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646 commits

Author SHA1 Message Date
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
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
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 
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 
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 
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 
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) 
* 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
Edmund Miller
6eeb930bdb
chore: Remove test directory from dummy tool 2020-11-24 21:09:55 -06:00
Edmund Miller
2fc39e02e2
test(trimgalore): Refactor se and pe to use pytest-workflow 2020-11-24 21:08:34 -06:00
Edmund Miller
b2cd464ad3
test(samtools): Refactor stats to use pytest-workflow 2020-11-24 21:08:34 -06:00
Edmund Miller
36bbf6baa3
test(samtools): Refactor sort to use pytest-workflow 
Pretty sure this is passing it a sorted bam though?
 2020-11-24 21:08:34 -06:00
Edmund Miller
6448638b55
test(samtools): Refactor index to use pytest-workflow 2020-11-24 21:08:34 -06:00
Edmund Miller
16cb794892
test(samtools): Refactor idxstats to use pytest-workflow 2020-11-24 21:08:34 -06:00
Edmund Miller
34d86427a6
test(samtools): Refactor flagstat to use pytest-workflow 2020-11-24 21:08:33 -06:00
Edmund Miller
7848019cdb
test(picard): Refactor markduplicates to use pytest-workflow 2020-11-24 21:08:33 -06:00
Edmund Miller
939f5ca744
test(picard): Refactor collectmultiplemetrics to use pytest-workflow 2020-11-24 21:03:40 -06:00
Edmund Miller
234e85bdce
test(picard): Refactor mergesamfiles to use pytest-workflow 2020-11-24 19:01:12 -06:00
Edmund Miller
016d8684f3
test(bwa): Refactor to use pytest-workflow 2020-11-24 19:00:11 -06:00
Edmund Miller
ba681c6f27 refactor(pytest-workflow): Move fastqc tests to tests/ 2020-11-24 20:26:04 +00:00
Edmund Miller
c264c66a49
test(fastqc): Use -entry to speed up tests 
`--wt, --workflow-threads` is now an option and can be used to run tests
simultaneously.
 2020-11-16 13:41:59 -06:00
Edmund Miller
a4544a11ad
chore(fastqc): Remove test output 2020-11-16 10:22:19 -06:00
drpatelh
a3f46865ff Remove Singularity image path 2020-11-12 14:55:16 +00:00
drpatelh
47d390772c Update picard version command and default container 2020-10-19 15:17:19 +01:00
drpatelh
29f9b05433 Update docs 2020-10-15 11:13:54 +01:00
drpatelh
530789ba85 Get tests passing 2020-10-15 10:47:15 +01:00
drpatelh
1d30e2c21a Update tools not in rnaseq pipeline too 2020-10-14 18:59:25 +01:00
drpatelh
14525ed50d Remove functions file 2020-10-14 18:29:50 +01:00
drpatelh
e9e81e8691 Revert RSeQC version 2020-10-12 17:47:13 +01:00
drpatelh
6bb3d5caea Update container 2020-10-12 16:20:35 +01:00
drpatelh
64377d4035 Bug fixes 2020-10-12 16:20:22 +01:00
drpatelh
a1b705d412 Update RSeQC version 2020-10-12 16:04:04 +01:00
drpatelh
436a1f983c Update trimgalore version 2020-10-12 15:59:46 +01:00
drpatelh
d19a8c702d Update picard version 2020-10-12 15:58:09 +01:00
drpatelh
74f27803b4 Update stringtie version 2020-10-12 15:55:07 +01:00
drpatelh
f4f96ff792 Update gffread version 2020-10-12 15:52:05 +01:00
Harshil Patel
0e11679748
Update main.nf 2020-09-18 10:39:41 +01:00
Harshil Patel
fb44f36f66
Update main.nf 2020-09-16 19:08:24 +01:00
drpatelh
e438d026bd Unify syntax 2020-09-10 16:45:11 +01:00
drpatelh
cbf8329ffd Add new modules 2020-09-10 16:09:54 +01:00
drpatelh
46edf8ae4c Update featurecounts module 2020-09-10 16:07:21 +01:00
drpatelh
473f1b192f Update functions script 2020-09-10 15:59:26 +01:00
