JoseEspinosa
3eedca9bb4
Add samtools_view
2021-01-29 17:18:45 +01:00
kevinmenden
e8bd730164
added quast tests
2021-01-29 16:14:33 +01:00
kevinmenden
10bb80743a
started adding quast modules
2021-01-29 16:06:14 +01:00
kevinmenden
bacebdfb47
added pangolin workf
2021-01-29 12:53:51 +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
kevinmenden
9156becd19
changed 'covid' to 'sarscov2'
2021-01-29 12:45:21 +01:00
kevinmenden
14ade8060f
added preliminary pangolin test
2021-01-29 11:12:22 +01:00
kevinmenden
d91cd73e52
added test workflow
2021-01-29 09:41:24 +01:00
kevinmenden
0780155dc4
added cutadapt module and tests
2021-01-29 09:33:45 +01:00
kevinmenden
3390f7621d
removed should_exist tag
2021-01-27 16:32:04 +01:00
kevinmenden
48c570d6ac
added file exist to test.yml
2021-01-27 08:56:25 +01:00
kevinmenden
431a2eb73b
added quant test workflow
2021-01-26 15:58:22 +01:00
kevinmenden
915e0574a2
added salmon index test workflow
2021-01-26 15:44:22 +01:00
kevinmenden
81bcf0da82
added test.yml and md5sums
2021-01-26 15:38:56 +01:00
kevinmenden
8d4b71355e
added test data and salmon tests
2021-01-26 15:24:06 +01:00
kevinmenden
5be1598b29
remove log.progress.out from test
2021-01-25 15:21:48 +01:00
kevinmenden
a1e1e27f67
updated test md5sums
2021-01-25 15:00:18 +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
Edmund Miller
cff3ac7e5f
ci: Make an edit to test pipeline trigger
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Plus this got clean up in 0c9f29e0a2
2021-01-24 10:37:29 -06:00
kevinmenden
f58c1c1e9e
added star genomegenerate test
2021-01-22 14:01:59 +01:00
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
Edmund Miller
daa25b9329
Merge branch 'preseq_test'
2021-01-15 17:41:13 -06:00
Edmund Miller
86850dc8a4
style: Remove old comment
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-15 10:32:20 -06:00
sruthipsuresh
7729fee5a9
Added gffread and gff3 file for testing
2021-01-15 10:32:20 -06:00
Edmund Miller
d7a78fa127
style: Fix indent
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-15 10:28:11 -06:00
sruthipsuresh
b95bd37780
Added ucsc module
2021-01-15 10:28:11 -06:00
Harshil Patel
27dbe8b52a
Merge pull request #115 from Functional-Genomics-Lab/stringtie_test
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Added testing for Stringtie
2021-01-15 16:09:39 +00:00
Edmund Miller
53830e05c7
test: Fix typo
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-15 10:07:44 -06:00
Edmund Miller
fe39c7822f
style: Fix indentation
2021-01-15 10:01:02 -06:00
Edmund Miller
b9e8f959b3
style: Standardize process names
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-01-15 10:00:40 -06:00
sruthipsuresh
ec91171152
Corrected naming to ensure test checks work
2021-01-15 09:38:13 -06:00
sruthipsuresh
5a1c1f90e5
removed md5sums for pdf, rdata
2021-01-15 09:38:13 -06:00
sruthipsuresh
3f814d1e2f
Workflow and md5sums added
2021-01-15 09:38:13 -06:00
sruthipsuresh
269d9888fe
Corrected bash error, tested process
2021-01-15 09:38:13 -06:00
Sruthi Suresh
b7435b0159
added test file for phantompeakqualtools for testing
2021-01-15 09:38:13 -06:00
sruthipsuresh
09d56efe12
Fixed with mr file for size issues
2021-01-14 02:12:57 -06:00
sruthipsuresh
00ef1d3863
Changed input to bed files
2021-01-15 16:52:17 -06:00
sruthipsuresh
a66618be98
Delete tests/software/phantompeakqualtools directory
2021-01-13 21:23:02 -06:00
sruthipsuresh
6f3cbfcd9a
Fixed test.yml
2021-01-12 18:14:28 -06:00
sruthipsuresh
b297f7aea1
Fixed test and removed phantompeak tests
2021-01-12 18:04:12 -06:00
sruthipsuresh
7c88cf4f67
Finished module with md5sums
2021-01-12 09:29:31 -06:00
sruthipsuresh
0a04c96357
Added module, TODO data
2021-01-12 09:13:37 -06:00
sruthipsuresh
3b581d1912
