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Author SHA1 Message Date
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
Matthias De Smet
fdaef46c90
Merge branch 'master' into subwf/bam_qc 2022-04-28 14:00:30 +02:00
Matthias De Smet
4618c542e9 fix metrics output 2022-04-28 13:59:46 +02:00
Matthias De Smet
2fc857955f fix index omission 2022-04-28 13:53:48 +02:00
Matthias De Smet
8ad861a645 add fasta index 2022-04-28 13:52:03 +02:00
Matthias De Smet
55dfe1d8ab fix hsmetrics input 2022-04-28 13:43:59 +02:00
Matthias De Smet
e0a8af8693 fix outputs 2022-04-28 13:42:24 +02:00
Praveen Raj S
68f1c27169
Changed tbi as optional output in GATK4 HaplotypeCaller (#1576) 
* 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
Matthias De Smet
dee8ec9e91 fix typos 2022-04-28 12:53:17 +02:00
Nicolas Vannieuwkerke
9df830f79d Added the .bai and .fai files 2022-04-28 10:23:07 +02:00
Matthias De Smet
b92efb7abf add nextflow.config 2022-04-28 10:21:47 +02:00
Matthias De Smet
881e9db4bf update tests 2022-04-28 10:19:30 +02:00
Matthias De Smet
3cbf5c63e5
Update subworkflows/nf-core/bam_qc_picard/main.nf 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-04-28 10:09:25 +02:00
Matthias De Smet
433aaece46
Update tests/subworkflows/nf-core/bam_qc_picard/main.nf 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-04-28 10:05:31 +02:00
Matthias De Smet
8fb8199f31 fix copilot suggestion 2022-04-28 10:05:07 +02:00
Matthias De Smet
2b29ff5883 drop params.options 2022-04-28 10:03:02 +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
Matthias De Smet
8303c509fe
Merge branch 'master' into subwf/bam_qc 2022-04-28 08:57:24 +02:00
Jill V. Hagey, PhD
b0c5f9422b
tmp/ to changed to output/ 2022-04-27 20:21:41 -04:00
Jill V. Hagey, PhD
ecd31fd3cd
remove whitespaces and prettier fix 2022-04-27 19:55:42 -04:00
Jill V. Hagey, PhD
a575b91254
Update test.yml 2022-04-27 19:54:33 -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) 
* 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
Jasmin F
9108e2e2ec
Update test output checksum 2022-04-27 12:22:05 +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
Jasmin F
31547edc1e
Update tool name 2022-04-27 10:14:14 +02:00
Jasmin F
d79433dcac
Apply suggestions from code review 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-04-27 10:08:07 +02:00
Jasmin F
259f993df7
Update tool name 2022-04-27 10:06:58 +02:00
James A. Fellows Yates
f03afbd337
Merge branch 'master' into antismash_db_output 2022-04-27 08:30:50 +02:00
Harshil Patel
85ec13ff1f
Add Trimgalore output for unpaired reads (#1568) 
* Add Trimgalore output for unpaired reads

* Use glob instead of outprefix
 2022-04-26 19:15:24 +01:00
James A. Fellows Yates
5bf24cdad7
Merge branch 'master' into antismash_db_output 2022-04-26 17:16:28 +02:00
jasmezz
cc05006dbb Update antismashlite module main.nf 2022-04-26 17:15:41 +02:00
jasmezz
134272c7ee Add missing container folders as output channels 2022-04-26 17:04:57 +02:00
Sofia Stamouli
1f77bc130b
Update minimap2/align module (#1537) 2022-04-26 16:32:20 +02:00