Mahesh Binzer-Panchal
e91e99db30
Add GeneScopeFK ( #1781 )
2022-06-14 20:49:06 +02:00
Mahesh Binzer-Panchal
8ded6d441a
Add MerquryFK ( #1778 )
...
* Add MerquryFK
* Change resource allocation
2022-06-14 16:36:02 +02:00
Mahesh Binzer-Panchal
fd5aea0b76
Add FastK/Histex ( #1776 )
2022-06-14 16:30:37 +02:00
nvnieuwk
1a4ab76618
new module rtgtools/pedfilter ( #1777 )
...
* new module rtgtools/pedfilter
* removed checksum due to the presence of a date in the file
2022-06-14 16:02:18 +02:00
Mahesh Binzer-Panchal
4e308c131e
FastK/fastK ( #1739 )
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* Add FastK/FastK
* Add ktab and prof outputs
* Add the hidden files necessary for the optional files
* Update image
* Apply suggestions from code review
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2022-06-14 13:39:52 +02:00
8b2a473f58
New module: krakentools/kreport2krona ( #1746 )
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* Add module definition for kreport2krona
* Add metadata for kreport2krona module
* Add tests for kreport2krona
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-06-13 20:14:44 +02:00
Maxime U. Garcia
b689b8ed88
TIDDIT - add --skip_assembly when no bwa specified ( #1769 )
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add --skip_assembly when no bwa specified
2022-06-13 17:02:59 +02:00
Maxime U. Garcia
680b6c5b04
Update tiddit to 3.1.0 ( #1767 )
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* update TIDDIT to 3.1.0
* update VCF too as version is in file
2022-06-13 16:24:34 +02:00
Merlin Szymanski
8f199c4fa4
Create atlas/splitmerge Module ( #1756 )
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* Add atlas/splitmerge module
* Finish the tests for atlas/splitmerge
* Prettier
* Update modules/atlas/splitmerge/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Remove curly brackets from meta.yml parameters
For single-file outputs, as reviewed
* Lintung: Remove trailing white-space
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-06-13 15:09:32 +02:00
Robert A. Petit III
81232af296
add module for mcroni ( #1750 )
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Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2022-06-13 15:04:01 +02:00
Mahesh Binzer-Panchal
c1761293d8
Merge branch 'master' into busco_md5sum_patch
2022-06-13 10:53:36 +02:00
Mahesh Binzer-Panchal
575b2f00d3
Change busco multi-fasta test md5sum to contains
2022-06-13 08:51:41 +00:00
WackerO
f1b3174501
Merge branch 'master' into mpileup_bgzip
2022-06-13 09:48:47 +02:00
FriederikeHanssen
5b27af025a
Merge branch 'master' into manta_convert
2022-06-13 09:29:50 +02:00
FriederikeHanssen
e5b0c7ed25
Update tests/modules/manta/convertinversion/main.nf
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-06-13 09:26:35 +02:00
WackerO
c3b6ec8f3b
Merge branch 'master' of https://github.com/nf-core/modules into mpileup_bgzip
2022-06-13 08:31:01 +02:00
WackerO
dc6c09e083
samtools mpileup now bgzips mpileup files
2022-06-11 13:32:53 +02:00
Rike
650076cacf
add manta conversion script
2022-06-11 13:01:18 +02:00
Taniguti
547f483b74
Merge branch 'master' into haplocheck
2022-06-10 20:39:33 -03:00
Jasmin F
7027719c67
Merge branch 'master' into r-ampir
2022-06-10 14:57:24 +02:00
jasmezz
088b5b14f6
Merge branch 'r-ampir' of github.com:jasmezz/modules into r-ampir
2022-06-10 12:54:47 +02:00
jasmezz
39388abc04
Add file name collision check + TSV output
2022-06-10 12:54:39 +02:00
Alexander Peltzer
a0747b1405
Remove empty file md5sum
2022-06-10 11:53:28 +02:00
Alexander Peltzer
63f47551a8
Fix empty test having md5sum
2022-06-10 11:52:30 +02:00
Alexander Peltzer
1fbe69cfcc
Updated and fixed tests
2022-06-10 11:46:23 +02:00
Alexander Peltzer
8dfe8b795f
Merge remote-tracking branch 'refs/remotes/origin/cellranger-7.0.0' into cellranger-7.0.0
2022-06-10 11:23:15 +02:00
Alexander Peltzer
4928dfad34
Trying to fix tests
2022-06-10 11:22:45 +02:00
Alexander Peltzer
570a43ba4c
Fix tests
2022-06-10 11:21:03 +02:00
Thiseas C. Lamnidis
9948e9fe21
Merge branch 'master' into sexdeterrmine
2022-06-10 11:03:18 +02:00
James A. Fellows Yates
c9db677a45
Merge branch 'master' into r-ampir
2022-06-09 19:28:37 +02:00
jasmezz
5841f11edb
Replace MD5 with contains check
2022-06-09 18:15:27 +02:00
jasmezz
ecf1d146ab
Add full user options for AMPir
2022-06-09 16:59:00 +02:00
Maxime U. Garcia
878a5a8093
Merge branch 'master' into update_spark
2022-06-09 15:49:31 +02:00
Rike
30262d1fdd
remove variable checksum
2022-06-09 15:44:12 +02:00
Rike
a5583143c4
update checksum
2022-06-09 15:38:28 +02:00
jasmezz
ba53e09b64
Implement suggestions from code review
2022-06-09 15:37:35 +02:00
Rike
95633c6853
update checksum
2022-06-09 15:30:47 +02:00
Nicolas Vannieuwkerke
c50df9ad04
fix test.yml
2022-06-09 15:14:37 +02:00
Nicolas Vannieuwkerke
81fff7384d
small fix and typo
2022-06-09 15:08:02 +02:00
Nicolas Vannieuwkerke
14d38e43cf
fix test.yml
2022-06-09 14:58:20 +02:00
nvnieuwk
bf73b6d376
Merge branch 'master' into new-module-gatk4/reblockgvcf
2022-06-09 14:57:20 +02:00
Nicolas Vannieuwkerke
fe9e4ece00
new module gatk4/reblockgvcf
2022-06-09 14:56:55 +02:00
nvnieuwk
6d10909e9f
Update tests/modules/ensemblvep/main.nf
...
