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
kevinmenden
956bf22a58
fixed bug; updated meta.yml
2021-02-01 07:44:26 +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
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
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
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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
Apply suggestions from code review
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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
Apply suggestions from code review
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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
...
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
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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
Edmund Miller
6eeb930bdb
chore: Remove test directory from dummy tool
2020-11-24 21:09:55 -06:00