Kevin Menden
17dbff52f4
added gatk4 variantfiltration ( #265 )
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* added gatk4 variantfiltration
* replace merge with filter
* Update software/gatk4/variantfiltration/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* updated input
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-17 09:42:35 +01:00
Harshil Patel
3df3d671f2
Fix nf-core modules lint tests ( #275 )
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* Fix Conda definition bug
* Add process label
2021-03-16 17:16:47 +00:00
Jose Espinosa-Carrasco
74ff11b07b
Fix bowtie builds ( #273 )
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* Fix bowtie build test
* Forgot to delete old bowtie_build
* Fix bowtie2 build tests
* Add initOptions include on hisat2 extractsplicesites
2021-03-15 15:39:42 +01:00
Harshil Patel
9b99b33401
Rename .github/filters.yml -> tests/config/pytest_software.yml ( #271 )
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* Rename pytest filters.yml
* Change filters.yml name
* Update resoures for ivar trim
2021-03-15 12:51:30 +00:00
Harshil Patel
d9396adbdf
Update software version command ( #269 )
2021-03-15 12:21:21 +00:00
Jose Espinosa-Carrasco
572abb00b3
Remove def from module options definition in main ( #270 )
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* Remove def from module options definition in main
* Fix bismark_deduplicate tests
* Fix bwameth_align tests
* Fixing gatk4 conda tests ("=" instead of ':' in build id)
* Same as previous commit (Fix gatk4 test)
* Fix qualimap bamqc test (no md5 check for pngs)
* Fix seqkit split2 tests. Changed to new test data
* Fix samtools tests. Some were missing initOptions include
* Removing TOOL SUBTOOL template module since now it is included on tools repo
2021-03-15 12:16:43 +00:00
Kevin Menden
0218824b86
add task.cpus to pangolin ( #263 )
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* add task.cpus to pangolin
* bumped pangolin to v2.3.2
2021-03-10 09:02:23 +01:00
Kevin Menden
a552d97849
Exchange VCF data by sarscov2 data ( #261 )
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* added sarscov2 vcf data; adjusted bcftools tests
* updated README.md
* deleted old VCF files; fixed mergevcfs
* fixed tabix
2021-03-09 10:04:08 +01:00
Maxime Garcia
05cbbbaded
Rename gatk/createsequencedictionary -> gatk4/createsequencedictionary ( #260 )
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* fix: update and sort filters
* fix: rename gatk/createsequencedictionary -> gatk4/createsequencedictionary
2021-03-08 14:45:46 +01:00
Maxime Garcia
ea6fde0193
Merge pull request #252 from MaxUlysse/master_tiddit
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New module: tiddit
2021-02-25 09:34:33 +01:00
MaxUlysse
f62196a4a6
feat: add tiddit_sv module
2021-02-24 15:59:10 +01:00
JoseEspinosa
e9fc285967
Fix conda version declaration
2021-02-24 15:52:25 +01:00
Harshil Patel
50b98d56a1
Merge pull request #246 from drpatelh/master
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Update iVar modules
2021-02-24 13:00:05 +00:00
drpatelh
1094af2206
Add missing docs
2021-02-24 12:54:45 +00:00
Harshil Patel
ca4b4eb78e
Merge pull request #248 from JoseEspinosa/fix_bcftools
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Add missing requirements to bcftools modules
2021-02-24 12:51:39 +00:00
FriederikeHanssen
4673c119c7
resolve merge conflicts
2021-02-24 10:03:16 +01:00
JoseEspinosa
ec674bb127
Add label to bcftools processes
2021-02-24 09:47:54 +01:00
JoseEspinosa
823a631afc
Fix tools entry on yml
2021-02-24 09:47:36 +01:00
Jose Espinosa-Carrasco
8f4363ccb5
Merge pull request #247 from JoseEspinosa/bcftools-mpileup
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Add bcftools mpileup module
2021-02-24 09:24:43 +01:00
JoseEspinosa
af7bc743bf
Correct yml file, add fasta to input and correct vcf on output
2021-02-24 09:15:18 +01:00
Harshil Patel
5287fe5f95
Merge pull request #245 from phue/bismark_deduplicate
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add bismark/deduplicate + tests
2021-02-23 21:08:24 +00:00
Harshil Patel
4703a60443
Merge pull request #220 from phue/bwameth
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add bwameth modules
2021-02-23 21:01:54 +00:00
JoseEspinosa
138be9f918
Adding label to the bcftools-mpileup process
2021-02-23 21:52:15 +01:00
drpatelh
89cd71309c
Output log file for MultiQC
2021-02-23 20:36:23 +00:00
drpatelh
9098ba41c8
Update ivar consensus
2021-02-23 20:36:03 +00:00
JoseEspinosa
035443b6e0
Add bcftools-mpileup module
2021-02-23 19:05:26 +01:00
phue
e73bda26f5
add bismark/deduplicate + tests
2021-02-23 18:02:16 +01:00
FriederikeHanssen
bf58948dad
remove todos, describe in/output
2021-02-23 15:41:11 +01:00
FriederikeHanssen
4e9d728108
allow fq.gz or gastq.gz as in/output
2021-02-23 15:40:22 +01:00
FriederikeHanssen
12137d6f3e
Remove trialing whitespace
2021-02-23 15:00:21 +01:00
FriederikeHanssen
e251a3bed5
Remove todos
2021-02-23 14:58:09 +01:00
FriederikeHanssen
13733b2581
Add beautiful md5sums
2021-02-23 14:57:07 +01:00
FriederikeHanssen
5e365d5eff
Make all these tests pass
2021-02-23 14:09:46 +01:00
FriederikeHanssen
25a2a16f2d
Try to make a single test pass
2021-02-23 13:34:50 +01:00
kevinmenden
3fee38ee2d
added gatk4 revertsam
2021-02-22 15:21:39 +01:00
kevinmenden
efd60d94ee
adding revertsam/ fix typo in mergevcfs
2021-02-22 15:10:20 +01:00
kevinmenden
69d7bb4fca
reformatted input to tuple
2021-02-22 13:31:54 +01:00
phue
bf0e0d857d
bwameth/align: fix fasta name retrieval
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apparently bwameth doesn't like './' in front of the filepath? I have no idea. This works however
2021-02-20 13:12:43 +01:00
phue
c67e591caf
apply suggestions from review
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thanks @drpatelh
2021-02-20 12:51:01 +01:00
kevinmenden
bb5c0ceca5
adding SplitNCigarReads
2021-02-19 14:59:29 +01:00
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
a963c67481
bwameth: pass genome index as directory
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instead of single files
2021-02-18 11:51:36 +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
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add qualimap/bamqc + test
2021-02-18 10:09:03 +01:00
phue
0606c06a25
qualimap/bamqc: remove unneeded variable definition
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can just use task.cpus directly
2021-02-18 10:00:49 +01:00
