1303 commits

Author	SHA1	Message	Date
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