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3140 commits 30 branches 0 tags 142 MiB
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1041 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
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
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
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
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
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