Updated test.yml
2021-01-12 08:56:11 -06:00
sruthipsuresh
a2faeb703f
Fixed md5sums
2021-01-12 08:50:20 -06:00
sruthipsuresh
cb39fcb915
Added preseq module and workflow
2021-01-12 08:41:09 -06:00
Chris Cheshire
7e9cbfc8d1
Merge remote-tracking branch 'nf-core/master'
2021-01-05 09:10:11 +00:00
sruthipsuresh
e1a3d1b18a
Corrected naming to ensure test checks work
2020-12-21 19:53:03 -06:00
sruthipsuresh
5319eabbc5
removed md5sums for pdf, rdata
2020-12-19 06:09:04 -06:00
sruthipsuresh
522b896534
Workflow and md5sums added
2020-12-19 06:09:04 -06:00
sruthipsuresh
8c088d473b
Corrected bash error, tested process
2020-12-19 06:09:04 -06:00
Sruthi Suresh
10d0058a1a
added test file for phantompeakqualtools for testing
2020-12-19 06:09:04 -06:00
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
8f75bac67e
update test.bam md5sums
2020-12-18 11:16:58 +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
07f0a2476a
fixed linting errors
2020-12-18 09:50:05 +01:00
Chris Cheshire
a57169a5da
seacr | updated test script
2020-12-17 14:23:20 +00:00
Chris Cheshire
b24834dfce
seacr | local testing implimented
2020-12-17 14:20:24 +00:00
Chris Cheshire
4e55bdcf84
seacr | removed test files
2020-12-17 14:20:02 +00:00
Chris Cheshire
a964d98d7f
seacr | Added test data
2020-12-17 13:55:58 +00:00
kevinmenden
f35850bf14
bowtie bam output
2020-12-16 11:02:58 +01:00
drpatelh
141ca290b7
Change md5sum for picard Markduplicates due to version bump
2020-12-14 00:44:49 +00:00
kevinmenden
0d7c8276b7
added test yml and md5s
2020-12-09 16:54:11 +01:00
kevinmenden
42020ce5ac
added tests for bowtie paired-end alignment; resolved index bug
2020-12-09 16:39:05 +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
fee0707af1
added bowtie_align workflow test
2020-12-08 14:19:34 +01:00
kevinmenden
6660a597a3
added tests for bowtie module
2020-12-08 13:59:14 +01:00
kevinmenden
9d67da2b2c
added module yml files
2020-12-08 13:40:32 +01:00
Abhinav Sharma
5949bfc15b
Edit the location of multiqc_config file
2020-12-04 22:55:15 +05:30
Abhinav Sharma
27b4b29976
Remove the extra data files
2020-12-04 20:20:59 +05:30
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
84c0bda00e
Apply suggestions from code review by @Emiller88
2020-12-03 12:57:24 +05:30
Abhinav Sharma
5fd3ba3ce6
Update the tests for MultiQC
2020-12-02 13:09:32 +05:30
Edmund Miller
6404c3390d
ci(fastqc): Remove md5sums
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These may not work across nextflow versions
2020-12-01 11:18:55 -06:00
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
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
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
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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
d1a77b2fb2
test(picard): Add failing test for markduplicates
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
d009420a0c
test(fastqc): Fix md5sums
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These must have gotten messed up at some point
83539fcdf2
is my guess
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
83539fcdf2
test(fastqc): restructure under software/fastqc
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2020-11-24 15:30:51 -06:00
Edmund Miller
b96f2d6a5e
test(config): One config to rule them all
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2020-11-24 20:26:04 +00:00
Edmund Miller
2e56022e31
test(fastqc): Remove input symlinks
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2020-11-24 20:26:04 +00:00
Edmund Miller
1fd97e8804
test(fastqc): Fix md5sums
2020-11-24 20:26:04 +00:00
Edmund Miller
ba681c6f27
refactor(pytest-workflow): Move fastqc tests to tests/
2020-11-24 20:26:04 +00:00