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406 commits

Author SHA1 Message Date
drpatelh
a37b116186 Fix bedtools merge module 2021-02-07 21:31:39 +00:00
drpatelh
4564ef0e54 Fix bedtools genomecov module 2021-02-07 21:31:21 +00:00
drpatelh
a0c08e0c06 Fix bedtools complement module 2021-02-07 21:31:02 +00:00
drpatelh
a9102c329c Fix bedtools complement module 2021-02-07 20:55:12 +00:00
drpatelh
81ae0089bc Fix merge conflicts 2021-02-05 10:06:39 +00:00
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
drpatelh
3ccf99d612 Fix module 2021-02-02 13:37:24 +00:00
drpatelh
6df54698d9 Remove fasta from input 2021-02-02 12:34:55 +00:00
drpatelh
dcb1dc5cd9 Remove fasta requirement from module 2021-02-02 12:34:42 +00:00
drpatelh
0d8bd42cca Create index in bwa directory 2021-02-02 12:34:23 +00:00
Maxime Garcia
e7474c3d98
Update main.nf 
Use same tag
 2021-02-02 12:13:14 +01:00
JoseEspinosa
3a40ec5664 Adding bcftools_isec taking a path with several vcfs and its tests 2021-02-02 10:50:45 +01:00
JoseEspinosa
c25f8f0f6c Fixing tests 2021-02-02 09:57:55 +01:00
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
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