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
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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
...
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