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-06-09 11:55:41 +02:00
nvnieuwk
e88a4ff70b
Merge branch 'master' into add-optional-fasta-parameter-to-ensemblvep
2022-06-09 11:54:22 +02:00
Nicolas Vannieuwkerke
e60323b757
typo
2022-06-09 11:53:59 +02:00
Nicolas Vannieuwkerke
7947bc662c
added an extra test without fasta
2022-06-09 11:53:16 +02:00
Nicolas Vannieuwkerke
a3202e41ec
prettier
2022-06-09 11:47:24 +02:00
Nicolas Vannieuwkerke
5ccf6fbcc9
add optional fasta argument to ensemblvep
2022-06-09 11:45:27 +02:00
SusiJo
0204d2374b
Merge remote-tracking branch 'origin/master' into gatk_spark
2022-06-09 09:33:17 +02:00
James Fellows Yates
4d7afa21e2
Add GATK indelrealigner tests
2022-06-08 21:14:08 +02:00
James A. Fellows Yates
1fc0d3de4b
Merge branch 'gatk3-indelrealigner' into upstream-for-indel
2022-06-08 20:30:19 +02:00
James A. Fellows Yates
4a2157e5ab
Merge branch 'master' into gatk-realigntargetcreator
2022-06-08 20:15:02 +02:00
Taniguti
89bffe3a5e
Merge branch 'master' into haplocheck
2022-06-08 15:00:06 -03:00
Ramprasad Neethiraj
1d67489056
update test
2022-06-08 16:36:02 +02:00
Ramprasad Neethiraj
0b090a6b6d
Merge branch 'master' of https://github.com/nf-core/modules into rhocall
2022-06-08 16:34:34 +02:00
Taniguti
d037f0ec97
Merge branch 'master' into haplocheck
2022-06-08 10:47:38 -03:00
Ramprasad Neethiraj
3cabdfac20
Merge branch 'master' into update_roh
2022-06-08 15:04:34 +02:00
Ramprasad Neethiraj
c079ee2025
fix test
2022-06-08 14:48:16 +02:00
Matthias De Smet
c005a5e007
formatting
2022-06-08 14:42:58 +02:00
Matthias De Smet
100b3f244c
Apply suggestions from code review
...
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
2022-06-08 14:24:55 +02:00
Lucas Taniguti
b2afb3b2ee
fix: string interpolation and test input access
2022-06-08 09:08:59 -03:00
Matthias De Smet
71e3056813
Merge branch 'master' into update/multiqc
2022-06-08 14:03:26 +02:00
Matthias De Smet
439d2a9e67
update mqc inputs
2022-06-08 13:48:27 +02:00
Lucas Taniguti
abaec30889
tests: add stub
2022-06-08 08:46:22 -03:00
Lucas Taniguti
f26979c44e
tests: add input to test_data.config
2022-06-08 08:10:25 -03:00
Taniguti
d5e077a2e9
Merge branch 'master' into haplocheck
2022-06-08 07:31:28 -03:00
Maxime U. Garcia
7230bf2174
Merge branch 'master' into update_tiddit
2022-06-08 11:16:01 +02:00
Taniguti
3be549534d
Apply suggestions from code review
...