Jeremy1805
789dc4f09a Changed options.publish_files definition in functions.nf/initOptions 2020-08-20 11:57:10 +01:00
drpatelh
08723c9d61 Add tests for mergesamfiles 2020-08-07 16:39:16 +01:00
drpatelh
3547b64eab Add docs and tests for markduplicates 2020-08-07 16:30:28 +01:00
drpatelh
cb85acddf0 Add docs and tests for collectmultiplemetrics 2020-08-07 16:29:37 +01:00
drpatelh
d6f7bb055b Fix indents 2020-08-07 15:27:35 +01:00
drpatelh
e648dc335c Add samtools stats commands 2020-08-07 15:23:39 +01:00
drpatelh
d5b16db27d Add samtools sort 2020-08-07 15:21:28 +01:00
drpatelh
0287cad1f8 Add samtools index tests 2020-08-07 15:17:46 +01:00
drpatelh
17b5f5ef3b Get samtools idxstats tests passing 2020-08-07 15:14:45 +01:00
drpatelh
46e4d35ec3 Get samtools flagstat passing 2020-08-07 15:12:03 +01:00
drpatelh
cf5cb8945c Get samtools flagstat passing 2020-08-07 15:11:31 +01:00
drpatelh
736a0aa43c Update indents and syntax 2020-08-07 15:05:25 +01:00
drpatelh
6333786d62 Add test BAM files 2020-08-07 14:04:39 +01:00
drpatelh
0ad26e3b19 Add output files 2020-08-07 13:28:18 +01:00
drpatelh
d10878f19d Change to SE 2020-08-07 13:27:06 +01:00
drpatelh
7ab1245eb5 Add test data 2020-08-07 13:24:39 +01:00
drpatelh
b5338efb7d Add tests for BWA mem 2020-08-07 13:24:24 +01:00
drpatelh
cff81ef875 Add test data 2020-08-07 12:57:32 +01:00
drpatelh
7604bd27fc Add test nextflow.config 2020-08-07 12:56:52 +01:00
drpatelh
f367f9ef69 Add main test script 2020-08-07 12:56:39 +01:00
drpatelh
375af1428e Minor change 2020-08-07 12:38:10 +01:00
drpatelh
a6fc702c8b Update bwa index docs 2020-08-07 12:38:01 +01:00
drpatelh
36f2544c36 Add single_end input file for testing 2020-08-07 12:19:47 +01:00
drpatelh
6522b04ee3 Remove old code 2020-08-07 12:19:28 +01:00
drpatelh
30256d8e81 Update tests 2020-08-07 12:18:53 +01:00
drpatelh
2c0f552908 Add output files 2020-08-07 12:18:43 +01:00
drpatelh
4df72f0396 Update nextflow.config 2020-08-07 12:14:12 +01:00
drpatelh
f32950d0f2 Update docs for trimgalore 2020-08-07 12:10:42 +01:00
drpatelh
a63897ee9c Add input output test folders 2020-08-07 11:40:51 +01:00
drpatelh
3a4fbf36ae Add test 2020-08-07 11:31:07 +01:00
drpatelh
b1381bb577 Add TODOs 2020-08-07 11:30:55 +01:00
drpatelh
e657363900 Add nextflow config to folder 2020-08-07 10:59:05 +01:00
drpatelh
bdfe187440 Add TODO comments 2020-08-07 10:58:36 +01:00
drpatelh
9296897009 Define options as input 2020-08-07 10:58:24 +01:00
drpatelh
4f76bb6b03 Add nextflow.config 2020-08-07 10:06:45 +01:00
drpatelh
7efd46b489 Add nextflow.config 2020-08-07 09:59:19 +01:00
drpatelh
fab020461b Add -with-docker 2020-08-07 09:44:16 +01:00
drpatelh
111b1505fa Add basedir 2020-08-07 09:40:02 +01:00
drpatelh
75e7e1573c Add output files 2020-08-07 09:32:28 +01:00
drpatelh
754fad7c8e Update output paths 2020-08-07 09:32:03 +01:00
drpatelh
b0abd14135 Update tests 2020-08-07 09:31:27 +01:00
drpatelh
0466d5249b Update docs 2020-08-07 00:50:49 +01:00
drpatelh
f014e67de6 Remove old outputs 2020-08-07 00:37:13 +01:00
drpatelh
2c7abca088 Move unit tests to deprecated 2020-08-07 00:36:05 +01:00
drpatelh
16d3ad5d06 Adapt script for meta 2020-08-07 00:35:34 +01:00
drpatelh
c98b32dfa8 Add link to functions file 2020-08-06 16:26:57 +01:00
drpatelh
e2b47a6fa3 Add software requirements section 2020-08-06 15:22:32 +01:00
drpatelh
2c9cd2d89b Update main script 2020-08-06 12:00:38 +01:00
drpatelh
530b4c1bd9 Add test directory 2020-08-06 11:32:38 +01:00
drpatelh
b7d0ee043e Initial commit 2020-08-06 11:32:18 +01:00
drpatelh
