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
|
114a54c8d5
|
spaces fix
|
2022-06-01 09:22:09 +02:00 |
|
James A. Fellows Yates
|
5a94794793
|
Merge branch 'master' into r-ampir
|
2022-06-01 09:18:54 +02:00 |
|
nvnieuwk
|
5b74a179c3
|
Update modules/gatk4/composestrtablefile/main.nf
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
|
2022-06-01 09:14:08 +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
|
d39ba08e02
|
Prepare main module code
|
2022-05-31 20:19:49 +02:00 |
|
James Fellows Yates
|
c1ac3fbb59
|
Skeleton
|
2022-05-31 20:13:48 +02:00 |
|
FriederikeHanssen
|
19037ed8f4
|
Merge branch 'master' into get_tbi_files_from_gatk4_mergevcfs
|
2022-05-31 17:42:27 +02:00 |
|
asp8200
|
4199a05aeb
|
Removing redundant empty line
|
2022-05-31 15:34:34 +00:00 |
|
Nicolas Vannieuwkerke
|
80366924fd
|
added gatk4/composestrtablefile
|
2022-05-31 16:08:13 +02:00 |
|
James Fellows Yates
|
089f761f0b
|
Actually add the changes
|
2022-05-31 15:49:57 +02:00 |
|
Anders Sune Pedersen
|
5513d095f5
|
Adding tbi-files to the output from GATK4_MERGEVCFS. #1709
|
2022-05-31 15:37:26 +02:00 |
|
SusiJo
|
49135415ae
|
Merge branch 'master' into gatk_spark
|
2022-05-31 15:36:55 +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 |
|
James A. Fellows Yates
|
0b895871d7
|
Merge branch 'master' into fix-filtlong
|
2022-05-31 14:49:44 +02:00 |
|
SusiJo
|
1e396d767f
|
Merge remote-tracking branch 'upstream/master' into gatk_spark
|
2022-05-31 14:36:14 +02:00 |
|
SusiJo
|
39e34418c9
|
added metrics as optional output
|
2022-05-31 14:34:50 +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 |
|
Sébastien Guizard
|
a3ae526521
|
Merge branch 'master' into bamtools/convert/remove_TODO
|
2022-05-30 17:36:36 +01:00 |
|
Sebastien Guizard
|
d463cd5dd6
|
👌 IMPROVE: Remove last TODO
|
2022-05-30 17:26:51 +01:00 |
|
jtangrot
|
5f0d75bb37
|
Merge branch 'vsearch_usearch_global' of https://github.com/jtangrot/nf-core_modules into vsearch_usearch_global
|
2022-05-30 13:05:00 +02:00 |
|
Jeanette Tångrot
|
69e00b55d3
|
Update modules/vsearch/usearchglobal/main.nf
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
|
2022-05-30 13:03:45 +02:00 |
|
jtangrot
|
c67c15f243
|
Make input tuple
|
2022-05-30 13:01:06 +02:00 |
|
Matthias De Smet
|
63db63757c
|
bump picard versions
|
2022-05-30 10:15:40 +02:00 |
|
jtangrot
|
2e16c90fce
|
Fix whitespace
|
2022-05-30 09:57:05 +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
|
fb6c7bca3d
|
Bump container version for STAR to 2.7.10a
|
2022-05-27 11:35:04 +01:00 |
|
Sateesh Peri
|
ead3679829
|
Merge branch 'master' into rp3-add-snippy
|
2022-05-26 03:04:19 -04:00 |
|
Harshil Patel
|
72a31b76eb
|
Update main.nf
|
2022-05-25 19:42:15 +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
|
b34e5ea6bf
|
rm unnecessary spark_user
|
2022-05-25 16:38:48 +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 |
|
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
|
fe90615f57
|
Merge branch 'rhocall' of github.com:genomic-medicine-sweden/modules into rhocall
|
2022-05-24 16:17:59 +02:00 |
|
Ramprasad Neethiraj
|
b0dba3ee75
|
update description
|
2022-05-24 16:17:15 +02:00 |
|
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 |
|
SusiJo
|
6b425735b9
|
Merge remote-tracking branch 'origin/master' into cnvkit/reference
|
2022-05-24 14:20:55 +02:00 |
|
SusiJo
|
749edce069
|
add prefix
|
2022-05-24 14:20:19 +02:00 |
|
Mahesh Binzer-Panchal
|
c8ffecfe86
|
Merge branch 'master' into kat_hist
|
2022-05-24 13:57:45 +02:00 |
|
Matthias De Smet
|
c51c047b2e
|
Merge branch 'master' into update/mosdepth
|
2022-05-24 13:50:22 +02:00 |
|
Matthias De Smet
|
a2a8e09762
|
Update modules/mosdepth/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2022-05-24 13:45:52 +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
|
7e777c6626
|
