Mahesh Binzer-Panchal
ddbe6e8f40
Merge branch 'master' into busco
2022-05-03 10:48:03 +02:00
Mahesh Binzer-Panchal
9a72548ee1
Update busco module
2022-05-03 08:42:56 +00:00
Lauri Mesilaakso
6367c6a1ad
Merge branch 'master' into add_compression_to_bam2fq
2022-05-03 11:41:25 +03:00
nvnieuwk
f85787b19e
Merge branch 'master' into vardict-java
2022-05-03 10:17:04 +02:00
nvnieuwk
8187641280
Update modules/vardictjava/meta.yml
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-03 10:16:45 +02:00
nvnieuwk
11c6faf433
Update modules/vardictjava/meta.yml
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-03 10:16:36 +02:00
nvnieuwk
01085b3e09
Update modules/vardictjava/meta.yml
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-03 10:16:30 +02:00
nvnieuwk
1609dfc96d
Update modules/vardictjava/meta.yml
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-03 10:16:20 +02:00
nvnieuwk
3cdbdf50fc
Update modules/vardictjava/meta.yml
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-03 10:16:14 +02:00
nvnieuwk
2dff193b54
Update modules/vardictjava/meta.yml
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-03 10:15:59 +02:00
nvnieuwk
7c89af359c
Update modules/vardictjava/meta.yml
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-03 10:15:51 +02:00
Nicolas Vannieuwkerke
49ba3adbde
Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java
2022-05-03 10:15:33 +02:00
Nicolas Vannieuwkerke
d33253513f
put the version on top of the file
2022-05-03 10:15:30 +02:00
Lauri Mesilaakso
773e6f8e93
Merge branch 'master' into add_compression_to_bam2fq
2022-05-03 11:13:55 +03:00
nvnieuwk
278d41b6bf
Merge branch 'master' into vardict-java
2022-05-03 09:59:05 +02:00
ljmesi
5503903457
Add compression for output fastq file
2022-05-03 09:46:04 +02:00
Ramprasad Neethiraj
6f787aea71
Merge branch 'master' into adding_stub_to_modules
2022-05-03 09:43:16 +02:00
Lauri Mesilaakso
77054795fb
Merge branch 'master' into add_handling_of_alternative_fn_suffix_for_metaphlan3
2022-05-03 09:38:51 +03:00
Nicolas Vannieuwkerke
71c5d21374
ran prettier
2022-05-03 08:34:12 +02:00
Nicolas Vannieuwkerke
9127f92ddd
Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java
2022-05-03 08:29:50 +02:00
Nicolas Vannieuwkerke
9a10e5beb5
Added the missing inputs in meta.yml + correct notation
2022-05-03 08:29:46 +02:00
Matthias De Smet
1687bfcb85
Merge branch 'master' into add-slimfastq
2022-05-03 08:22:49 +02:00
Matthias De Smet
a67c06af81
Merge branch 'master' into vardict-java
2022-05-03 08:22:19 +02:00
Nicolas Vannieuwkerke
d8782d7976
Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java
2022-05-03 08:20:13 +02:00
Nicolas Vannieuwkerke
b8a59c2b17
Fixed version annotation
2022-05-03 08:20:10 +02:00
Moritz E. Beber
16aa3915e3
feat: add module for slimfastq
2022-05-02 23:16:59 +02:00
Ramprasad Neethiraj
3194729f82
Merge branch 'master' into adding_stub_to_modules
2022-05-02 18:31:55 +02:00
JIANHONG OU
5735f515f8
fix a typo in version export.
2022-05-02 12:25:48 -04:00
Sateesh Peri
c56b371713
Merge branch 'master' into srst2/srst2
2022-05-02 12:13:11 -04:00
Carpanzano
c07ae8c483
fixed lint in ktimporttaxonomy
2022-05-02 17:47:45 +02:00
Simone Carpanzano
3d9c8a6bb1
Merge branch 'master' into firstbranch
2022-05-02 17:43:33 +02:00
jvhagey
24dc2d2113
added tests
2022-05-02 11:30:19 -04:00
Jasmin F
235944f797
Merge branch 'master' into antismash_db_output
2022-05-02 17:11:51 +02:00
Jasmin F
8db0b754c0
Fix commented-out command
2022-05-02 16:56:39 +02:00
jasmezz
6a9f2077cf
Fix unbound variable crash
2022-05-02 16:41:59 +02:00
Lucpen
62c6123ec4
fix gatk4_mutect2 test by changing main.nf
2022-05-02 15:11:57 +02:00
JIANHONG OU
250d64dfde
fix the typo of motus_downloadb.
