197 commits

Author	SHA1	Message	Date
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	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
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