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1113 commits 30 branches 0 tags 142 MiB
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476 commits

Author SHA1 Message Date
Kevin Menden
0202162b17
Merge branch 'master' into gatk4-mergevcfs 2021-02-19 14:11:30 +01:00
kevinmenden
02abe106ec added optional reference dictionary as input 2021-02-19 14:09:32 +01:00
kevinmenden
c288e081b4 initial commit adding mergevcfs 2021-02-19 13:29:08 +01:00
Kevin Menden
5c325f2942
Merge branch 'master' into master 2021-02-19 13:08:43 +01:00
kevinmenden
bd8ba42a8d added gatk4 SamToFastq 2021-02-19 12:41:29 +01:00
kevinmenden
6dcaf5ffc8 add gatk4 bedtointervallist 2021-02-19 11:26:31 +01:00
phue
0d8f5f0572 add bismark/genome_preparation + tests 2021-02-18 10:56:36 +01:00
Patrick Hüther
dba295155e
Merge pull request #219 from phue/qualimap_bamqc 
add qualimap/bamqc + test
 2021-02-18 10:09:03 +01:00
phue
0606c06a25 qualimap/bamqc: remove unneeded variable definition 
can just use task.cpus directly
 2021-02-18 10:00:49 +01:00
Harshil Patel
5695e4ccce
Merge pull request #222 from phue/methyldackel 
add methyldackel modules
 2021-02-17 22:17:26 +00:00
Harshil Patel
ecd26b388d
Merge pull request #221 from heuermh/seqwish 
Add module for seqwish/induce
 2021-02-17 22:14:49 +00:00
phue
52b00d4286 add methyldackel/mbias + tests 2021-02-17 19:27:57 +01:00
phue
5ad7c6bc51 add methyldackel/extract + tests + testdata 2021-02-17 19:18:55 +01:00
Michael L Heuer
206b605666 Add module for seqwish/induce 2021-02-17 11:19:47 -06:00
phue
b5b259a2d9 add qualimap/bamqc + test 2021-02-17 17:34:51 +01:00
phue
aafc6949d3 faidx: add process label 2021-02-17 16:56:45 +01:00
phue
3b1d126a0e add samtools/faidx + tests 2021-02-17 16:46:34 +01:00
drpatelh
d47f9bb909 @kevinmenden sanity fix 2021-02-16 23:58:52 +00:00
drpatelh
dcc580e4fb Remove Conda build ids for all modules 2021-02-16 23:58:23 +00:00
Harshil Patel
412172cda6
Merge pull request #180 from MaxUlysse/master_tabix_bgzip 
Replace bcftools/bgzip by tabix/bgzip
 2021-02-16 23:32:23 +00:00
MaxUlysse
596bb18394 fix: rename file to input and gz, plus fix tests 2021-02-17 00:28:32 +01:00
Harshil Patel
a282ecd8c7
Merge pull request #172 from andersgs/ivar-variant 
Add ivar variants
 2021-02-16 23:20:30 +00:00
Harshil Patel
b07ad23efa
Merge pull request #179 from MaxUlysse/master_htslib_tabix 
Replace bcftools/tabix by tabix/tabix
 2021-02-16 22:30:45 +00:00
Harshil Patel
d6d34a4b5b
Merge pull request #177 from MaxUlysse/master_gatk_createsequencedictionary 
Add gatk/createsequencedictionary
 2021-02-16 22:21:38 +00:00
Harshil Patel
a6d6c0b973
Update software/gatk/createsequencedictionary/main.nf 2021-02-16 22:08:11 +00:00
Harshil Patel
7c64e70c9e
Update software/gatk/createsequencedictionary/meta.yml 2021-02-16 22:07:51 +00:00
Harshil Patel
e558d5fb57
Merge pull request #174 from andersgs/ivar_consensus_fix 
ivar consensus: Add save mpileup as optional in output directive
 2021-02-16 22:04:38 +00:00
MaxUlysse
6a147b8aaa chores: replace bcftools/bgzip by tabix/bgzip cf #179 2021-02-16 19:11:36 +01:00
MaxUlysse
edf5fa3cf6 fix: merge bcftools/tabix and htslib/tabix into tabix/tabix 2021-02-16 18:27:13 +01:00
MaxUlysse
f660324508 chores: move file 2021-02-16 18:20:43 +01:00
MaxUlysse
274897f1fd fix: ECLint: Wrong line endings or new final newline 2021-02-16 17:11:50 +01:00
MaxUlysse
5e71dc94d6 fix: make HTSLIB_TABIX more modular 2021-02-16 17:06:55 +01:00
MaxUlysse
10524e3515 chores: add modules for htslib/tabix 2021-02-16 14:47:53 +01:00
MaxUlysse
28dc9227d7 fix: remove memory requirements and simplify URI 2021-02-16 13:54:40 +01:00
MaxUlysse
30e3f2c5f5 fix: ECLint check: trailing whitespace 2021-02-16 13:42:34 +01:00
MaxUlysse
7f35a1742d chores: add gatk/createsequencedictionary module 2021-02-16 13:40:06 +01:00
Maxime Garcia
d8706c12b3
Update meta.yml 
typo
 2021-02-16 11:22:15 +01:00
Anders Goncalves da Silva
fd854c333e
Add save mpileup as optional in output directive 2021-02-15 21:07:31 -08:00
Anders Goncalves da Silva
89f65e0875 Merge branch 'master' into ivar-variant 2021-02-15 20:50:35 -08:00
Anders Goncalves da Silva
7cae9b1842
Add gff to meta yaml 2021-02-15 20:49:37 -08:00
Anders Goncalves da Silva
26189f4132
Change ternary expressions back to traditional format 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:56:22 -08:00
Anders Goncalves da Silva
4f8ab8bd69
Rename gff to features 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:53:30 -08:00
Anders Goncalves da Silva
8c483d4c6a
Add gff as input for proper staging 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:53:13 -08:00
Anders Goncalves da Silva
6259b72081
Fix output format 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:52:30 -08:00
Anders Goncalves da Silva
ef1e1b2539
Fix indentation 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:51:45 -08:00
Harshil Patel
8eb3acc43f
Merge pull request #171 from JoseEspinosa/mosdepth 
Add mosdepth module
 2021-02-15 23:13:01 +00:00
Harshil Patel
f97c78b3fb
Update software/mosdepth/main.nf 2021-02-15 22:49:53 +00:00
Anders Goncalves da Silva
f841483a70
Fix URL for containers 2021-02-15 13:23:35 -08:00
Anders Goncalves da Silva
e8d1171b5d
Make gff a param and not an optional input 2021-02-15 11:50:52 -08:00
Anders Goncalves da Silva
9e3c4e598c
Add meta to ivar variants 2021-02-15 09:29:10 -08:00