add error is is provided twice
|
2022-05-24 12:25:31 +02:00 |
|
Matthias De Smet
|
b5850fd471
|
add stub
|
2022-05-24 12:16:03 +02:00 |
|
Harshil Patel
|
393f23274d
|
Merge branch 'master' into cnvkit/reference
|
2022-05-24 11:14:50 +01:00 |
|
Harshil Patel
|
29a4f112be
|
Update main.nf
|
2022-05-24 11:14:32 +01:00 |
|
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 |
|
SusiJo
|
5db94ea0ee
|
changed tag of module
|
2022-05-24 10:17:41 +02:00 |
|
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
|
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
|
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
|
58c5ec2f4e
|
rm line
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
|
2022-05-23 18:53:28 +02:00 |
|
SusiJo
|
86b5951c14
|
rm line
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
|
2022-05-23 18:48:30 +02:00 |
|
SusiJo
|
24905e26e2
|
rm line
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
|
2022-05-23 18:48:13 +02:00 |
|
SusiJo
|
ddb964a4bf
|
rm line
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
|
2022-05-23 18:48:04 +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 |
|
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 |
|
Ramprasad Neethiraj
|
9fb327fec7
|
Merge branch 'master' of https://github.com/nf-core/modules into rhocall
|
2022-05-23 13:06:00 +02:00 |
|
Rike
|
175ea9b7f9
|
fix version
|
2022-05-23 12:15:33 +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 |
|
Rike
|
5d72500d60
|
remove variables used for test data generation, add tbi
|
2022-05-22 13:34:56 +02:00 |
|
Matthias De Smet
|
c390385cf5
|
revert wgsmetrics'
|
2022-05-22 06:44:17 +02:00 |
|
Matthias De Smet
|
d6a0238cd1
|
Merge branch 'master' into update/picard
|
2022-05-21 08:34:33 +02:00 |
|
Matthias De Smet
|
a5a6973fcf
|
picard: make reference sequence optional
|
2022-05-21 08:33:49 +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
|
9096be5464
|
improve readability
|
2022-05-20 13:29:49 +02:00 |
|
SusiJo
|
bdf222649d
|
remove unnecessary if statement
|
2022-05-20 13:25:57 +02:00 |
|
SusiJo
|
153c900d0e
|
refine comment
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
|
2022-05-20 13:08:38 +02:00 |
|
SusiJo
|
2e5aa0dbb4
|
refine comment
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
|
2022-05-20 13:08:26 +02:00 |
|
SusiJo
|
3b3921cfa3
|
refine comment
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
|
2022-05-20 13:07:57 +02:00 |
|
SusiJo
|
f392c4bed5
|
removed params section & added description fasta
|
2022-05-20 13:05:43 +02:00 |
|
SusiJo
|
129270d7bc
|
adjusted conda env & singularity container
|
2022-05-20 10:37:46 +02:00 |
|
SusiJo
|
dd2f48810a
|
Merge branch 'nf-core:master' into cnvkit_bam
|
2022-05-20 09:14:21 +02:00 |
|
SusiJo
|
5a1297cc7d
|
added optional pdf/png outputs
|
2022-05-20 09:12:47 +02:00 |
|
SusiJo
|
064712c4ea
|
added cram_bam conversion & tumor_only check
|
2022-05-20 09:11:45 +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 |
|
Rike
|
10840a0562
|
Conda not suported
|
2022-05-18 14:26:21 +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
|
05837a011d
|
Add comment
|
2022-05-17 23:06:52 +02:00 |
|
Rike
|
15fba1dd7c
|
add filter variant tranches
|
2022-05-17 23:01:24 +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
|
f48790a728
|
replace regex with fixed extensions
|
2022-05-17 09:54:06 +02:00 |
|
Matthias De Smet
|
94733a85c0
|
Update modules/biobambam/bammerge/main.nf
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
|
2022-05-17 09:46:19 +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
|
00204fa82b
|
Update main.nf
|
2022-05-16 15:20:15 +00:00 |
|
Subazini TK
|
a0b46d3f03
|
Update meta.yml
|
2022-05-16 15:20:15 +00:00 |
|
Subazini TK
|
eaf81f6835
|
Update meta.yml
|
2022-05-16 15:20:15 +00:00 |
|
Subazini TK
|
1c42c97504
|
Update meta.yml
|
2022-05-16 15:20:15 +00:00 |
