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668 commits 30 branches 0 tags 142 MiB
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270 commits

Author SHA1 Message Date
JoseEspinosa
cee37852cd Merge remote-tracking branch 'upstream/master' into bcftools_viralrecon 2021-02-02 09:15:20 +01:00
JoseEspinosa
579de3e038 bcftools_tabix generic for any TAB-delimited genome position file 2021-02-01 21:59:39 +01:00
drpatelh
f84e5b59ca Rename bowtie_index to bowtie_build 2021-02-01 17:53:31 +00:00
Harshil Patel
0a41130276
Merge pull request #131 from KevinMenden/fastp-module 
Adding fastp module
 2021-02-01 13:43:35 +00:00
Harshil Patel
e851da8640
Merge pull request #130 from KevinMenden/master 
Adding a QUAST module
 2021-02-01 13:17:57 +00:00
Kevin Menden
f6c4e9d9c1
Update software/quast/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-01 14:03:36 +01:00
Kevin Menden
9885da628e
Update software/quast/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-01 14:03:22 +01:00
Kevin Menden
c807c6c438
Update software/quast/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-01 14:03:15 +01:00
Kevin Menden
d88bf3bdda
Update software/quast/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-01 14:03:06 +01:00
Kevin Menden
c43fe85a0c
Update software/quast/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-01 14:02:57 +01:00
kevinmenden
038381de99 added fastp module 2021-02-01 13:54:08 +01:00
kevinmenden
b5298f94d8 refactored quast module 2021-02-01 13:13:21 +01:00
Harshil Patel
2c962f34df
Merge pull request #110 from luslab/master 
Add SEACR module containing a single CALLPEAK process
 2021-02-01 09:48:15 +00:00
JoseEspinosa
0a8915ae77 Adding bcftools_tabix module 2021-02-01 10:07:35 +01:00
JoseEspinosa
52b0b8094d Adding bcftools_stats module 2021-02-01 10:03:25 +01:00
JoseEspinosa
0423e686a6 Adding bcftools_isec module 2021-02-01 09:46:24 +01:00
JoseEspinosa
da7598272e Adding bcftools_filter module 2021-02-01 09:41:08 +01:00
JoseEspinosa
eb12f4610d Fixing meta ymls 2021-02-01 09:28:51 +01:00
kevinmenden
956bf22a58 fixed bug; updated meta.yml 2021-02-01 07:44:26 +01:00
JoseEspinosa
b6ef06c6cd Add bcftools_consensus module 2021-01-31 22:23:26 +01:00
Harshil Patel
eadbea4b83
Merge pull request #127 from JoseEspinosa/bowtie2_viralrecon 
Bowtie2 viralrecon
 2021-01-30 13:22:30 +00:00
Harshil Patel
eab633776e
Update software/bowtie2/build/meta.yml 2021-01-30 13:21:56 +00:00
JoseEspinosa
500481833f Adding bcftools_bgzip module 2021-01-30 11:22:25 +01:00
JoseEspinosa
986b72cee9 Fix error on previous commit 2021-01-30 09:35:25 +01:00
JoseEspinosa
29989035a5 Remove author entry from yml (copy-pasted :P) 2021-01-30 09:29:53 +01:00
JoseEspinosa
ddbe8055c2 Adding tests 2021-01-29 19:31:33 +01:00
JoseEspinosa
43f9815621 Adding module bowtie2 align 2021-01-29 19:29:32 +01:00
Harshil Patel
bd59706d51
Merge pull request #118 from heuermh/dsh-bio 
Added dsh-bio filter-bed as dsh_filterbed
 2021-01-29 18:15:24 +00:00
Harshil Patel
7ab3217f16
Update software/dsh/filterbed/main.nf 2021-01-29 18:14:13 +00:00
Harshil Patel
cf5e38f48b
Update software/dsh/filterbed/main.nf 2021-01-29 18:14:08 +00:00
Harshil Patel
0fcbc4233c
Merge pull request #126 from JoseEspinosa/samtools_viralrecon 
Samtools viralrecon
 2021-01-29 18:12:48 +00:00
Harshil Patel
eb7a3861db
Update software/samtools/mpileup/meta.yml 2021-01-29 18:12:17 +00:00
JoseEspinosa
2f9934c563 Adding bowtie2_build module 2021-01-29 18:57:27 +01:00
JoseEspinosa
13e9f81160 Fixing lint tests 2021-01-29 18:01:58 +01:00
JoseEspinosa
22dcdc692d Adding samtools_mpileup module 2021-01-29 17:58:42 +01:00
JoseEspinosa
3eedca9bb4 Add samtools_view 2021-01-29 17:18:45 +01:00
kevinmenden
10bb80743a started adding quast modules 2021-01-29 16:06:14 +01:00
Michael L Heuer
d2723408ad
Apply suggestions from code review 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-01-29 09:01:21 -06:00
kevinmenden
d30994c6ef Merge branch 'pangolin-module' of https://github.com/KevinMenden/modules into pangolin-module 2021-01-29 12:54:38 +01:00
kevinmenden
44df90a795 Merge branch 'master' of https://github.com/nf-core/modules into pangolin-module 2021-01-29 12:50:24 +01:00
Harshil Patel
5da41ecb26
Merge pull request #122 from KevinMenden/master 
Added tests and meta.yml files for Salmon
 2021-01-29 11:49:03 +00:00
Harshil Patel
59e3e8202b
Update software/pangolin/main.nf 2021-01-29 11:43:42 +00:00
Kevin Menden
afaef3c30d
Apply suggestions from code review 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-01-29 12:40:15 +01:00
kevinmenden
a22f430674 updated input description 2021-01-29 12:34:23 +01:00
Kevin Menden
8f2f936cd4
Apply suggestions from code review 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-01-29 12:33:37 +01:00
kevinmenden
69a41cadbc added pangolin module 2021-01-29 11:03:54 +01:00
kevinmenden
0780155dc4 added cutadapt module and tests 2021-01-29 09:33:45 +01:00
kevinmenden
3750bea2dd fixed typo 2021-01-26 16:18:46 +01:00
kevinmenden
a3185732ff added meta.yml files 2021-01-26 16:12:41 +01:00
kevinmenden
84355f674d added optional output files 2021-01-26 13:31:30 +01:00