Commit graph

327 commits

Author SHA1 Message Date
drpatelh
26e04dd298 rsem - add build info for mulled container 2021-02-03 11:04:51 +00:00
drpatelh
3d1b9371f2 hisat2 - add build info for mulled container 2021-02-03 11:04:35 +00:00
drpatelh
98158064a7 bwa - add build info for mulled container 2021-02-03 11:04:25 +00:00
drpatelh
630b4be938 bowtie2 - add build info for mulled container 2021-02-03 11:04:02 +00:00
drpatelh
415d0265db Add build to Conda 2021-02-03 11:03:36 +00:00
drpatelh
3ae4c51f42 various - add build to conda definition 2021-02-03 09:20:34 +00:00
drpatelh
c0926b0b6b various - add build to conda definition 2021-02-03 09:19:46 +00:00
drpatelh
daab19a849 picard - add build to conda definition 2021-02-03 09:18:37 +00:00
drpatelh
773d4d89f2 rseqc - add build to conda definition 2021-02-03 09:18:20 +00:00
drpatelh
383d35bc7d samtools - add build to conda definition 2021-02-03 09:17:38 +00:00
drpatelh
ce3edcc994 deeptools - add build to conda definition 2021-02-03 09:16:59 +00:00
drpatelh
c089edc670 cutadapt - add build to conda definition 2021-02-03 09:16:33 +00:00
drpatelh
b41c3d63ec bwa index - add build to conda definition 2021-02-03 09:16:22 +00:00
drpatelh
f913a55d85 bowtie2 build - add build to conda definition 2021-02-03 09:16:10 +00:00
drpatelh
a536c85ec0 bowtie - add build to conda definition 2021-02-03 08:49:18 +00:00
Maxime Garcia
e7474c3d98
Update main.nf
Use same tag
2021-02-02 12:13:14 +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
kevinmenden
956bf22a58 fixed bug; updated meta.yml 2021-02-01 07:44:26 +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
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
Kevin Menden
8e2749beb7
Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-26 12:46:30 +01:00
kevinmenden
272de7c021 Added meta.yml files for align and genomegenerate 2021-01-25 15:14:57 +01:00
kevinmenden
71e0de733c adapdted star for mutliple output BAMs 2021-01-25 14:09:03 +01:00
kevinmenden
6444af7b36 star module tests 2021-01-25 09:02:03 +01:00
Michael L Heuer
e6547d5b16 Update dsh-bio version to 2.0 2021-01-22 12:12:56 -06:00
Michael L Heuer
23f9284aae Added dsh-bio split-bed as dsh_splitbed 2021-01-21 16:34:49 -06:00
Michael L Heuer
eb6408f3dc Added dsh-bio filter-bed as dsh_filterbed 2021-01-21 15:16:20 -06:00
Chris Cheshire
f6432d3c9c seacr | updated whitespace 2021-01-05 10:22:37 +00:00
Chris Cheshire
d9818cf3ab seacr | updated whitespace 2021-01-05 10:21:32 +00:00
Chris Cheshire
6d34e6964f seacr | added new line at end 2021-01-05 10:20:13 +00:00
Chris Cheshire
e25edbf7b8 seacr | Added meta file 2021-01-05 10:18:11 +00:00
Chris Cheshire
c110088b5e Updated line endings 2021-01-05 09:56:15 +00:00
Chris Cheshire
37840b3855 seacr | updated trailing whitespace 2021-01-05 09:54:44 +00:00
Chris Cheshire
9c00d1722c seacr | PR review changes 2021-01-05 09:50:47 +00:00
Chris Cheshire
7e9cbfc8d1 Merge remote-tracking branch 'nf-core/master' 2021-01-05 09:10:11 +00:00
Harshil Patel
c98f9284a2
Merge pull request #89 from KevinMenden/master
Add bowtie module
2020-12-18 14:56:29 +00:00
kevinmenden
32f6191ff3 editorconfig 2020-12-18 11:11:19 +01:00
kevinmenden
db0b631906 removed index from test output 2020-12-18 11:06:02 +01:00
kevinmenden
299a3fa07e adding .index back 2020-12-18 10:58:37 +01:00
kevinmenden
0be13edc52 next try at editorconfig 2020-12-18 09:52:38 +01:00
kevinmenden
07f0a2476a fixed linting errors 2020-12-18 09:50:05 +01:00
kevinmenden
0eb20c14bf fixed unaligned output 2020-12-18 09:20:35 +01:00
kevinmenden
1c89c9717b Merge branch 'master' of https://github.com/KevinMenden/modules 2020-12-18 09:16:17 +01:00
kevinmenden
f840325ead added unaligned output 2020-12-18 09:14:40 +01:00
Kevin Menden
7805d25cc5
Update software/bowtie/align/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2020-12-18 09:13:48 +01:00
Kevin Menden
a7f1ff29d7
Update software/bowtie/align/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2020-12-18 09:13:42 +01:00
Kevin Menden
dc4108fd9b
Update software/bowtie/align/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2020-12-18 09:13:35 +01:00
Kevin Menden
41329b8982
Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2020-12-18 08:16:18 +01:00
Edmund Miller
d76638d6f8
style(#77): Fix editorconfig errors 2020-12-17 17:50:24 -06:00
Chris Cheshire
6f1c66f22f Merge remote-tracking branch 'nf-core/master' 2020-12-17 14:29:20 +00:00
Chris Cheshire
b24834dfce seacr | local testing implimented 2020-12-17 14:20:24 +00:00
Chris Cheshire
74e7b5385f seacr | Added main process structure 2020-12-17 13:54:48 +00:00
Harshil Patel
b236d0c834
Update main.nf 2020-12-17 10:24:01 +00:00
kevinmenden
57ab6dbcbf groovy formatting 2020-12-17 10:24:48 +01:00
kevinmenden
d75cb75111 added singularity; edge NXF version 2020-12-17 07:33:44 +01:00
Chris Cheshire
3ff2b558e0 seacr | Added callpeak skeleton 2020-12-16 11:05:06 +00:00
kevinmenden
f35850bf14 bowtie bam output 2020-12-16 11:02:58 +01:00
drpatelh
200c946693 Add --singularity_pull_docker_container to module yml 2020-12-14 00:34:24 +00:00
drpatelh
99a2364a26 Update all other modules 2020-12-14 00:05:48 +00:00
drpatelh
047dbde0af Add singularity containers for rnaseq pipeline modules 2020-12-13 23:41:53 +00:00
drpatelh
115efec15c Update Salmon quant to use BAM input 2020-12-09 21:20:52 +00:00
drpatelh
37b8b82c98 Fix tyop 2020-12-09 21:20:26 +00:00
drpatelh
42f318fe75 Update Salmon modules 2020-12-09 21:20:11 +00:00