f021ab119b Initial commit 2020-08-06 11:32:11 +01:00
drpatelh
ab512be9aa Initial commit 2020-08-06 11:31:52 +01:00
drpatelh
f315a7b3c4 Hard copy files 2020-08-05 18:38:27 +01:00
drpatelh
ab8a9025a0 Copy across test data and docs for trimgalore 2020-08-05 17:28:25 +01:00
drpatelh
50fce8b3cf Copy across test data and docs for samtools sort 2020-08-05 17:28:09 +01:00
drpatelh
de9d33da12 Copy across test data and docs for samtools index 2020-08-05 17:27:58 +01:00
drpatelh
fb697eca2f Copy across test data and docs for bwa mem 2020-08-05 17:27:42 +01:00
drpatelh
da4dcee934 Copy across test data and docs for bwa index 2020-08-05 17:27:28 +01:00
drpatelh
5d224740cd Change path 2020-08-05 17:17:58 +01:00
drpatelh
137db462a7 Add samtools 2020-08-05 17:17:47 +01:00
drpatelh
993d0d5743 Add picard 2020-08-05 17:17:41 +01:00
drpatelh
9d168cf29e Add deeptools 2020-08-05 17:17:34 +01:00
drpatelh
f481899049 Add subread 2020-08-05 17:17:19 +01:00
drpatelh
20e6d847a3 Add trimgalore 2020-08-05 17:17:12 +01:00
drpatelh
c5bb9c2fde Add macs2 2020-08-05 17:17:05 +01:00
drpatelh
f61ad7506a Add homer 2020-08-05 17:16:56 +01:00
drpatelh
71d7aecf74 Add preseq 2020-08-05 17:16:45 +01:00
drpatelh
e94676a2b2 Add phantompeakqualtools 2020-08-05 17:16:34 +01:00
drpatelh
6fe4ec16df Add ucsc 2020-08-05 17:16:23 +01:00
drpatelh
3b1669c317 Add bwa mem 2020-08-05 17:16:08 +01:00
drpatelh
7938a60a02 Add bwa index 2020-08-05 17:15:56 +01:00
drpatelh
7f5ca56413 Soft-link functions to top-level module dir 2020-08-05 17:03:04 +01:00
drpatelh
3ec4f63fd8 Use correct link to fastqc 2020-08-05 16:28:42 +01:00
drpatelh
c08e6959a5 Reorganise everything 2020-08-05 16:09:25 +01:00
Harshil Patel
95a91032ce
Merge pull request #42 from JoseEspinosa/bedtools_dev 
Add modules complement, genomecov, intersect, merge, sort for bedtools
 2020-08-05 15:45:17 +01:00
Paolo Di Tommaso
70daf8be30
Minor style improvents 
This commit provides a minor refactoring with som
Nextflow code style improvments:
- Replaces `.toGiga()` with `.giga`
- Replaces `tag { foo }` with `tag "$foo"`
- Move publishDir before input declarations. Directives should be
  before the first input. Tho this is not enforced, it may be in
  future versions.
- Replaces input `file` with `path`
- Remove unnecessary parentheses
 2020-07-27 12:11:42 +02:00
Phil Ewels
3406ed4da0 Merge branch 'master' into fastqc-unit-test 2020-07-17 16:00:59 +02:00
Phil Ewels
f01b3f13a6 Remove debugging statement 2020-07-17 16:00:08 +02:00
Phil Ewels
2d1252c804 FastQC tests - disable hash check 2020-07-17 11:30:28 +02:00
Phil Ewels
dcc4beacb1 Fix FastQC test 2020-07-17 11:26:50 +02:00
JoseEspinosa
a09e3a633d I forgot to uncomment output 2020-07-16 16:38:37 +02:00
JoseEspinosa
d30089f12d Very preliminary implementation of passing optional params to bedtools/intersect modules 2020-07-16 16:37:33 +02:00
Stephen Kelly
846a862513 move md5 function to lib dir and symlink to fastqc test dir, rename md5 function 2020-07-16 09:17:48 -04:00
Phil Ewels
9dfafb4a19
Merge pull request #46 from stevekm/fastqc-unit-test 
add FastQC output validation and md5 checksum hash checks
 2020-07-16 15:13:44 +02:00
Stephen Kelly
45fbbb538c add FastQC output validation and md5 checksum hash checks 2020-07-16 08:20:37 -04:00
JoseEspinosa
759dd85c92 Removing biocontainer in favor of nf-core container 2020-07-16 10:22:09 +02:00
JoseEspinosa
6d8b616975 Bedtools sort adapted to the current module standard 2020-07-15 18:16:12 +02:00
JoseEspinosa
4d2e375a0d Bedtools merge adapted to the current module standard 2020-07-15 18:16:01 +02:00
