 'master' into update/bowtie2-align 2022-05-11 19:08:23 +02:00
Moritz E. Beber
98d8a741ec tests: add missing paths to config 2022-05-11 18:17:27 +02:00
Moritz E. Beber
888620063b tests: delete settings for conda 2022-05-11 17:44:49 +02:00
Moritz E. Beber
b2dbaa9930 refactor: rename module 2022-05-11 17:33:45 +02:00
Moritz E. Beber
23091aabda refactor: move files to custom section 2022-05-11 17:33:45 +02:00
Moritz E. Beber
a83dd33a7e tests: use remove settings file 2022-05-11 17:33:45 +02:00
Moritz E. Beber
e4551a9ab3 refactor: always output settings 2022-05-11 17:33:45 +02:00
Moritz E. Beber
64ff23f3c1 feat: add module that verifies NCBI settings 2022-05-11 17:33:45 +02:00
Mahesh Binzer-Panchal
0199d0efd2
Merge branch 'master' into kat_hist 2022-05-11 16:56:29 +02:00
Harshil Patel
4e603393c3
Merge branch 'master' into update/bowtie2-align 2022-05-11 15:47:37 +01:00
Jasmin F
853e3ec087
Remove commented code 
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
 2022-05-11 15:56:10 +02:00
Mahesh Binzer-Panchal
fbe2f85e7b Fix path 2022-05-11 13:53:38 +00:00
Matthias De Smet
94e8c3a882
Update tests/modules/bowtie2/align/test.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-05-11 13:56:03 +02:00
Matthias De Smet
0d00452eca
Update tests/modules/bowtie2/align/test.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-05-11 13:55:45 +02:00
Matthias De Smet
dcffd93875
Merge branch 'master' into update/bowtie2-align 2022-05-11 13:34:24 +02:00
CMGG ICT Team
3ae8cbfad7 bowtie2: remove code duplication 2022-05-11 13:32:56 +02:00
Moritz E. Beber
0cdf7767a7 refactor: require NCBI user settings always 2022-05-11 13:02:52 +02:00
Moritz E. Beber
eae7161a32 tests: add settings input or not and test all branches 2022-05-11 12:47:54 +02:00
Mahesh Binzer-Panchal
fd579ebbb3
Merge branch 'master' into kat_hist 2022-05-11 12:43:11 +02:00
Mahesh Binzer-Panchal
00fcdd0cba
Merge branch 'master' into genomescope2 2022-05-11 12:42:39 +02:00
Mahesh Binzer-Panchal
d54cf467f4 Update outputs and test data set 2022-05-11 10:42:17 +00:00
Harshil Patel
7be7f404d5
Merge branch 'master' into refactor-prefetch 2022-05-11 11:28:02 +01:00
jasmezz
2b746abfbe Fix Prettier linting issue 2022-05-11 12:09:52 +02:00
jasmezz
5d76f1c7ff Add fasta/gff input option 2022-05-11 12:06:02 +02:00
Jasmin F
9cce4a00b2
Merge branch 'nf-core:master' into antismashlite 2022-05-11 12:03:30 +02:00
Mahesh Binzer-Panchal
0774704038
Merge branch 'master' into genomescope2 2022-05-11 11:38:36 +02:00
Robert A. Petit III
56e94f625e remove empty file md5 2022-05-10 21:47:11 +00:00
Robert A. Petit III
44e13ae439 add module for snippy 2022-05-10 21:31:43 +00:00
Mahesh Binzer-Panchal
7a16ece747 Change md5sum to contains 2022-05-10 15:13:25 +00:00
Mahesh Binzer-Panchal
cd32c7f744
Merge branch 'master' into kat_hist 2022-05-10 17:03:00 +02:00
Mahesh Binzer-Panchal
9b4923dcd5 Change test files 2022-05-10 15:02:37 +00:00
Mahesh Binzer-Panchal
b875cfb744
Merge branch 'master' into kat_hist 2022-05-10 14:36:18 +02:00
Praveen Raj S
237971cd15
Merge branch 'master' into master 2022-05-10 14:35:41 +02:00
Nicolas Vannieuwkerke
b7134855e4 Small update on the output channels 2022-05-10 12:34:52 +02:00
Moritz E. Beber
1b228835e9 refactor: require settings input always 2022-05-10 12:29:42 +02:00
Moritz E. Beber
a303904eb0 chore: add settings file to test data config 2022-05-10 12:19:25 +02:00
