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376 commits

Author SHA1 Message Date
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
sruthipsuresh
e360617ac6 Fixed images, genomecov 2021-01-29 23:17:44 -06:00
sruthipsuresh
e3bbbb48fc Fixed slop file 2021-01-29 23:17:44 -06:00
sruthipsuresh
957983bd99 Fixed and tested 4 modules, keeping with fastp module syntax 2021-01-29 23:17:44 -06:00
sruthipsuresh
295fff35ec Corrected containers and tested 2021-01-29 23:17:44 -06:00
sruthipsuresh
19b55fc67c Fixed intersect, complement indentation issues 2021-01-29 23:17:44 -06:00
sruthipsuresh
3da39dfc88 Fixed bedtools complement module 2021-01-29 23:17:44 -06:00
sruthipsuresh
8496427c56 Update software/bedtools/complement/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-01-29 23:17:44 -06:00
sruthipsuresh
fc8cdde2b4 Apply suggestions from code review 
Add all initial suggestions from review (syntax issues)

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-01-29 23:17:44 -06:00
sruthipsuresh
e5c21d15a3 Update software/bedtools/complement/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-01-29 23:17:44 -06:00
sruthipsuresh
bf2703f396 Update software/bedtools/complement/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-01-29 23:17:44 -06:00
sruthipsuresh
93f640154a Update software/bedtools/complement/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-01-29 23:17:44 -06:00
sruthipsuresh
ced2458d78 Update software/bedtools/complement/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-01-29 23:17:44 -06:00
sruthipsuresh
29639c522f Corrected sort 2021-01-29 23:17:44 -06:00
sruthipsuresh
70de0331a5 Corrected pytest and config 2021-01-29 23:17:44 -06:00
sruthipsuresh
2f19b4279c All modules corrected, TODO config 2021-01-29 23:17:44 -06:00
sruthipsuresh
6e7feb9e57 Update main.nf 
Fixed prefix
 2021-01-29 23:17:44 -06:00
sruthipsuresh
672f94f2af rebased and updated all bedtools testing and modules 2021-01-29 23:17:44 -06:00
sruthipsuresh
78473edb72 Removed large testing files, will convert to updated testing 2021-01-29 23:17:44 -06:00
Sruthi Suresh
4fca435120 Fixed naming issues and links in meta.yml 2021-01-29 23:17:44 -06:00
Edmund Miller
178becdd69 style: Run yaml-lint against files 2021-01-29 23:17:44 -06:00
Edmund Miller
b16226c09c fix(bedtools): Add header param 2021-01-29 23:17:44 -06:00
Sruthi Suresh
a984c1be7c Added all modules with basic functionality and updated meta.yml files. 2021-01-29 23:17:44 -06:00
Sruthi Suresh
89e5473b44 Updated modules with the changed container format 2021-01-29 23:17:44 -06:00
Sruthi Suresh
6677c98b11 Updated complement and completed slop module with all parameters available. 2021-01-29 23:17:44 -06:00
Sruthi Suresh
199dfc5ea3 Added complement module with necessary test dir/parameters 2021-01-29 23:17:44 -06:00
Sruthi Suresh
709970e9af Completed slop module for modules with test directory and updated meta.yml file 2021-01-29 23:17:44 -06:00
Sruthi Suresh
5205ce286a Added all modules using bedtools in the enhancer transcript identification section 2021-01-29 23:17:44 -06:00
Sruthi Suresh
637b545168 Removed extraneous modules and updated removegenes module 2021-01-29 23:17:44 -06:00
Sruthi Suresh
1426d89440 Completed sloprefseq and removegenes modules (main.nf, meta.yml and functiosn.nf file). Also added the test directory with input/output/main.nf files. 2021-01-29 23:17:44 -06:00
Sruthi Suresh
5b2633757e updated test file and main.nf file 2021-01-29 23:17:44 -06:00
sruthipsuresh
521c87f999 Updated test.mainnf file. 
