Commit graph

1940 commits

Author SHA1 Message Date
FriederikeHanssen
25a2a16f2d Try to make a single test pass 2021-02-23 13:34:50 +01:00
FriederikeHanssen
a0c9777d60 add seqkit to GHA 2021-02-23 12:43:30 +01:00
FriederikeHanssen
312bf85f70 use reasonable option params 2021-02-23 11:26:54 +01:00
FriederikeHanssen
9c51e05125 remove wrong md5 sums 2021-02-23 11:25:45 +01:00
FriederikeHanssen
c7d2bc8d43 Add tests for different options 2021-02-23 11:14:51 +01:00
Kevin Menden
0e594eadc3
Merge pull request #240 from KevinMenden/revertsam
Added GATK4 Revertsam
2021-02-23 08:25:36 +01:00
FriederikeHanssen
ec63f335d5 Add split2 options 2021-02-22 22:43:32 +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
Kevin Menden
5fb90932f7
Merge pull request #238 from KevinMenden/splitcigar
Splitcigar
2021-02-22 13:59:38 +01:00
kevinmenden
bd585265ce added entry to filters.yml 2021-02-22 13:36:49 +01:00
kevinmenden
69d7bb4fca reformatted input to tuple 2021-02-22 13:31:54 +01:00
kevinmenden
43446bc37e added sarscov2 fastq and bam files 2021-02-22 13:19:12 +01:00
Kevin Menden
c606ea42e7
Merge pull request #237 from KevinMenden/gatk4-mergevcfs
Gatk4 mergevcfs
2021-02-22 12:53:57 +01:00
phue
bf0e0d857d bwameth/align: fix fasta name retrieval
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
2d8baa8b75 bwameth/index: update test.yml 2021-02-20 12:55:09 +01:00
phue
c67e591caf apply suggestions from review
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
MaxUlysse
2bf3890afb Merge remote-tracking branch 'upstream/master' into master_tiddit 2021-02-19 13:37:45 +01:00
kevinmenden
3ac5c5fad6 working test 2021-02-19 13:36:42 +01:00
Kevin Menden
7996a46178
Merge pull request #235 from KevinMenden/master
add gatk4 bedtointervallist
2021-02-19 13:35:15 +01:00
kevinmenden
c0693fa3db remove whitespace 2021-02-19 13:30:40 +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
Kevin Menden
134f0ac78c
Merge pull request #236 from KevinMenden/gatk4-bamtofastq
added gatk4 SamToFastq
2021-02-19 13:07:10 +01:00
kevinmenden
908e55ee5c fixed tag 2021-02-19 12:46:59 +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
MaxUlysse
eaff4eb0ff fix: order alphabetically 2021-02-19 10:56:04 +01:00
Harshil Patel
01c0d335ca
Merge pull request #223 from phue/bismark_genome_preparation
add bismark/genome_preparation + test
2021-02-18 19:08:00 +00:00
phue
a963c67481 bwameth: pass genome index as directory
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
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
phue
1a414261c4 bwameth/align: update checksums 2021-02-17 18:35:39 +01:00
phue
84a5da0d91 add bwameth/align module + tests 2021-02-17 18:23:11 +01:00
Michael L Heuer
206b605666 Add module for seqwish/induce 2021-02-17 11:19:47 -06:00
phue
180b1cf36b add bwameth/index module + test 2021-02-17 18:03:48 +01:00
Patrick Hüther
78cf182ed4
Merge pull request #218 from phue/samtools_faidx
add samtools/faidx + tests
2021-02-17 17:37:16 +01:00
phue
b5b259a2d9 add qualimap/bamqc + test 2021-02-17 17:34:51 +01:00
FriederikeHanssen
5f9aa7264e Add tests 2021-02-17 17:25:41 +01:00
Patrick Hüther
0cbe0a4173
Update tests/software/samtools/faidx/main.nf
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
2021-02-17 17:24:50 +01:00
FriederikeHanssen
2654c52ed1 Use list of reads as input, similar to dedup/extract 2021-02-17 17:15:02 +01:00
FriederikeHanssen
bedc2972eb Add seqkit split2 2021-02-17 17:09:24 +01:00