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651 commits

Author SHA1 Message Date
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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
JoseEspinosa
2fa14f2ec8 Adding conda build to bcftools modules 2021-02-09 23:00:19 +01:00
Harshil Patel
3f431014a4
Update software/bedtools/getfasta/main.nf 2021-02-09 21:34:40 +00:00
Anders Goncalves da Silva
8f546a1f95 Add ivar consensus 2021-02-09 10:26:35 -08:00
JoseEspinosa
68b85d9191 Merge remote-tracking branch 'upstream/master' into bedtools_getfasta 2021-02-09 18:23:24 +01:00
JoseEspinosa
e118bc049a Add bedtools getfasta module 2021-02-09 17:56:51 +01:00
JoseEspinosa
12ae7b0bff Adding blast blastn module 2021-02-09 16:58:36 +01:00
JoseEspinosa
c23b355b35 Add blast makeblastdb module 2021-02-09 15:44:34 +01:00
JoseEspinosa
c93e96101a Add untar module 2021-02-09 11:50:32 +01:00
JoseEspinosa
20771ae1bc Remove meta from input/output meta.yml 2021-02-09 11:02:31 +01:00
JoseEspinosa
b09416a0d0 Correcting meta.yml 2021-02-09 10:51:57 +01:00
JoseEspinosa
f7f06dd6e8 Add gunzip module 2021-02-09 10:05:55 +01:00
Harshil Patel
46e5df2cf7
Merge pull request #151 from drpatelh/bedtools 
Follow up fixes for bedtools modules added in #79
 2021-02-09 01:54:31 +00:00
Harshil Patel
84cf5ea2ef
Merge pull request #153 from JoseEspinosa/bedtools_maskfasta 
Add bedtools maskfasta module
 2021-02-08 23:11:00 +00:00
JoseEspinosa
02d10c25a3 Add bedtools maskfasta module 2021-02-08 23:41:10 +01:00
JoseEspinosa
f4e322f88d Merging upstream changes 
# Conflicts:
#	.github/filters.yml
 2021-02-08 18:09:41 +01:00
JoseEspinosa
fe412797dd Adressing general comments on PR #134 2021-02-08 15:11:36 +01:00
JoseEspinosa
5071bf5914 Merge remote-tracking branch 'upstream/master' into bcftools_viralrecon 2021-02-08 10:45:57 +01:00
drpatelh
c9cfdd31f3 Fix barfing linters 2021-02-08 00:57:06 +00:00
drpatelh
83a50d8ae0 Rename SOFTWARE_TOOL to TOOL_SUBTOOL 2021-02-07 23:20:53 +00:00
drpatelh
a34d74188d Really fix Editor Config 2021-02-07 21:49:20 +00:00
drpatelh
ef0a984cc0 Fix Editor config tests 2021-02-07 21:44:45 +00:00
drpatelh
5779b180da Fix bedtools sort module 2021-02-07 21:32:43 +00:00
drpatelh
f3b5af4ed5 Fix bedtools slip module 2021-02-07 21:32:20 +00:00
drpatelh
38964ecfc0 Fix bedtools intersect module 2021-02-07 21:32:01 +00:00
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
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
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