Moritz E. Beber
145e2f80e9 tests: run prefetch with and without given settings 2022-05-10 12:16:57 +02:00
Nicolas Vannieuwkerke
3a064b0a99 Split the output to different channels 2022-05-10 12:05:42 +02:00
Nicolas Vannieuwkerke
6008619603 test issue fix? 2022-05-10 10:20:54 +02:00
Nicolas Vannieuwkerke
96c3f895b9 test issue fix? 2022-05-10 10:19:13 +02:00
Nicolas Vannieuwkerke
42fbf80c72 Fixed a test issue with wrong md5sum 2022-05-10 09:57:49 +02:00
Nicolas Vannieuwkerke
f0e8f6ce4d Linting 2022-05-10 09:36:54 +02:00
Nicolas Vannieuwkerke
e5d091ad4b Merge branch 'new-module-rtg/vcfeval' of github.com:nvnieuwk/modules into new-module-rtg/vcfeval 2022-05-10 09:35:44 +02:00
Nicolas Vannieuwkerke
c69d5cc23e Added evaluation-regions and adjusted the output to now contain all output (and not only the summary) 2022-05-10 09:35:42 +02:00
nvnieuwk
95103fbd79
Merge branch 'master' into new-module-rtg/vcfeval 2022-05-10 09:06:34 +02:00
Praveen Raj S
459a2d1759
Merge branch 'master' into master 2022-05-09 22:16:59 +02:00
Mahesh Binzer-Panchal
f65d896f57 create genomescope2 module 2022-05-09 15:09:15 +00:00
Mahesh Binzer-Panchal
705ad7c3a1
Merge branch 'master' into meryl_unionsum 2022-05-09 16:20:01 +02:00
nvnieuwk
aceb5220cf
Merge branch 'master' into new-module-rtg/vcfeval 2022-05-09 16:18:00 +02:00
Mahesh Binzer-Panchal
83a266ea70
Merge branch 'master' into meryl_unionsum 2022-05-09 16:16:08 +02:00
FriederikeHanssen
adc4ff868c
Merge branch 'master' into samtools_convert 2022-05-09 16:15:24 +02:00
nvnieuwk
4b8bd9ebf9
Merge branch 'master' into new-module-rtg/vcfeval 2022-05-09 15:51:31 +02:00
Mahesh Binzer-Panchal
da93beaf60 Update pytests 2022-05-09 13:50:49 +00:00
Nicolas Vannieuwkerke
f6262b4a10 fixed some issues 2022-05-09 15:47:07 +02:00
Mahesh Binzer-Panchal
8d86988632
Merge branch 'master' into meryl/histogram 2022-05-09 15:39:32 +02:00
nvnieuwk
d6dd4c2e2d
Update tests/modules/rtgtools/vcfeval/test.yml 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-09 15:35:16 +02:00
Rike
ef5f145342 Generalize Bam2Cram do either conversion 2022-05-09 15:22:54 +02:00
Annick Renevey
ac3034696b update md5sum 2022-05-09 15:19:16 +02:00
Mahesh Binzer-Panchal
0c567f5474
Merge branch 'master' into meryl_unionsum 2022-05-09 15:03:27 +02:00
Mahesh Binzer-Panchal
f0f414d519 Update pytests 2022-05-09 13:00:10 +00:00
Annick Renevey
eed874ace7 update arriba tests 2022-05-09 14:55:59 +02:00
Mahesh Binzer-Panchal
6621768550 Update pytest outputs 2022-05-09 12:54:31 +00:00
Jasmin F
453d5b66a4
Add Bacteroides fragilis GFF file 2022-05-09 14:46:18 +02:00
Mahesh Binzer-Panchal
ce97c87b5d
Merge branch 'master' into meryl_unionsum 2022-05-09 13:51:55 +02:00
Mahesh Binzer-Panchal
7a5d5f5766
Merge branch 'master' into kat_hist 2022-05-09 13:18:18 +02:00
Mahesh Binzer-Panchal
a43bc940d6 Add suggestions from code review 2022-05-09 11:15:14 +00:00
Mahesh Binzer-Panchal
129f57ccd9 Add meryl histogram 2022-05-09 08:50:28 +00:00
Mahesh Binzer-Panchal
ad4f8389cb Add meryl unionsum 2022-05-09 08:33:21 +00:00
Mahesh Binzer-Panchal
32b0fdc9d9
Merge branch 'master' into meryl_count 2022-05-09 10:05:28 +02:00
Mahesh Binzer-Panchal
9ebeb6a702 Update test 2022-05-09 08:05:07 +00:00
Matthias De Smet
3dc18365f6
Merge branch 'master' into new-module-rtg/vcfeval 2022-05-09 10:04:29 +02:00
Mahesh Binzer-Panchal
