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Author	SHA1	Message	Date
Edmund Miller	937344236c	chore(codeowners): Add @drpatelh as owner of lib	2020-12-10 12:15:56 -06:00
Edmund Miller	5ff08c3bdc	chore(codeowners): Add module owners ... This will default to any place in the modules that has that folder name. So it will pick up the module and the tests.	2020-12-10 12:14:07 -06:00
Edmund Miller	371abd5c95	chore: Add CODEOWNERS test ... I'm not sure if the syntax is proper.	2020-12-09 10:16:24 -06:00
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
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
Harshil Patel	cd2cf9cf2f	Merge pull request #85 from nf-core/pytest-workflow-refactor ... Refactor all tests to use pytest-workflow	2020-12-04 14:30:00 +00:00
Edmund Miller	6d8ba714d5	ci(fastqc): Use 20.10.0 => ''	2020-12-04 08:23:19 -06:00
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	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	65697532a1	ci: Get rid of software folder	2020-12-01 11:40:16 -06:00
Edmund Miller	6404c3390d	ci(fastqc): Remove md5sums ... These may not work across nextflow versions	2020-12-01 11:18:55 -06:00
Edmund Miller	8cd635f757	ci(fastqc): Fix test matrix	2020-12-01 11:13:43 -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
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) ... * 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
Edmund Miller	98c629583a	ci: Test whether subdirectories are breaking workflows	2020-11-30 19:03:56 -06:00
Edmund Miller	7d2b74a5f7	ci(fastqc): Use a test matrix for NXF versions	2020-11-30 18:57:56 -06:00
Harshil Patel	e02f0de514	Merge pull request #87 from drpatelh/rsem_index ... Use STAR to build initial index for RSEM	2020-11-30 14:45:32 +00:00
drpatelh	e5c7ecc89c	Use STAR to build initial index for RSEM	2020-11-30 11:29:24 +00:00
Edmund Miller	036427d73c	ci(pytest-workflow): Fix trigger paths	2020-11-24 21:24:55 -06:00
Edmund Miller	6eeb930bdb	chore: Remove test directory from dummy tool	2020-11-24 21:09:55 -06:00
Edmund Miller	86219a586b	ci(trimgalore): Use pytest-workflow	2020-11-24 21:08:34 -06:00
Edmund Miller	2fc39e02e2	test(trimgalore): Refactor se and pe to use pytest-workflow	2020-11-24 21:08:34 -06:00
Edmund Miller	445498d0c3	ci(samtools): Run tests with 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	ebf3a4529f	ci(picard): Update markduplicates	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	dfc8528df9	ci: Remove docker workflow ... This only applies to deprecated software	2020-11-24 18:58:02 -06:00
Edmund Miller	691df9d469	style(actions): Create seperate software dir ... For future subworkflows	2020-11-24 18:57:53 -06:00
Harshil Patel	794a5cbd0c	Merge pull request #80 from nf-core/pytest-workflow ... Pytest-workflow	2020-11-24 22:55:07 +00:00
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