Patrick Hüther
f9ce8664ba
add bismark/report ( #297 )
...
* add bismark/align module
* bismark/align: add tests
* bismark/align: update meta.yml
* bismark/align: skip checksum for alignment logs
they contain timestamps
* bismark/align: restore correct checksum
caused some mixup in the last commit
* bismark/align: add genome_preparation to filters
* Fix conda version pin
* change options to be a global var
* remove params from meta.yml
* add bismark/report
* fix test filepaths
* remove mysterious index files
2021-03-22 13:38:08 +01:00
Patrick Hüther
04704c2034
add bismark/methylation_extractor ( #274 )
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* add bismark/methylation_extractor
* add tests for bismark/methylation_extractor
* bismark/methylation_extractor: add genome_preparation to filters
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* remove params from meta.yml
* pytest: remove md5sum checks for gzipped output
gzip stores timestamps in the file header, so the checksum will be different each time
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-20 23:54:42 +00:00
Patrick Hüther
8a44258548
remove params section from meta.yml ( #282 )
2021-03-19 13:16:50 +01:00
Edmund Miller
36593aa43e
chore: Remove stray functions file ( #279 )
2021-03-19 05:49:02 +00:00
Jose Espinosa-Carrasco
72e81d6e90
Add spades module ( #277 )
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* Add spades module
* Reorder gatk4 modules alphabetically
* Update software/spades/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-18 13:48:38 +00:00
Jose Espinosa-Carrasco
313241749c
Add kraken2 run module ( #266 )
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* Add kraken2 run module
* Add kraken2 run module
* Add coronavirus kraken2 db
* Adding kraken2 run tests
* Update software/kraken2/run/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Fixing files commited by mistake
* Remove params for meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-18 13:08:06 +00:00
Michael L Heuer
1845db4043
Update dsh-bio to 2.0.3 ( #276 )
2021-03-18 13:06:56 +00:00
Kevin Menden
a90332906b
add mergebamalignment ( #259 )
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* add mergebamalignment
* fix test.yml
* update to latest gatk4 version
* Update software/gatk4/mergebamalignment/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/data/README.md
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gatk4/mergebamalignment/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gatk4/mergebamalignment/meta.yml
* fixed unmapped/unaligned
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-17 15:56:56 +01:00
Kevin Menden
3c4d9466f4
Adding minia for viralrecon ( #267 )
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* initial 'modules create' of minia
* fixed tests
* finished meta.yml
* fixed filters.yml
* resolved issues in pytest_software.yml
* add newline
* Update software/minia/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-17 12:54:15 +01:00
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
...
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
...
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
...
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
Harshil Patel
5695e4ccce
Merge pull request #222 from phue/methyldackel
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add methyldackel modules
2021-02-17 22:17:26 +00:00
Harshil Patel
ecd26b388d
Merge pull request #221 from heuermh/seqwish
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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
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
phue
b5b259a2d9
add qualimap/bamqc + test
2021-02-17 17:34:51 +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
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
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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
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Add ivar variants
2021-02-16 23:20:30 +00:00
Harshil Patel
b07ad23efa
Merge pull request #179 from MaxUlysse/master_htslib_tabix
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
Anders Goncalves da Silva
2fe3210f88
Add ivar variants
2021-02-15 09:27:59 -08:00
JoseEspinosa
6e92a6a080
Adding mosdepth module
2021-02-15 14:33:44 +01:00
Maxime Garcia
ec0bf0145e
Merge branch 'master' into master_bwa-mem2
2021-02-15 13:08:52 +01:00