4591ea2205 atomize 2022-05-09 07:58:58 +00:00
Matthias De Smet
2b91985aa0
Merge branch 'master' into new-module-rtg/vcfeval 2022-05-09 09:43:48 +02:00
Nicolas Vannieuwkerke
d18af7358a Moved untarring the genome sdf folder to the test itself 2022-05-09 09:20:42 +02:00
Lucpen
bdaed264a7
Merge branch 'master' into correcting_stubs 2022-05-09 08:54:22 +02:00
James A. Fellows Yates
8a83ad0518
Merge branch 'master' into motus_profile 2022-05-09 08:16:16 +02:00
MaxUlysse
3d428e2933 fix spacing 2022-05-07 15:28:40 +02:00
MaxUlysse
1013be2623 fix path to script 2022-05-07 15:22:52 +02:00
Jose Espinosa-Carrasco
e2acf28c8f
Merge branch 'master' into maxulysse-patch-1 2022-05-06 23:53:27 +02:00
Matthias De Smet
0752b82c9f
Merge branch 'master' into update/snapaligner 2022-05-06 18:57:37 +02:00
Matthias De Smet
dd458e3388 fix tags 2022-05-06 18:57:17 +02:00
Maxime U. Garcia
ac217479e9
Update tests/config/test_data.config 
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
 2022-05-06 18:18:32 +02:00
Maxime U. Garcia
ec7b460fa4
add missing file 2022-05-06 17:54:35 +02:00
Mahesh Binzer-Panchal
67481c6d54 Start Meryl count 2022-05-06 15:04:04 +00:00
Mahesh Binzer-Panchal
1e55ad987f
Merge branch 'master' into kat_hist 2022-05-06 16:35:51 +02:00
nvnieuwk
5153e10840
Merge branch 'master' into new-module-rtg/vcfeval 2022-05-06 16:19:17 +02:00
Nicolas Vannieuwkerke
8c857dee3a Fixed the sdf folder fetching 2022-05-06 16:16:57 +02:00
Lucpen
8e5fda3b10
Merge branch 'master' into correcting_stubs 2022-05-06 15:37:08 +02:00
Lucpen
971a17a3ab fix datatest for stubs 2022-05-06 15:34:18 +02:00
Mahesh Binzer-Panchal
7a85760d08 remove 'auto' test 2022-05-06 13:33:27 +00:00
Lucpen
0fa36e6777 fix added correct entry workflow in test.yml 2022-05-06 15:26:34 +02:00
JIANHONG OU
9b50036e9b add test_bam and -m parameter for motus_profile 2022-05-06 08:56:42 -04:00
JIANHONG OU
c301a406dd
Merge branch 'nf-core:master' into motus_profile 2022-05-06 08:33:43 -04:00
Nicolas Vannieuwkerke
84b354ab6a Added the rtgtools/vcfeval module 2022-05-06 14:23:40 +02:00
JIANHONG OU
26d5b4da72
Update tests/modules/motus/profile/main.nf 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-06 08:19:54 -04:00
Matthias De Smet
26d2231e85 fix linting 2022-05-06 14:16:38 +02:00
Matthias De Smet
3930ba227b merge snapaligner modes into one 2022-05-06 14:10:44 +02:00
Mahesh Binzer-Panchal
a9f23bb477
Merge branch 'master' into busco 2022-05-06 13:49:01 +02:00
Mahesh Binzer-Panchal
35c5828f43 Add --auto-lineage option and remove single_end 
Co-authored-by: Jill V. Hagey, PhD <jvhagey@gmail.com>
 2022-05-06 11:48:21 +00:00
Jose Espinosa-Carrasco
035655e35d
Merge branch 'master' into modules/md5sum 2022-05-06 12:34:14 +02:00
Mahesh Binzer-Panchal
c19e7da59d
Apply suggestions from code review 
Remove versions md5sum

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-06 10:55:48 +02:00
Matthias De Smet
09e729ad41 added sha256sum 2022-05-06 10:28:14 +02:00
Mahesh Binzer-Panchal
d83281eac9
Merge branch 'master' into kat_hist 2022-05-06 10:02:44 +02:00
Mahesh Binzer-Panchal
9194fb845e Add module kat hist 2022-05-06 07:54:10 +00:00
Matthias De Smet
853b623969 new module: md5sum 2022-05-06 09:20:40 +02:00
Ramprasad Neethiraj
db56d80060 Merge branch 'master' of https://github.com/nf-core/modules into feat/update_cnvpytor 2022-05-06 00:10:28 +02:00