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Author SHA1 Message Date
JoseEspinosa
4b3c86ed9f Add tests for bcftools-mpileup 2021-02-23 19:05:57 +01:00
JoseEspinosa
035443b6e0 Add bcftools-mpileup module 2021-02-23 19:05:26 +01:00
Gregor Sturm
f4af709634
Merge pull request #244 from grst/fix-conda 
Only use one thread for pytest-workflow
 2021-02-23 14:15:05 +01:00
Gregor Sturm
38349417ad
Update .github/workflows/pytest-workflow.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-23 14:14:29 +01:00
Gregor Sturm
94bdc62123 Only use one thread for pytest-workflow 
This avoids a race condition on the conda cache.
 2021-02-23 14:06:52 +01:00
Kevin Menden
0e594eadc3
Merge pull request #240 from KevinMenden/revertsam 
Added GATK4 Revertsam
 2021-02-23 08:25:36 +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
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
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
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
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
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
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
phue
a156bdfc03 faidx: add filter 2021-02-17 17:01:22 +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
Harshil Patel
ed573db194
Merge pull request #184 from MaxUlysse/master_fix_ci 
fix: update checksum or filename
 2021-02-17 10:54:38 +00:00
Harshil Patel
4d656c8f5f
Merge pull request #181 from drpatelh/fixes 
Fix tests for iVar variants
 2021-02-17 10:08:57 +00:00
MaxUlysse
28fb5e8cbd fix: update checksum or filename 2021-02-17 01:34:50 +01:00
Harshil Patel
f677a6a05e
Merge pull request #183 from nf-core/MaxUlysse-patch-1 
Update .markdownlint.yml
 2021-02-17 00:20:51 +00:00
Harshil Patel
67d4dab632
Merge pull request #182 from drpatelh/rm_build 
Remove Conda build ids for all modules
 2021-02-17 00:20:00 +00:00
Maxime Garcia
4c511757f3
Update .markdownlint.yml 
fix typo
 2021-02-17 01:15:21 +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
Maxime Garcia
842173be9f
Merge pull request #175 from MaxUlysse/master_ISSUE_TEMPLATE 
fix: add guidelines to PRs and issues
 2021-02-17 00:36:35 +01:00
MaxUlysse
ebb6d5de1f fix: Apply suggestions from code review 2021-02-17 00:34:55 +01:00