|
Subazini TK
|
8b4c5742c9
|
Update main.nf
|
2022-05-16 15:20:15 +00:00 |
|
Subazini TK
|
2a15bc2ac0
|
Update main.nf
|
2022-05-16 15:20:15 +00:00 |
|
Subazini TK
|
78dc1af1e6
|
Update main.nf
|
2022-05-16 15:20:15 +00:00 |
|
sysbiocoder
|
26f026683b
|
hmtnote
|
2022-05-16 15:20:15 +00:00 |
|
sysbiocoder
|
31fc8b560f
|
hmtnote
|
2022-05-16 15:20:15 +00:00 |
|
Veit Schwämmle
|
85345e5f61
|
Merge branch 'master' into maxquant
|
2022-05-16 16:06:32 +02:00 |
|
Praveen Raj S
|
df2620cfc7
|
Merge branch 'master' into process_lable_markdup
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2022-05-16 15:53:26 +02:00 |
|
Matthias De Smet
|
98f204fd1f
|
Update modules/biobambam/bammerge/main.nf
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
|
2022-05-16 15:13:54 +02:00 |
|
Matthias De Smet
|
cdbe648400
|
align
|
2022-05-16 14:44:32 +02:00 |
|
Matthias De Smet
|
2cca156fed
|
linting
|
2022-05-16 14:42:34 +02:00 |
|
Matthias De Smet
|
af69ea749d
|
add module: biobambam/bammerge
|
2022-05-16 14:39:58 +02:00 |
|
veitveit
|
12815af53e
|
ran prettier
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2022-05-16 14:30:40 +02:00 |
|
Veit Schwämmle
|
74a1c1400e
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Merge branch 'master' into maxquant
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2022-05-16 13:26:35 +02:00 |
|
Jasmin F
|
982c9183fa
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Merge branch 'master' into antismashlite
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2022-05-16 11:42:44 +02:00 |
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Jasmin F
|
adcfae6cd4
|
Merge branch 'master' into antismashlite
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2022-05-16 10:38:01 +02:00 |
|
Rike
|
ba14355891
|
revert markduplciatespark changes
|
2022-05-16 09:54:40 +02:00 |
|
FriederikeHanssen
|
8b4d021189
|
Merge branch 'master' into gatk_426
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2022-05-16 09:50:13 +02:00 |
|
Taniguti
|
ac7fe89a78
|
Merge branch 'master' into haplocheck
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2022-05-13 11:24:10 -03:00 |
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JIANHONG OU
|
fadb83cf44
|
Merge branch 'master' into motus_profile
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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
|
6427eeeca0
|
added tmp-dir + alignment correction
|
2022-05-13 14:35:22 +02:00 |
|
Nicolas Vannieuwkerke
|
1c2a991429
|
fixed memory warning
|
2022-05-13 14:25:53 +02:00 |
|
Nicolas Vannieuwkerke
|
d1f824ae66
|
updated meta.yml
|
2022-05-13 14:21:48 +02:00 |
|
Praveen
|
e0dccbb5dd
|
Changed process label to Medium for GATK4/MarkDuplicates
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2022-05-13 13:55:14 +02:00 |
|
Nicolas Vannieuwkerke
|
4f6264f7c3
|
Merge branch 'new-module-gatk4/splitintervals' of github.com:nvnieuwk/modules into new-module-gatk4/splitintervals
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2022-05-13 13:48:35 +02:00 |
|
Nicolas Vannieuwkerke
|
9d53577282
|
linting
|
2022-05-13 13:48:33 +02:00 |
|
nvnieuwk
|
1d4862ba60
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Merge branch 'master' into new-module-gatk4/splitintervals
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2022-05-13 13:47:20 +02:00 |
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Nicolas Vannieuwkerke
|
8a17b6dd0e
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added gatk4/splitintervals
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2022-05-13 13:46:34 +02:00 |
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Chris Cheshire
|
9f6a1ae4a4
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Merge branch 'master' into bowtie2-test-fix
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2022-05-13 12:05:48 +01:00 |