2022-05-02 08:52:54 -04:00
JIANHONG OU
b14f30936e
Merge branch 'nf-core:master' into motus_downloaddb
2022-05-02 08:42:09 -04:00
JIANHONG OU
31dd31079d
update teh versions.yml
2022-05-02 08:41:41 -04:00
jasmezz
0fc352188b
Fix conda antismash path
2022-05-02 14:40:35 +02:00
Jasmin F
5cd517e759
Apply suggestions from code review
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-02 14:31:40 +02:00
Lucpen
dfabf960dc
Merge branch 'master' into adding_stub_to_modules
2022-05-02 14:20:03 +02:00
ljmesi
ed4dd1a928
Add additional handling of fq.gz file name suffix
2022-05-02 14:16:12 +02:00
Lucpen
f231291e77
fix gatk4_reversam test
2022-05-02 12:58:12 +02:00
James A. Fellows Yates
575258332a
Merge branch 'master' into diamond-update
2022-05-02 12:41:37 +02:00
James Fellows Yates
bd3bfe0817
Add warn of default being used
2022-05-02 12:41:24 +02:00
James Fellows Yates
67b074382e
Fix tests
2022-05-02 12:29:00 +02:00
James Fellows Yates
58e5c6aece
Make variables consistent
2022-05-02 11:55:43 +02:00
James Fellows Yates
6986975bc0
Fix output channels allow BLAST table customisation
2022-05-02 11:39:07 +02:00
Praveen
0511e7fbbf
Changed BAI as optional output to handle large genome
2022-05-02 11:35:15 +02:00
Lucpen
8a5bcbc325
fix the stub of gatk4_revertsam
2022-05-02 11:06:08 +02:00
Matthias De Smet
bf416f2307
Merge branch 'master' into vardict-java
2022-05-02 10:43:47 +02:00
Lucpen
6b64f9cb6c
feat added stub to modules
2022-05-02 10:34:14 +02:00
Ramprasad Neethiraj
d2004a2b76
update cnvpytor
2022-05-01 21:14:01 +02:00
James Fellows Yates
44ed38beb8
Merge branch 'diamond-update' of github.com:jfy133/nf-core-modules into diamond-update
2022-04-29 21:06:09 +02:00
James Fellows Yates
39530b5ca7
Bump DIAMOND version to 2.0.15
2022-04-29 21:05:12 +02:00
Harshil Patel
4df985a065
Merge branch 'master' into tool/bamtools-split
2022-04-29 16:38:59 +01:00
James A. Fellows Yates
23c42e9b76
Merge branch 'master' into tool/elprep-merge
2022-04-29 15:11:09 +02:00
Matthias De Smet
9d0f03d96a
Update modules/elprep/merge/main.nf
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-29 15:07:09 +02:00
Matthias De Smet
7de207f93f
Merge branch 'master' into diamond-update
2022-04-29 15:02:54 +02:00
Matthias De Smet
bdbf629d93
Merge branch 'master' into tool/bamtools-split
2022-04-29 14:33:28 +02:00
Matthias De Smet
edadc9d216
Merge branch 'master' into tool/elprep-merge
2022-04-29 14:32:12 +02:00
Matthias De Smet
771d5a19f1
fix reference arg
2022-04-29 11:12:24 +02:00
Matthias De Smet
20ebb89ff9
update to long args
2022-04-29 10:52:40 +02:00
James A. Fellows Yates
983d61763d
Merge branch 'master' into diamond-update
2022-04-29 10:28:38 +02:00
James Fellows Yates
42564565b9
Update diamond/blastx diamond/blastp to support all possible output formats
2022-04-29 10:26:17 +02:00
Matthias De Smet
e263f267a7
Merge branch 'master' into bump/picard
2022-04-29 09:48:15 +02:00
Lauri Mesilaakso
1a5a9e7b40
Fix typo ( #1586 )
2022-04-29 09:37:23 +02:00
Matthias De Smet
ec10f98d55
picard CollectWgsMetrics: update to new cli args ( #1578 )
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* update to new cli args
* remove bam index from tuple, not needed by program
* bump picard version
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-04-29 09:32:32 +02:00
Matthias De Smet
00467ac64a
update command line syntax for all tools
2022-04-29 07:57:11 +02:00
Matthias De Smet
6ca6de91f8
bump picard version across the board
2022-04-29 07:47:24 +02:00
Simone Carpanzano
2efa5a09ab