Harshil Patel
4af9417b6d
Update software/ivar/trim/main.nf
2021-02-13 08:20:06 +00:00
Harshil Patel
a5686ed14e
Update software/ivar/trim/main.nf
2021-02-13 08:19:55 +00:00
Harshil Patel
25f3d46f68
Update software/ivar/trim/meta.yml
2021-02-13 08:17:03 +00:00
Anders Goncalves da Silva
bbdca4fa76
Fix output files
2021-02-12 16:14:46 -08:00
Anders Goncalves da Silva
7c9766962d
Add ivar trim meta.yml
2021-02-12 16:02:48 -08:00
Anders Goncalves da Silva
6dca7799e6
Add ivar trim
2021-02-12 16:02:10 -08:00
Harshil Patel
63a20e7b5c
Merge pull request #168 from JoseEspinosa/bcftools_merge
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Add bcftools merge module
2021-02-12 23:20:30 +00:00
Harshil Patel
c0d128fd39
Update software/bcftools/merge/main.nf
2021-02-12 23:16:52 +00:00
Anders Goncalves da Silva
9268851cde
Remove samtools option
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-12 15:09:50 -08:00
Anders Goncalves da Silva
1f66954180
Relabel input parameter
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-12 15:09:35 -08:00
JoseEspinosa
5313698705
Add bcftools merge module
2021-02-13 00:08:57 +01:00
Harshil Patel
0580fd8ded
Update software/ivar/consensus/main.nf
2021-02-12 23:02:04 +00:00
Harshil Patel
9e4539473e
Update software/ivar/consensus/main.nf
2021-02-12 23:01:53 +00:00
Harshil Patel
bc5e073cdb
Update software/ivar/consensus/main.nf
2021-02-12 22:57:06 +00:00
Anders Goncalves da Silva
cb19c7b056
Fix trailing whitespace
2021-02-12 14:46:13 -08:00
Anders Goncalves da Silva
b08bf1ea5c
Remove ref to conda build and additional params
2021-02-12 14:43:50 -08:00
Anders Goncalves da Silva
24b212318b
Merge branch 'master' into ivar-consensus
2021-02-12 11:51:24 -08:00
Anders Goncalves da Silva
bfc13d3379
Add options to make samtools more flexible
2021-02-12 11:50:33 -08:00
Anders Goncalves da Silva
a4bba006bd
Add reference fasta as input
2021-02-12 11:26:55 -08:00
Anders Goncalves da Silva
6b22bb9782
Add meta.yml
2021-02-12 11:25:40 -08:00
JoseEspinosa
0688230863
Revert since fixes to test were not working
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This reverts commit d7a219e88d
2021-02-12 18:02:32 +01:00
JoseEspinosa
8e23e1839d
Trying to fix tests
2021-02-12 17:56:51 +01:00
JoseEspinosa
6e8b63fc26
Add cat fastq module
2021-02-12 17:22:07 +01:00
MaxUlysse
9c98194d3c
chores: remove fasta file from bwamem2 mem process
2021-02-12 16:00:59 +01:00
MaxUlysse
0afddf6ca4
fix: CI is working
2021-02-12 15:24:09 +01:00
Maxime Garcia
c1ff201518
Apply suggestions from code review
...
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-12 13:24:10 +01:00
MaxUlysse
6b34ddf239
chores: bwa-mem2 -> bwamem2
2021-02-12 13:08:44 +01:00
MaxUlysse
a910d1a608
chores: add bwa-mem2 index + mem
2021-02-12 13:00:02 +01:00
Maxime Garcia
27be87ac72
Merge pull request #135 from drpatelh/bwa
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Update indices syntax for BWA index and mem modules
2021-02-12 12:45:38 +01:00
Anders Goncalves da Silva
e9aa037e7b
Add function to enable output of mpileup
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-10 10:02:06 -08:00
Anders Goncalves da Silva
06770d5f02
Specify the exact bioconda recipe build
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-10 10:01:25 -08:00
Anders Goncalves da Silva
362a630f8b
Change suffix of mpileup ouput file
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-10 10:00:54 -08:00
Anders Goncalves da Silva
884c4658b8
Make mpileup saving optional
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-10 10:00:22 -08:00
Jose Espinosa-Carrasco
1e771ac8a0
Merge pull request #164 from drpatelh/fixes
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Add missing build ids and rename *.txt channels
2021-02-10 14:19:00 +01:00
drpatelh
b9afca2b05
Underscore not .
2021-02-10 12:53:17 +00:00
drpatelh
d2508e3c03
Amend prefix for bcftools stats
2021-02-10 12:51:47 +00:00
drpatelh
e63279e6a2
Pin pangoLearn version
2021-02-10 10:28:27 +00:00
drpatelh
b03846600d
Tidy up
2021-02-09 23:26:45 +00:00
drpatelh
6795fe04b8
Rename output channel
2021-02-09 23:26:18 +00:00
drpatelh
2b9129b3f9
Change txt channel output
2021-02-09 23:09:22 +00:00
drpatelh
d50d070c06
Change txt channel output
2021-02-09 23:09:18 +00:00
drpatelh
0b33b6d081
Add missing build ids
2021-02-09 23:03:13 +00:00
JoseEspinosa
e8dc199dc8
Adding conda build to blast modules
2021-02-09 23:04:12 +01:00