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
2022-06-07 14:09:04 -03:00
Ramprasad Neethiraj
16e5e6093c
Merge branch 'master' of https://github.com/nf-core/modules into rhocall
2022-06-07 14:45:09 +02:00
SusiJo
745e47cd33
add versions.yml
2022-06-07 14:38:43 +02:00
Ramprasad Neethiraj
65a0fb959f
rhocall
2022-06-07 14:37:03 +02:00
SusiJo
e78ad2f88b
Merge remote-tracking branch 'origin' into gatk_spark
2022-06-07 14:00:26 +02:00
Matthias De Smet
bffd1c562b
Merge branch 'master' into update/multiqc
2022-06-07 13:59:00 +02:00
SusiJo
dbca9e8b36
adjusted prefix + test + authors
2022-06-07 13:58:57 +02:00
Matthias De Smet
e5bf87aec3
possible fix for name collisions
2022-06-07 13:58:27 +02:00
Taniguti
a2e2d50494
Merge branch 'master' into haplocheck
2022-06-07 08:16:22 -03:00
Ramprasad Neethiraj
9d6697bdea
template
2022-06-07 12:14:40 +02:00
Nicolas Vannieuwkerke
771425e7a0
add threads to calibratedragstrmodel
2022-06-07 12:11:18 +02:00
SusiJo
1368956d88
Merge remote-tracking branch 'origin/master' into gatk_spark
2022-06-07 11:00:33 +02:00
James A. Fellows Yates
d292f822e4
Merge branch 'master' into gatk-realigntargetcreator
2022-06-03 21:33:22 +02:00
James A. Fellows Yates
d2b240a17a
Merge branch 'master' into gatk-unifiedgenotyper
2022-06-03 21:24:09 +02:00
Robert A. Petit III
24ca2ed464
Merge branch 'master' into rp3-add-snippy
2022-06-03 13:01:05 -06:00
MaxUlysse
97e66015ca
add test + fix issues
2022-06-03 15:51:02 +02:00
SusiJo
230224700e
change prefix
2022-06-03 13:20:45 +02:00
SusiJo
1db7771ea9
Merge branch 'nf-core:master' into gatk_spark
2022-06-03 13:17:35 +02:00
MaxUlysse
f1a5cc07db
restructure tiddit/sv + test (just one for now)
2022-06-03 13:00:29 +02:00
MaxUlysse
40996cdbe1
update tiddit/cov + more tests
2022-06-03 12:07:16 +02:00
MaxUlysse
36ffd4fbf7
Merge remote-tracking branch 'upstream/master' into update_tiddit
2022-06-03 11:38:33 +02:00
Rike
2c9e2f5e73
Update TIDDIT to 3.0.0
2022-06-03 10:52:50 +02:00
James Fellows Yates
a565d9072a
Add GATK UnifiedGenotyper
2022-06-02 21:39:39 +02:00
James Fellows Yates
544b62df45
Star work on GATK UG
2022-06-02 21:11:17 +02:00
James Fellows Yates
9a4f22e8d1
Merge branch 'gatk-realigntargetcreator' of github.com:jfy133/nf-core-modules into gatk-realigntargetcreator
2022-06-02 20:32:03 +02:00
James Fellows Yates
c469a2b35e
Fux tests
2022-06-02 20:32:00 +02:00
James A. Fellows Yates
abc619a3e2
Merge branch 'master' into gatk-realigntargetcreator
2022-06-02 20:24:24 +02:00
SusiJo
1b93cde9ff
Merge branch 'master' into gatk_spark
2022-06-02 16:24:39 +02:00
Nicolas Vannieuwkerke
b4b1f3b81d
add intervals to calibratedragstrmodel
2022-06-02 16:20:12 +02:00
nvnieuwk
e107d61069
Update tests/modules/gatk4/haplotypecaller/test.yml
...
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-06-02 14:20:15 +02:00
nvnieuwk
e419d306df
Update tests/modules/gatk4/haplotypecaller/test.yml
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-06-02 14:20:10 +02:00
nvnieuwk
2ce1cf3329
Update tests/modules/gatk4/haplotypecaller/test.yml
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-06-02 14:20:04 +02:00
nvnieuwk
a6c4276ad7
Update tests/modules/gatk4/haplotypecaller/test.yml
...
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-06-02 14:19:57 +02:00
Nicolas Vannieuwkerke
e53d091a6d
added dragstr model to haplotypecaller
2022-06-02 14:08:09 +02:00
nvnieuwk
a339f9818a
Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel
2022-06-02 13:42:56 +02:00
nvnieuwk
4b430e8ece
Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel
2022-06-02 13:41:20 +02:00
Matthias De Smet
f58771c47f
Merge branch 'master' into update/untar
2022-06-02 13:38:53 +02:00
nvnieuwk
eadab8e002
Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel
2022-06-02 13:18:36 +02:00
Nicolas Vannieuwkerke
2a45d42868
added the calibratedragstrmodel module
2022-06-02 13:17:06 +02:00
SusiJo
2f3ddc90fb
added fasta_fai as input + changed if statements
2022-06-02 12:57:50 +02:00
Matthias De Smet
51be617b1c
fix untar output dir
2022-06-02 11:09:55 +02:00
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