Update main.nf
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$args line 28
2022-04-29 00:00:13 +02:00
Matthias De Smet
4d913d337d
Merge branch 'master' into tool/bamtools-split
2022-04-28 21:17:46 +02:00
Matthias De Smet
a7ed1477ee
Merge branch 'master' into tool/elprep-merge
2022-04-28 21:14:30 +02:00
Jill V. Hagey, PhD
218769d7df
Update modules/srst2/srst2/main.nf
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Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-04-28 14:41:37 -04:00
Jill V. Hagey, PhD
842ae3982b
Update meta.yml
2022-04-28 14:39:02 -04:00
Jill V. Hagey, PhD
9e7e10305b
Update modules/srst2/srst2/meta.yml
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Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-04-28 14:02:28 -04:00
Sateesh Peri
f5c4aecde5
Merge branch 'master' into srst2/srst2
2022-04-28 13:49:51 -04:00
Jill V. Hagey, PhD
e29a69077d
add doi
2022-04-28 12:30:04 -04:00
Jill V. Hagey, PhD
5be6afd6b1
changed container
2022-04-28 12:29:39 -04:00
Robert A. Petit III
4b6ee6fc14
Merge branch 'master' into rp3-add-shigatyper
2022-04-28 09:51:36 -06:00
Jasmin F
c740853874
Antismash db output patch 1 ( #3 )
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* Update main.nf
* Update meta.yml
* Update test.yml
2022-04-28 16:42:44 +02:00
Nicolas Vannieuwkerke
4b04ca22dd
Variable name change for var2vcf conversion arguments
2022-04-28 16:38:49 +02:00
Nicolas Vannieuwkerke
d626a1dcd3
Removed a whitespace in meta.yml...
2022-04-28 15:41:43 +02:00
nvnieuwk
a6397fac8f
Merge branch 'master' into vardict-java
2022-04-28 15:34:46 +02:00
Nicolas Vannieuwkerke
bdff37c3d7
Added the statistical tests and conversion to vcf
2022-04-28 15:33:27 +02:00
Nicolas Vannieuwkerke
6678ad4426
Added a header to the VCF
2022-04-28 14:54:20 +02:00
Praveen Raj S
b3e9b88e80
csi output in TABIX ( #1579 )
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* Added: csi output to TABIX
* Added: tests for csi
* Fix tiddit/sv (#1580 )
* Fix fasta ref option for TIDDIT_SV
* Add md5sum's to tiddit/sv tests
Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>
* Fix: prettier issues
Co-authored-by: Daniel Cooke <daniel.cooke@invitae.com>
Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>
2022-04-28 14:41:01 +02:00
nvnieuwk
c9404ed266
Merge branch 'master' into vardict-java
2022-04-28 14:30:19 +02:00
Nicolas Vannieuwkerke
40e6e5273d
fix for a linting issue
2022-04-28 14:30:04 +02:00
Nicolas Vannieuwkerke
c6ea41948d
Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java
2022-04-28 14:29:39 +02:00
Nicolas Vannieuwkerke
bf18604471
fix for a linting issue
2022-04-28 14:29:37 +02:00
JIANHONG OU
cdefbec669
add kimporttext module ( #1560 )
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* add kimporttext module
* fix the Prettier error.
* fix the Prettier error.
* fix the test.yml
* fix the test.yml
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* update the test files;
simplify the main script of krona/ktimporttext.
* update the test file url for krona ktimporttext
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-28 08:16:26 -04:00
JIANHONG OU
24fb7c89aa
Update modules/motus/downloaddb/main.nf
...
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-04-28 08:14:30 -04:00
Matthias De Smet
c7806e7bef
Merge branch 'master' into vardict-java
2022-04-28 14:12:07 +02:00
Nicolas Vannieuwkerke
8c98a78d2a
Fixed the issue with the BED file
2022-04-28 14:07:55 +02:00
Daniel Cooke
57cb730e78
Fix tiddit/sv ( #1580 )
...
