drpatelh
ff23473e82
Restructure tests to run individually for each module
2021-02-03 16:02:58 +00:00
drpatelh
8be5e05111
Remove bam md5sum check for bowtie
2021-02-03 13:46:44 +00:00
drpatelh
1512c9af74
Unable to test BAM due to command
2021-02-03 12:26:10 +00:00
Edmund Miller
467d1595c4
test: Use docker image with singularity
2021-02-02 18:14:39 -06:00
Edmund Miller
72b4fb35aa
test: Fix profile logic order
2021-02-02 17:32:21 -06:00
Edmund Miller
67deb0d47a
ci: Add singularity tmp dir
...
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-02 17:25:58 -06:00
Edmund Miller
6b675eef6d
ci: Set pull docker container to false
...
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-02 17:00:40 -06:00
Edmund Miller
688cc05fe8
tests: Remove -profile in tests
...
See ddbca7b467
for more info
2021-02-02 15:30:59 -06:00
Edmund Miller
ddbca7b467
test: Use profile ENV variable hack
...
The user will now set the env variable and pass it to pytest. You also
can't set the env variable ahead of time, it has to be run with pytest.
Example:
PROFILE=conda pytest --tag fastqc --symlink --kwd
2021-02-02 12:44:30 -06:00
Harshil Patel
e7b1241449
Merge pull request #120 from nf-core/composite-runs
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Universal CI job
2021-02-02 18:26:02 +00:00
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
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Adding fastp module
2021-02-01 13:43:35 +00:00
Harshil Patel
e851da8640
Merge pull request #130 from KevinMenden/master
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Adding a QUAST module
2021-02-01 13:17:57 +00:00
Kevin Menden
0bd8506ea1
Update tests/software/quast/main.nf
...
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-01 14:04:08 +01:00
Kevin Menden
05370b5e16
Update tests/software/quast/main.nf
...
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-01 14:03:49 +01:00
kevinmenden
e9e795633d
added fastp tests
2021-02-01 14:02:06 +01:00
kevinmenden
a342296d70
fixed test md5s
2021-02-01 13:36:25 +01:00
kevinmenden
b5298f94d8
refactored quast module
2021-02-01 13:13:21 +01:00
Harshil Patel
c74d8a1711
Merge pull request #128 from JoseEspinosa/bowtie2_viralrecon
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Bowtie2 viralrecon 2
2021-02-01 09:56:11 +00:00
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
JoseEspinosa
8fb6b80abd
Fixing some md5 hashes
2021-01-30 23:08:17 +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
JoseEspinosa
ddbe8055c2
Adding tests
2021-01-29 19:31:33 +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
0fcbc4233c
Merge pull request #126 from JoseEspinosa/samtools_viralrecon
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Samtools viralrecon
2021-01-29 18:12:48 +00:00
JoseEspinosa
720db2bed5
Fixing samtools_mpileup test
2021-01-29 18:21:03 +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
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
...
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
...
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
...
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
...
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
...
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
...
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
...
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