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 )
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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
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
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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
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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
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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 )
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* 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
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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 )
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* 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
jasmezz
1acde9a7a1
Fix container volume mounts
2022-04-26 16:28:39 +02:00
Jose Espinosa-Carrasco
6a46e7cf11
Allow to pass arguments to the phantompeakqualtools script itself ( #1562 )
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* 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 )
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* 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
Jasmin F
6467e23809
Merge branch 'nf-core:master' into antismashlite
2022-04-25 14:21:54 +02:00
JIANHONG OU
98d318c0e0
init
2022-04-24 07:55:17 -04:00
Matthias De Smet
978f665c0a
Merge branch 'master' into tool/elprep-merge
2022-04-24 10:08:29 +02:00