* Fix fasta ref option for TIDDIT_SV
* Add md5sum's to tiddit/sv tests
Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>
2022-04-28 14:06:38 +02:00
Praveen Raj S
68f1c27169
Changed tbi as optional output in GATK4 HaplotypeCaller ( #1576 )
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* Changed tbi as optional output. HC cannot index a VCF from large chromosomes.
* Apply suggestions from code review
* Update modules/gatk4/haplotypecaller/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-04-28 13:41:20 +02:00
Nicolas Vannieuwkerke
45b4a61a15
Some small updates
2022-04-28 13:31:37 +02:00
Nicolas Vannieuwkerke
9df830f79d
Added the .bai and .fai files
2022-04-28 10:23:07 +02:00
Matthias De Smet
484c8f5dfa
Update meta.yml
2022-04-28 09:29:27 +02:00
Matthias De Smet
def580ddb7
Add gzip for compressed output
2022-04-28 09:28:57 +02:00
Nicolas Vannieuwkerke
db43095b1a
Split the bed file into a seperate input
2022-04-28 09:18:15 +02:00
nvnieuwk
1fd4719e9d
Merge branch 'master' into vardict-java
2022-04-28 09:09:07 +02:00
Nicolas Vannieuwkerke
fc942e062a
Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java
2022-04-28 09:08:03 +02:00
Nicolas Vannieuwkerke
85c49a971f
Fixed an issue with wrong file order
2022-04-28 09:07:52 +02:00
Jill V. Hagey, PhD
ecd31fd3cd
remove whitespaces and prettier fix
2022-04-27 19:55:42 -04:00
Jill V. Hagey, PhD
5b6d4fdace
Merge branch 'nf-core:master' into srst2/srst2
2022-04-27 18:19:18 -04:00
jvhagey
839ee59ca1
adding srst2 module
2022-04-27 18:01:28 -04:00
Simone Carpanzano
a5e7943f2b
update krona module
...
add "$args" to the module
2022-04-27 22:43:31 +02:00
Harshil Patel
1b5d3f5ac2
Bump STAR version to 2.7.10a for RSEM modules ( #1573 )
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* Bump STAR version to 2.7.10a for RSEM modules
* Fix tests
2022-04-27 19:21:26 +01:00
Robert A. Petit III
30bd93602f
Merge branch 'master' into rp3-add-shigatyper
2022-04-27 11:37:13 -06:00
Harshil Patel
2134031879
Bump SAMtools version for custom/getchromsizes ( #1572 )
2022-04-27 19:15:11 +02:00
Maxime U. Garcia
10ca39a86f
add intervals possibilities to splitncigarreads ( #1571 )
2022-04-27 16:03:44 +02:00
Matthias De Smet
d9b2c6af1a
Merge branch 'master' into vardict-java
2022-04-27 14:04:05 +02:00
Nicolas Vannieuwkerke
7956d38e61
Fixed the test on nextflow level
2022-04-27 13:18:46 +02:00
Jasmin F
61e740f79c
Add antismash download DB: missing container folders as output channels ( #1567 )
...
* Add missing container folders as output channels
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update tool name
* Update test output checksum
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-27 12:40:04 +02:00
Matthias De Smet
d57664b576
cleanup TODO's
2022-04-27 11:18:58 +02:00
nvnieuwk
dc62de1a78
Merge branch 'master' into vardict-java
2022-04-27 11:17:33 +02:00
Nicolas Vannieuwkerke
024c992ca7
created the module
2022-04-27 11:12:58 +02:00
Harshil Patel
85ec13ff1f
Add Trimgalore output for unpaired reads ( #1568 )
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* Add Trimgalore output for unpaired reads
* Use glob instead of outprefix
2022-04-26 19:15:24 +01:00
Sofia Stamouli
1f77bc130b
Update minimap2/align module ( #1537 )
2022-04-26 16:32:20 +02:00
Jose Espinosa-Carrasco
6a46e7cf11
Allow to pass arguments to the phantompeakqualtools script itself ( #1562 )
...
