125 commits

Author	SHA1	Message	Date
drpatelh	f079ce9d1f	Fix preseq tests	2021-02-03 17:28:44 +00:00
drpatelh	f37fb66f40	Fix bwa mem tests	2021-02-03 17:26:43 +00:00
drpatelh	8a15852756	Fix salmon index tests	2021-02-03 17:13:47 +00:00
drpatelh	058d7b397c	Fix fastqc test	2021-02-03 17:03:30 +00:00
drpatelh	39b8600dbb	Fix trimgalore test	2021-02-03 17:02:52 +00:00
drpatelh	305d47fc87	Change path to tests	2021-02-03 16:44:56 +00:00
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	688cc05fe8	tests: Remove -profile in tests ... See ddbca7b467 for more info	2021-02-02 15:30:59 -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	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
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