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382 commits

Author SHA1 Message Date
drpatelh
a87d584c48 Change path to bowtie tests 2021-02-03 16:39:00 +00:00
drpatelh
9b153f296d Add check to see if bowtie bam files exists 2021-02-03 16:26:10 +00:00
drpatelh
239cbe17ad Fix relative paths 2021-02-03 16:20:02 +00:00
drpatelh
38c3ecfac6 Merge branch 'master' of https://github.com/nf-core/modules into split_tests 2021-02-03 16:05:06 +00:00
drpatelh
743ba37d4b Update filters paths 2021-02-03 16:04:43 +00:00
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 
Universal CI job
 2021-02-02 18:26:02 +00:00
drpatelh
6ac252e407 Change singularity to docker again 2021-02-02 13:38:34 +00:00
drpatelh
838defa350 Update md5sums 2021-02-02 13:37:40 +00:00
drpatelh
05b15df17e Remove file extension 2021-02-02 12:46:34 +00:00
drpatelh
d63d40827e Fix bwa index tests 2021-02-02 12:40:55 +00:00
drpatelh
ade6124a84 Change tests 2021-02-02 12:35:06 +00:00
JoseEspinosa
26829497d5 Fixing typo on path for md5 check 2021-02-02 12:19:57 +01:00
JoseEspinosa
e7f15feccf Adding --no-version to bcftools_isec for tests md5 check 2021-02-02 11:00:02 +01:00
JoseEspinosa
3a40ec5664 Adding bcftools_isec taking a path with several vcfs and its tests 2021-02-02 10:50:45 +01:00
JoseEspinosa
8e4764b8ed bcftools_filter adding argument to test to enable md5 check 2021-02-02 10:19:34 +01:00
JoseEspinosa
c25f8f0f6c Fixing tests 2021-02-02 09:57:55 +01:00
JoseEspinosa
382ea31e7e Adding bcftools test data 2021-02-02 09:18:28 +01:00
JoseEspinosa
cee37852cd Merge remote-tracking branch 'upstream/master' into bcftools_viralrecon 2021-02-02 09:15:20 +01:00
JoseEspinosa
a3ce63c79c Adding tests for bcftools 2021-02-02 09:14:00 +01:00
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 
Adding fastp module
 2021-02-01 13:43:35 +00:00
Harshil Patel
e851da8640
Merge pull request #130 from KevinMenden/master 
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 
Bowtie2 viralrecon 2
 2021-02-01 09:56:11 +00:00
Harshil Patel
2c962f34df
Merge pull request #110 from luslab/master 
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 
Bowtie2 viralrecon
 2021-01-30 13:22:30 +00:00
sruthipsuresh
7a1c2a2eb5 Fixed slop module 2021-01-29 23:17:44 -06:00
sruthipsuresh
93e414635b Fixed md5sum, fixed filters, fixed slop input 2021-01-29 23:17:44 -06:00
sruthipsuresh
78ac4435be Added new tests, todo: fix md5sums 2021-01-29 23:17:44 -06:00
Edmund Miller
2b0d51ca9c test(bedtools): Remove old style tests 
AKA how the tests were done last week.
 2021-01-29 23:17:44 -06:00
Edmund Miller
7d52907d1c test(bedtools): Fix typo on yaml indentation 2021-01-29 23:17:44 -06:00
sruthipsuresh
ac7f634675 Added complement test 2021-01-29 23:17:44 -06:00
sruthipsuresh
e360617ac6 Fixed images, genomecov 2021-01-29 23:17:44 -06:00
sruthipsuresh
e3bbbb48fc Fixed slop file 2021-01-29 23:17:44 -06:00
sruthipsuresh
29639c522f Corrected sort 2021-01-29 23:17:44 -06:00
sruthipsuresh
a108bd407e Corrected md5sum and output 2021-01-29 23:17:44 -06:00
sruthipsuresh
2f19b4279c All modules corrected, TODO config 2021-01-29 23:17:44 -06:00
sruthipsuresh
32564137fd Corrected workflows and ran editor config 2021-01-29 23:17:44 -06:00
sruthipsuresh
672f94f2af rebased and updated all bedtools testing and modules 2021-01-29 23:17:44 -06:00
Harshil Patel
b260192942
Merge pull request #149 from heuermh/minimap2 
Add minimap2 align module
 2021-02-07 16:37:26 +00:00
Michael L Heuer
6b873d7d33 Remove single_end if/else 2021-02-05 11:35:11 -06:00
Michael L Heuer
50bebac136 Remove pairwise test 2021-02-04 15:22:12 -06:00
Michael L Heuer
061b13bf25 Fix md5 --> md5sum 2021-02-04 13:48:56 -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
Harshil Patel
bd59706d51
Merge pull request #118 from heuermh/dsh-bio 
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 
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 
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 
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 
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
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 
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) 
* 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 
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 
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 
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 
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 
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
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
29937fe198
test(fastqc): Add expected files and md5sums 
The md5 sums change for the zip files every run so it's difficult to hit
a moving target.
 2020-11-16 10:20:29 -06:00
Edmund Miller
07017f401e
test(fastqc): Add initial pytest-workflow 2020-11-16 09:35:01 -06:00
drpatelh
29f1585068 Remove test functions folder 2020-08-07 14:05:55 +01:00
drpatelh
6333786d62 Add test BAM files 2020-08-07 14:04:39 +01:00
drpatelh
953256f967 Reformat paired-end fastqs 2020-08-07 13:46:23 +01:00
drpatelh
0cbefde4b0 Add index test data for BWA 2020-08-07 13:25:02 +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
FelixKrueger
9402a2efbe Still fixing linting 2020-07-16 09:06:59 +01:00
FelixKrueger
c6f73f9d56 Trying to trigger CI tests 2020-07-16 09:01:29 +01:00
JoseEspinosa
1273c31294 Adding files for bedtools testing 2020-07-15 18:13:51 +02:00
FelixKrueger
684005f2cb Fixing markdown lint 2 2020-07-15 16:00:21 +01:00
FelixKrueger
4f8b7a90aa Trying to fix markdown linting 2020-07-15 15:59:17 +01:00
FelixKrueger
02156d6b0d Removing old subsampled SRR files 2020-07-15 15:48:09 +01:00
FelixKrueger
1c84a234ec Adding back in all input files we had before 2020-07-15 15:12:04 +01:00
Gregor Sturm
f7c42ac4fd Add tests for fastqc module 2020-07-15 09:48:14 +02:00
Gregor Sturm
4ee6ddc7ab Update README 2020-07-14 10:55:38 +02:00
Phil Ewels
d3f3432451 Update test file imports 2020-07-11 14:33:12 +02:00
Phil Ewels
cffb8b63ab Move to new tests/ folder 2020-07-11 14:28:26 +02:00