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Author SHA1 Message Date
Rike
a694267b4b fix empty index input 2022-05-12 17:01:03 +02:00
Rike
b3bd55da76 getpileupsummaries requires intervals files 2022-05-12 16:51:17 +02:00
Rike
f40cfefc08 leftover fixes from refactoring 2022-05-12 16:47:17 +02:00
Rike
15fbf21b28 double tmpdir args removed, porb leftover after massive refactor where we decided to make it mandatory everywhere 2022-05-12 16:16:53 +02:00
Rike
fef5434c4c Update md5sums 2022-05-12 16:07:12 +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
Mahesh Binzer-Panchal
2061a41803
Merge pull request #1634 from mahesh-panchal/meryl_unionsum 
Add meryl unionsum
 2022-05-09 16:33:04 +02:00
Mahesh Binzer-Panchal
705ad7c3a1
Merge branch 'master' into meryl_unionsum 2022-05-09 16:20:01 +02:00
FriederikeHanssen
36962150ce
Merge pull request #1639 from FriederikeHanssen/samtools_convert 
Samtools convert
 2022-05-09 16:17:25 +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
Mahesh Binzer-Panchal
3f95464f05
Merge pull request #1636 from mahesh-panchal/meryl/histogram 
Add meryl histogram
 2022-05-09 16:15:13 +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
Mahesh Binzer-Panchal
da93beaf60 Update pytests 2022-05-09 13:50:49 +00:00
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
FriederikeHanssen
52a62c238b
Merge branch 'nf-core:master' into master 2022-05-09 15:05:58 +02:00
Mahesh Binzer-Panchal
0c567f5474
Merge branch 'master' into meryl_unionsum 2022-05-09 15:03:27 +02:00
Mahesh Binzer-Panchal
f0f414d519 Update pytests 2022-05-09 13:00:10 +00:00
Jasmin F
6b8e7ea8e3
Merge pull request #1637 from jasmezz/test_data_bacteroides 
Update test_data.config: Add Bacteroides fragilis GFF file
 2022-05-09 14:59:15 +02:00
Mahesh Binzer-Panchal
57fee2b3d6 Add description pattern 2022-05-09 12:56:22 +00:00
Mahesh Binzer-Panchal
6621768550 Update pytest outputs 2022-05-09 12:54:31 +00:00
Jasmin F
453d5b66a4
Add Bacteroides fragilis GFF file 2022-05-09 14:46:18 +02:00
Mahesh Binzer-Panchal
ce97c87b5d
Merge branch 'master' into meryl_unionsum 2022-05-09 13:51:55 +02:00
Harshil Patel
eb084d1dc0
Merge pull request #1626 from mahesh-panchal/meryl_count 
Meryl Count
 2022-05-09 12:21:09 +01:00
Mahesh Binzer-Panchal
a43bc940d6 Add suggestions from code review 2022-05-09 11:15:14 +00:00
Mahesh Binzer-Panchal
129f57ccd9 Add meryl histogram 2022-05-09 08:50:28 +00:00
Mahesh Binzer-Panchal
ad4f8389cb Add meryl unionsum 2022-05-09 08:33:21 +00:00
Mahesh Binzer-Panchal
32b0fdc9d9
Merge branch 'master' into meryl_count 2022-05-09 10:05:28 +02:00
Mahesh Binzer-Panchal
9ebeb6a702 Update test 2022-05-09 08:05:07 +00:00
Lucpen
38d4f81d20
Merge pull request #1623 from nf-core/correcting_stubs 
fix added correct entry workflow in test.yml
 2022-05-09 10:02:56 +02:00
Mahesh Binzer-Panchal
4591ea2205 atomize 2022-05-09 07:58:58 +00:00
Lucpen
bdaed264a7
Merge branch 'master' into correcting_stubs 2022-05-09 08:54:22 +02:00
Maxime U. Garcia
9cfa06878e
Merge pull request #1629 from maxulysse/master_typos 
fix typos and spacing
 2022-05-08 12:23:23 +02:00
MaxUlysse
3d428e2933 fix spacing 2022-05-07 15:28:40 +02:00
MaxUlysse
1013be2623 fix path to script 2022-05-07 15:22:52 +02:00
Jose Espinosa-Carrasco
2c5ecc87ed
Merge pull request #1628 from nf-core/maxulysse-patch-1 
add missing file
 2022-05-06 23:54:04 +02:00
Jose Espinosa-Carrasco
e2acf28c8f
Merge branch 'master' into maxulysse-patch-1 2022-05-06 23:53:27 +02:00
Harshil Patel
e36489d9e4
Merge pull request #1627 from nf-core/fix-prefetch 
Use a template to add retrying to prefetch
 2022-05-06 19:43:43 +01:00
Harshil Patel
2676f8eef4
Merge branch 'master' into fix-prefetch 2022-05-06 19:33:44 +01:00
Matthias De Smet
b6dd8d2854
Merge pull request #1622 from matthdsm/update/snapaligner 2022-05-06 19:34:09 +02:00
Matthias De Smet
0752b82c9f
Merge branch 'master' into update/snapaligner 2022-05-06 18:57:37 +02:00
Matthias De Smet
dd458e3388 fix tags 2022-05-06 18:57:17 +02:00
Maxime U. Garcia
ac217479e9
Update tests/config/test_data.config 
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
 2022-05-06 18:18:32 +02:00
Maxime U. Garcia
ec7b460fa4
add missing file 2022-05-06 17:54:35 +02:00
Moritz E. Beber
ea41c753c0 fix: remove retry label 
Call gets retried by bash script
 2022-05-06 17:28:56 +02:00