Added the necessary chrom sizes input and changed test file to directory (as specified in nfcore).
 2021-01-29 23:17:44 -06:00
sruthipsuresh
fefbdb9893 Created test file for checking code. 
Still need to add parameters map and chrom sizes path.
 2021-01-29 23:17:44 -06:00
Sruthi Suresh
185ca19930 Added module for slopRefseq, including meta.yml, functions and main 2021-01-29 23:17:44 -06:00
Sruthi Suresh
352a48741f updated test file and main.nf file 2021-01-29 23:17:44 -06:00
Sruthi Suresh
5a997c5ac6 Updated module, need to fix cardinality of tuple 2021-01-29 23:17:44 -06:00
Sruthi Suresh
022b0bfe54 Updated test directory with input files, corrected main.nf and config. Additionally, main.nf for the process was updated. 2021-01-29 23:17:44 -06:00
sruthipsuresh
74f1a62fa4 Corrected errors in naming. 2021-01-29 23:17:44 -06:00
sruthipsuresh
ec6ebe086f Updated test.mainnf file. 
Added the necessary chrom sizes input and changed test file to directory (as specified in nfcore).
 2021-01-29 23:17:44 -06:00
sruthipsuresh
898c0775c6 Main.nf for bedtools module added. 2021-01-29 23:17:44 -06:00
sruthipsuresh
a654c0f5fa Created fixbedcoordinates functions.nf file 2021-01-29 23:17:44 -06:00
sruthipsuresh
c8f30720a1 Created meta file for the fixbedcoordinates module. 2021-01-29 23:17:44 -06:00
sruthipsuresh
8d6d48f067 Created test file for checking code. 
Still need to add parameters map and chrom sizes path.
 2021-01-29 23:17:44 -06:00
sruthipsuresh
5f705f69e1 Fixed version error in bedtools. 2021-01-29 23:17:44 -06:00
sruthipsuresh
fe2e27c793 Update main.nf 
Updated bedtools module with updated container version and upstream/downstream values.
 2021-01-29 23:17:44 -06:00
Sruthi Suresh
69f9f1cc89 Updated with removegenes folder (with meta, main and generic function file). 2021-01-29 23:17:44 -06:00
Sruthi Suresh
cfe8a490d8 Added module for slopRefseq, including meta.yml, functions and main 2021-01-29 23:17:44 -06:00
Harshil Patel
b260192942
Merge pull request #149 from heuermh/minimap2 
Add minimap2 align module
 2021-02-07 16:37:26 +00:00
Michael L Heuer
35ed09b06e Fix CI test failure 2021-02-05 11:41:36 -06:00
Michael L Heuer
6b873d7d33 Remove single_end if/else 2021-02-05 11:35:11 -06:00
Harshil Patel
31520fce97
Update software/minimap2/align/main.nf 2021-02-05 10:45:34 +00:00
Michael L Heuer
bbc8c725a2 Fix lint errors 2021-02-04 13:45:39 -06:00
Michael L Heuer
d5f2f5e32d Add minimap2 align module 2021-02-04 13:42:08 -06:00
Michael L Heuer
37a9f6f456 Address review comments 2021-02-04 12:10:54 -06:00
Kevin Menden
f298c594fe
Update meta.yml 
Just a small edit, we want to keep this consistent for linting
 2021-02-04 07:34:08 +01:00
Michael L Heuer
05d257e8f5 Fix lint errors 2021-02-03 19:34:25 -06:00
Michael L Heuer
c466255f6f Add bandage image module 2021-02-03 19:31:58 -06:00
drpatelh
673d463208 bowtie - add mulled build info 2021-02-03 11:33:31 +00:00
drpatelh
423144808c seacr - add build info for mulled container 2021-02-03 11:05:10 +00:00
drpatelh
34e451dd2e rsem - add build info for mulled container 2021-02-03 11:04:59 +00:00
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
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