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Author SHA1 Message Date
Francesco L
97f318eea6
Merge branch 'master' into firstbranch 2022-05-05 14:25:00 +02:00
Maxime U. Garcia
448934b749
Merge pull request #1613 from maxulysse/master_snpeff_vep_improved 
update ensemblvep and snpeff modules
 2022-05-05 14:24:47 +02:00
Carpanzano
a700a9c15e Merge branch 'firstbranch' of github.com:carpanz/modules into firstbranch 2022-05-05 13:52:45 +02:00
Carpanzano
9083d3bb3d integrating suggestions from PR comments, including recovery of tests for kronadb and more detailed explanation of input database in yml file 2022-05-05 13:51:41 +02:00
MaxUlysse
40dd662fd2 update ensemblvep and snpeff modules 2022-05-05 12:57:14 +02:00
James A. Fellows Yates
e60c6f9bfd
Merge branch 'master' into firstbranch 2022-05-05 10:57:27 +02:00
Carpanzano
204dfba2d8 fixing ktupdatetaxonomy/meta.yml as suggested in PR 2022-05-05 10:51:22 +02:00
Lauri Mesilaakso
6bb9be38c5
Merge pull request #1606 from Genomic-Medicine-Linkoping/add_compression_to_bam2fq 
update samtools/bam2fq: add compression for output fastq file
 2022-05-05 09:37:36 +03:00
ljmesi
888e122f05 Merge branch 'add_compression_to_bam2fq' of https://github.com/Genomic-Medicine-Linkoping/modules into add_compression_to_bam2fq 2022-05-05 08:32:48 +02:00
ljmesi
be8ce6de2a Remove variable md5sum from the tests 2022-05-05 08:32:45 +02:00
Lauri Mesilaakso
e757966566
Merge branch 'master' into add_compression_to_bam2fq 2022-05-04 18:41:36 +03:00
Carpanzano
a6086f549d recovered process name 2022-05-04 17:28:24 +02:00
Carpanzano
38faf040ec missing change in ext.args config 2022-05-04 16:54:15 +02:00
Carpanzano
e7b92a7616 fixing md5sum changes 2022-05-04 16:43:22 +02:00
Carpanzano
8b1711d8a1 recovering old module name 2022-05-04 16:38:10 +02:00
Simone Carpanzano
162f8edf54
Merge branch 'master' into firstbranch 2022-05-04 16:35:25 +02:00
Carpanzano
6b8ca501ed fixing suggestions from PR 2022-05-04 16:34:52 +02:00
nvnieuwk
486cc1d142
Merge pull request #1611 from nvnieuwk/split-hap.py-into-two-modules 
Split hap.py into two parts
 2022-05-04 15:49:31 +02:00
Nicolas Vannieuwkerke
42bdc5471e Changed the pytest location of happy 2022-05-04 15:40:34 +02:00
Nicolas Vannieuwkerke
f875aec46b Split the module into two parts 2022-05-04 15:29:48 +02:00
nvnieuwk
994cd6d171
Merge pull request #1610 from nvnieuwk/new-module-hap.py 
New module hap.py
 2022-05-04 15:00:45 +02:00
Nicolas Vannieuwkerke
3c66138672 Linting issue + removed the contains lines 2022-05-04 14:49:17 +02:00
Nicolas Vannieuwkerke
5889d6c923 Another possible fix for the pytest issues 2022-05-04 14:46:15 +02:00
Nicolas Vannieuwkerke
583ea13800 Another try to fix the pytest issues 2022-05-04 14:22:55 +02:00
Nicolas Vannieuwkerke
17dbd2bb82 Linting issue fixed 2022-05-04 14:18:56 +02:00
Nicolas Vannieuwkerke
505ab03803 fixed a description 2022-05-04 14:14:53 +02:00
Nicolas Vannieuwkerke
c1393bf999 Possible fix for the pytest errors? 2022-05-04 14:14:01 +02:00
Nicolas Vannieuwkerke
177a7e49f2 Fixed a linting issue 2022-05-04 14:06:42 +02:00
Nicolas Vannieuwkerke
000b8ee2e0 Merge branch 'new-module-hap.py' of github.com:nvnieuwk/modules into new-module-hap.py 2022-05-04 14:05:23 +02:00
Nicolas Vannieuwkerke
065a5d6a7f Fixed a linting issue 2022-05-04 14:05:21 +02:00
nvnieuwk
c9808cb97f
Merge branch 'master' into new-module-hap.py 2022-05-04 14:01:02 +02:00
Nicolas Vannieuwkerke
37338ecee3 Finished the module 2022-05-04 14:00:02 +02:00
Nicolas Vannieuwkerke
c517ce9b4d Added the module and some simple testing 2022-05-04 13:42:12 +02:00
Lauri Mesilaakso
530b5ac661
Merge branch 'master' into add_compression_to_bam2fq 2022-05-04 09:53:46 +03:00
Chris Cheshire
7949c1f048
Merge pull request #1607 from luslab/expected_error_fix 
Bowtie2 - Added support for large indexes and improved error reporting
 2022-05-03 22:27:45 +01:00
Chris Cheshire
79e64cdd1f
Merge branch 'master' into expected_error_fix 2022-05-03 22:21:28 +01:00
Lauri Mesilaakso
12f79c2101
Merge branch 'master' into add_compression_to_bam2fq 2022-05-03 17:03:02 +03:00
ljmesi
a39fa4e003 Fix checksum for one file 2022-05-03 15:47:49 +02:00
nvnieuwk
1f906a7c6a
Merge pull request #1608 from nvnieuwk/vardict-java-update 
Small update to vardict-java
 2022-05-03 15:37:52 +02:00
Nicolas Vannieuwkerke
96d4a31cc1 Moved the BED file to the main tuple 2022-05-03 15:31:05 +02:00
ljmesi
034352dbbf Merge branch 'add_compression_to_bam2fq' of https://github.com/Genomic-Medicine-Linkoping/modules into add_compression_to_bam2fq 2022-05-03 15:18:12 +02:00
ljmesi
5510ea39fe Test --no-name to solve inconsistent checksums 2022-05-03 15:18:09 +02:00
Lauri Mesilaakso
a65e76e3dd
Merge branch 'master' into add_compression_to_bam2fq 2022-05-03 14:30:54 +03:00
Chris Cheshire
6f35537d40
Merge branch 'master' into expected_error_fix 2022-05-03 12:21:51 +01:00
Chris Cheshire
1baf143607
Merge pull request #1548 from rpetit3/rp3-add-shigatyper 
add module for shigatyper
 2022-05-03 12:21:43 +01:00
Chris Cheshire
829183ee84
Merge branch 'master' into rp3-add-shigatyper 2022-05-03 12:16:54 +01:00
Chris Cheshire
b3ee6384e6
Merge pull request #1604 from nf-core/add-slimfastq 
feat: add module for slimfastq
 2022-05-03 12:16:41 +01:00
Chris Cheshire
6015478b72
Merge branch 'master' into add-slimfastq 2022-05-03 12:11:19 +01:00
Chris Cheshire
d7fb969a74
Merge branch 'master' into rp3-add-shigatyper 2022-05-03 12:10:23 +01:00
Chris Cheshire
40e6bd9dc1 bowtie2|fix tags error 2022-05-03 12:07:04 +01:00