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Taniguti
|
4728b2bcd2
|
Merge branch 'master' into haplocheck
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2022-05-13 07:49:55 -03:00 |
|
Lucas Taniguti
|
86343cb034
|
feat: add haplocheck
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2022-05-13 07:42:09 -03:00 |
|
Mahesh Binzer-Panchal
|
00826dc2e9
|
Merge branch 'master' into genomescope2
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2022-05-13 11:28:47 +02:00 |
|
Nicolas Vannieuwkerke
|
6fa1c8089a
|
Added memory allocation to VCFeval
|
2022-05-13 10:03:20 +02:00 |
|
FriederikeHanssen
|
868150e1af
|
Merge branch 'master' into gatk_426
|
2022-05-12 19:33:07 +02:00 |
|
Rike
|
5f7b02189a
|
reverse again, why did tests pass before
|
2022-05-12 18:35:51 +02:00 |
|
Rike
|
e3a17b699e
|
update version
|
2022-05-12 18:19:33 +02:00 |
|
Rike
|
99880654bf
|
add output default bam
|
2022-05-12 18:06:15 +02:00 |
|
Rike
|
3fda3903dc
|
revert markduplciatespark container
|
2022-05-12 17:40:42 +02:00 |
|
Mahesh Binzer-Panchal
|
308ab8801d
|
Merge branch 'master' into kat_hist
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2022-05-12 16:52:05 +02:00 |
|
Rike
|
f40cfefc08
|
leftover fixes from refactoring
|
2022-05-12 16:47:17 +02:00 |
|
Rike
|
fd7ee6799a
|
update version also for spark containers
|
2022-05-12 15:55:11 +02:00 |
|
Rike
|
169b2b96c1
|
update gatk version
|
2022-05-12 15:45:21 +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 |
|
JIANHONG OU
|
6b960f0e75
|
fix the typo in motus_profile.
|
2022-05-12 09:20:32 -04:00 |
|
James A. Fellows Yates
|
3c02e6056c
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Merge branch 'master' into antismashlite
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2022-05-12 14:53:52 +02:00 |
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Chris Cheshire
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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
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2022-05-12 10:56:48 +02:00 |
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JIANHONG OU
|
a2dbef3de3
|
remove the wrong quotes for motus_profile.
|
2022-05-11 17:49:12 -04:00 |
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Robert A. Petit III
|
8b6e1aff38
|
Merge branch 'master' into rp3-add-snippy
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2022-05-11 12:28:27 -06:00 |
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JIANHONG OU
|
aca4b48842
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Merge branch 'motus_profile' of github.com:jianhong/modules into motus_profile
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2022-05-11 14:23:25 -04:00 |
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JIANHONG OU
|
ae81311a78
|
fix the typo when using getExtension for motus_profile.
|
2022-05-11 14:23:09 -04:00 |
|
Matthias De Smet
|
dcf9c07fc9
|
Merge branch 'master' into update/bowtie2-align
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2022-05-11 19:08:23 +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
|
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
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2022-05-11 16:56:29 +02:00 |
|
Matthias De Smet
|
c8d3de2ad9
|
restore samtools cmd to defaults
|
2022-05-11 16:17:30 +02:00 |
|
Jasmin F
|
853e3ec087
|
Remove commented code
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
|
2022-05-11 15:56:10 +02:00 |
|
Matthias De Smet
|
bcd7fe55b1
|
Update modules/bowtie2/align/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2022-05-11 13:59:03 +02:00 |
|
Matthias De Smet
|
9097abf277
|
Update modules/bowtie2/align/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2022-05-11 13:58:58 +02:00 |
|
Matthias De Smet
|
971a889e2a
|