JoseEspinosa
98c8f44130 Bedtools intersect adapted to the current module standard 2020-07-15 18:15:49 +02:00
JoseEspinosa
0b123f9e13 Bedtools genomecov adapted to the current module standard 2020-07-15 18:15:32 +02:00
JoseEspinosa
2cbc988d5f Bedtools complement adapted to the current module standard 2020-07-15 18:15:16 +02:00
FelixKrueger
e90164dd0b Adding back tool specific input output and index files 2020-07-15 15:46:45 +01:00
drpatelh
532859d437 Update path 2020-07-15 14:07:19 +01:00
JoseEspinosa
7f8b8189f8 Merge remote-tracking branch 'upstream/master' into bedtools_dev 2020-07-15 15:05:26 +02:00
Gregor Sturm
a2bcb5c36a Update module according to discussion on Slack 2020-07-15 13:04:49 +02:00
Gregor Sturm
01a926866e
Update software/fastqc/test/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-07-15 12:48:21 +02:00
Gregor Sturm
9d7cece077
Update software/fastqc/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-07-15 12:48:11 +02:00
Gregor Sturm
5a8803ee2f
Update software/fastqc/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-07-15 12:48:03 +02:00
Gregor Sturm
a3db769a93
Update software/fastqc/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-07-15 12:47:52 +02:00
Gregor Sturm
180310bf0a
Update software/fastqc/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-07-15 12:47:42 +02:00
Gregor Sturm
6ad2b570c2
Update software/fastqc/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-07-15 12:47:30 +02:00
Gregor Sturm
53897f4d97
Update software/fastqc/meta.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2020-07-15 12:47:19 +02:00
Gregor Sturm
b00bb83532 Document params 2020-07-15 11:01:15 +02:00
Gregor Sturm
86d6daf9de Implement publish_results parameter 2020-07-15 10:55:52 +02:00
Gregor Sturm
1dc47e7cd3 Make publishDir more flexible 2020-07-15 10:16:48 +02:00
Gregor Sturm
dd34fa5853 Use moduleDir for conda env 2020-07-15 09:48:17 +02:00
Gregor Sturm
f7c42ac4fd Add tests for fastqc module 2020-07-15 09:48:14 +02:00
Gregor Sturm
167067a92e Clean up module file 2020-07-15 09:47:41 +02:00
JoseEspinosa
c485d56972 Indentation error in yml 2020-07-14 18:00:23 +02:00
JoseEspinosa
562fc74550 Indentation error in yml 2020-07-14 17:57:42 +02:00
JoseEspinosa
39b9ca205c Correcting path to test data 2020-07-14 17:42:03 +02:00
JoseEspinosa
b38135ff6b Moving bedtools/intersectbed to bedtools/intersect 2020-07-14 17:40:17 +02:00
JoseEspinosa
c059a485b9 Using bedtools{_,-}genomecov instead of genomecov alone 2020-07-14 17:31:40 +02:00
JoseEspinosa
71eaa83bf6 bedtoools/complementBed changed to bedtools/complement 2020-07-14 17:26:45 +02:00
JoseEspinosa
8c3d7aa2d8 Standardizing process names to BEDTOOLS_FOO and same with some variables 2020-07-14 17:25:32 +02:00
JoseEspinosa
99a8196776 Module bedtools-sort added 2020-07-14 17:20:12 +02:00
JoseEspinosa
cf9d87c977 Module bedtools-merge added 2020-07-14 16:49:06 +02:00
JoseEspinosa
708cee9cae Module bedtools-intersectbed added 2020-07-14 16:49:05 +02:00
JoseEspinosa
5f80a900e9 Changing fasta_sizes by chrom_sizes input path for genomecov 2020-07-14 16:47:27 +02:00
JoseEspinosa
f2eb3f68c0 Module bedtools-genomecov added 2020-07-14 16:47:26 +02:00
JoseEspinosa
f6894c7d3a Module complementbed added 2020-07-14 15:50:35 +02:00
Phil Ewels
31c0f617b9 Fix up cutadapt tests 2020-07-11 17:14:14 +02:00
Phil Ewels
f36902b9af Cutadapt - merge tests into one 2020-07-11 17:09:06 +02:00
Phil Ewels
d3f3432451 Update test file imports 2020-07-11 14:33:12 +02:00
Phil Ewels
014fef2e92 Rename tools to software 2020-07-11 14:27:21 +02:00