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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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# 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
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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
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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
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Adding fastp module
2021-02-01 13:43:35 +00:00
Harshil Patel
e851da8640
Merge pull request #130 from KevinMenden/master
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Adding a QUAST module
2021-02-01 13:17:57 +00:00
Kevin Menden
f6c4e9d9c1
Update software/quast/meta.yml
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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.
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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.
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
kevinmenden
42020ce5ac
added tests for bowtie paired-end alignment; resolved index bug
2020-12-09 16:39:05 +01:00
kevinmenden
cc72028d3d
output index as directory
2020-12-09 15:58:56 +01:00
Kevin Menden
560a6a578b
Apply suggestions from code review
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2020-12-09 15:45:05 +01:00
Harshil Patel
79a0ce79ab
Merge pull request #82 from abhi18av/master
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Add multiqc module
2020-12-09 11:31:07 +00:00
Abhinav Sharma
0c9f29e0a2
Give finishing touches after the review
2020-12-08 19:08:00 +05:30
Abhinav Sharma
b56a0322ab
Apply suggestions from code review by @drpatelh
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2020-12-08 18:57:14 +05:30
kevinmenden
9d67da2b2c
added module yml files
2020-12-08 13:40:32 +01:00
kevinmenden
508761e05c
Added bowtie index and align modules
2020-12-08 12:57:00 +01:00
Harshil Patel
cd2cf9cf2f
Merge pull request #85 from nf-core/pytest-workflow-refactor
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Refactor all tests to use pytest-workflow
2020-12-04 14:30:00 +00:00
Abhinav Sharma
3da7aec183
Update the signatures
2020-12-04 12:25:16 +05:30
Abhinav Sharma
a30df8a59b
Iterate again on MultiQC
2020-12-04 12:11:17 +05:30
Abhinav Sharma
5fd3ba3ce6
Update the tests for MultiQC
2020-12-02 13:09:32 +05:30
Abhinav Sharma
4e657c82e2
Move the MultiQC test files to data folder
2020-12-01 12:27:31 +05:30
Abhinav Sharma
b43c1f3937
Refactor the multiqc test code
2020-12-01 12:19:52 +05:30
Abhinav Sharma
131609dc05
Tweak the output section to make the tests pass
2020-12-01 12:03:37 +05:30
Paolo Cozzi
835ac48565
Fixing MULTIQC module and adding tests ( #1 )
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* fix multiqc process
* fix multiqc tests
* move multiqc test input data into tests/data/fastqc/ folder
Move input tests data into tests/data/fastqc/ and linking those files into software/multiqc/test/input/ as stated from the project documentation
* add multiqc github workflow
* remove unused file
* generalize multiqc input data
User must collect all desidered files in a channel (as described in https://seqera.io/training/#_multiqc_report
* update meta information
2020-12-01 12:03:37 +05:30
Abhinav Sharma
2783913122
initial attempt for multiqc module
2020-12-01 12:03:37 +05:30
drpatelh
e5c7ecc89c
Use STAR to build initial index for RSEM
2020-11-30 11:29:24 +00:00