Update modules/bowtie2/align/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2022-05-11 13:57:27 +02:00 |
|
Matthias De Smet
|
b456d8fa0a
|
Update modules/bowtie2/align/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2022-05-11 13:57:19 +02:00 |
|
Matthias De Smet
|
ff4b297827
|
Update modules/bowtie2/align/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2022-05-11 13:57:11 +02:00 |
|
Matthias De Smet
|
9dd083fa94
|
Update modules/bowtie2/align/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2022-05-11 13:55:55 +02:00 |
|
Matthias De Smet
|
dcffd93875
|
Merge branch 'master' into update/bowtie2-align
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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
|
d4f13ebfff
|
refactor: create new settings input
|
2022-05-11 12:47:54 +02:00 |
|
Moritz E. Beber
|
5d593bdb45
|
docs: correct license and input description
|
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
|
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
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2022-05-11 11:38:36 +02:00 |
|
Robert A. Petit III
|
ef2996e4a5
|
match names in meta and main
|
2022-05-10 21:47:57 +00:00 |
|
Robert A. Petit III
|
f15848d477
|
fix typo
|
2022-05-10 21:44:40 +00:00 |
|
Robert A. Petit III
|
44e13ae439
|
add module for snippy
|
2022-05-10 21:31:43 +00:00 |
|
Mahesh Binzer-Panchal
|
cd32c7f744
|
Merge branch 'master' into kat_hist
|
2022-05-10 17:03:00 +02:00 |
|
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
|
fa7c947c35
|
Adjusted meta
|
2022-05-10 13:33:37 +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 |
|
Nicolas Vannieuwkerke
|
c18391aa49
|
Updated meta.yml
|
2022-05-10 12:26:13 +02:00 |
|
nvnieuwk
|
2eb77bd64e
|
Update modules/rtgtools/vcfeval/main.nf
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
|
2022-05-10 12:22:56 +02:00 |
|
nvnieuwk
|
29f2d3c284
|
Update modules/rtgtools/vcfeval/main.nf
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
|
2022-05-10 12:22:49 +02:00 |
|
Nicolas Vannieuwkerke
|
ef4857ec54
|
Updated meta.yml
|
2022-05-10 12:20:01 +02:00 |
|
Moritz E. Beber
|
09bfe3c618
|
Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2022-05-10 12:16:57 +02:00 |
|
Moritz E. Beber
|
b1e134fdd7
|
docs: describe new file input
|
2022-05-10 12:16:57 +02:00 |
|
Moritz E. Beber
|
f6936e5270
|
refactor: accept settings as input
|
2022-05-10 12:16:57 +02:00 |
|
Moritz E. Beber
|
46a9aabfa3
|
chore: improve license description
|
2022-05-10 12:16:57 +02:00 |
|
Nicolas Vannieuwkerke
|
f3d5584ab0
|
Linting
|
2022-05-10 12:08:23 +02:00 |
|
Nicolas Vannieuwkerke
|
5db26f9f35
|
Linting
|
2022-05-10 12:07:11 +02:00 |
|
Nicolas Vannieuwkerke
|
3a064b0a99
|
Split the output to different channels
|
2022-05-10 12:05:42 +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 |
|
Rike
|
da79396f06
|
rename aligned to alignment
|
2022-05-09 16:07:49 +02:00 |
|
Rike
|
5bd456e5e8
|
rename file_type to output extension
|
2022-05-09 16:06:22 +02:00 |
|
Rike
|
1de1c2253e
|
Combine output after code review
|
2022-05-09 16:04:58 +02:00 |
|
Nicolas Vannieuwkerke
|
bd7e1414a4
|
Fixed meta.yml
|
2022-05-09 15:55:48 +02:00 |
|
nvnieuwk
|
4b8bd9ebf9
|
Merge branch 'master' into new-module-rtg/vcfeval
|
2022-05-09 15:51:31 +02:00 |
|
Nicolas Vannieuwkerke
|
1b63d03f8e
|
adjusted the bed variable name
|
2022-05-09 15:51:19 +02:00 |
|
Nicolas Vannieuwkerke
|
f6262b4a10
|
fixed some issues
|
2022-05-09 15:47:07 +02:00 |
|
Rike
|
24d5e7feed
|
Code review suggestions
|
2022-05-09 15:42:55 +02:00 |
|
Mahesh Binzer-Panchal
|
8d86988632
|
Merge branch 'master' into meryl/histogram
|
2022-05-09 15:39:32 +02:00 |
|
Rike
|
ef5f145342
|
Generalize Bam2Cram do either conversion
|
2022-05-09 15:22:54 +02:00 |
|
Mahesh Binzer-Panchal
|
57fee2b3d6
|
Add description pattern
|
2022-05-09 12:56:22 +00:00 |
|