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
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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
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
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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
...
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
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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
...
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 )
...
* 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
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Add modules complement, genomecov, intersect, merge, sort for bedtools
2020-08-05 15:45:17 +01:00
Paolo Di Tommaso
70daf8be30
Minor style improvents
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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
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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
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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