* Allow to pass arguments to the script itself
* Place args2 correctly
* Define args2 aaaaarrrrgggg
* Testing locally before commiting is a good practice
* Update modules/phantompeakqualtools/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-25 19:07:43 +02:00
Maxime U. Garcia
569e07f0af
add samtools/bamtocram modules ( #1561 )
...
* add new samtools/bamtocram module
* fix md5sum
* remove md5sum
* Update modules/samtools/bamtocram/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-25 14:32:49 +02:00
Matthias De Smet
978f665c0a
Merge branch 'master' into tool/elprep-merge
2022-04-24 10:08:29 +02:00
Sateesh Peri
378fa5fbb4
new module: GAMMA ( #1532 )
...
* initial version of gamma module
* remove trailing whitespace
* prettier fix
* hardcode version number
* Update modules/gamma/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/gamma/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/gamma/meta.yml
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* update meta and prettier
* add whitespaces
* add fasta output and tests
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-23 10:12:06 -04:00
Matthias De Smet
c3f13fdaf6
Merge branch 'master' into tool/bamtools-split
2022-04-22 19:36:18 +02:00
Matthias De Smet
da56a2d509
Update modules/bamtools/split/main.nf
...
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-22 19:36:08 +02:00
Matthias De Smet
2d32267fcd
Update modules/bamtools/split/main.nf
...
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-22 19:36:01 +02:00
Matthias De Smet
7bcede7474
Update modules/bamtools/split/meta.yml
...
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-22 19:34:14 +02:00
Matthias De Smet
2a2ac290c3
Update modules/bamtools/split/meta.yml
...
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-22 19:34:00 +02:00
Robert A. Petit III
a83202e710
Merge branch 'master' into rp3-add-shigatyper
2022-04-22 08:49:50 -06:00
Robert A. Petit III
c2d2399107
Update modules/shigatyper/main.nf
...
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-04-22 08:49:44 -06:00
Jose Espinosa-Carrasco
b3e56c83c6
Remove task.cpus from the command ( #1559 )
2022-04-22 15:29:49 +01:00
Harshil Patel
6d88f2da8c
Rename process from STRINGTIE to STRINGTIE_STRINGTIE ( #1546 )
...
* Rename process from STRINGTIE to STRINGTIE_STRINGTIE
* Bump Stringtie version to 2.2.1 and remove empty files in tests
* Fix tests for stringtie/merge
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
2022-04-22 15:13:06 +01:00
Harshil Patel
9aadd9a6d3
Replace vanilla Linux Biocontainer with Ubuntu ( #1557 )
2022-04-22 14:50:07 +01:00
CMGG ICT Team
b4af3f1475
test fixes
2022-04-22 15:02:41 +02:00
Sateesh Peri
8f2561c07f
Merge branch 'master' into rp3-add-shigatyper
2022-04-22 09:01:36 -04:00
Matthias De Smet
7e883da904
Revert "make use of dependent on input array size"
...
This reverts commit 413980e93a
2022-04-22 14:50:50 +02:00
Matthias De Smet
413980e93a
make use of dependent on input array size
2022-04-22 14:33:16 +02:00
Matthias De Smet
a6e7ecb3a3
Merge branch 'master' into tool/bamtools-split
2022-04-22 13:07:16 +02:00
Matthias De Smet
d57024ddc0
Merge branch 'master' into tool/elprep-merge
2022-04-22 13:05:30 +02:00
Matthias De Smet
c17d1a7a7b
fix output glob ( #1552 )
2022-04-22 13:04:41 +02:00
Matthias De Smet
d9348f3714
Merge branch 'master' into tool/bamtools-split
2022-04-22 13:04:16 +02:00
Matthias De Smet
b1749445d7
fix output glob ( #1551 )
2022-04-22 12:50:17 +02:00
Matthias De Smet
fefffb9bb0
fix output glob
2022-04-22 12:36:32 +02:00
Matthias De Smet
20728acde6
Merge branch 'master' into tool/bamtools-split
2022-04-22 11:57:22 +02:00
Matthias De Smet
2f6382168c
update meta.yml
2022-04-22 11:51:54 +02:00
Matthias De Smet
c4072f274c
fix formatting, fix code style
2022-04-22 11:39:22 +02:00
Matthias De Smet
b4d2e374a0
Merge branch 'master' into tool/elprep-merge
2022-04-22 11:35:48 +02:00
