335 commits

Author	SHA1	Message	Date
JoseEspinosa	12ae7b0bff	Adding blast blastn module	2021-02-09 16:58:36 +01:00
JoseEspinosa	c23b355b35	Add blast makeblastdb module	2021-02-09 15:44:34 +01:00
JoseEspinosa	c93e96101a	Add untar module	2021-02-09 11:50:32 +01:00
JoseEspinosa	9b65961828	Fix file output path on test	2021-02-09 10:22:50 +01:00
JoseEspinosa	f7f06dd6e8	Add gunzip module	2021-02-09 10:05:55 +01:00
Harshil Patel	46e5df2cf7	Merge pull request #151 from drpatelh/bedtools ... Follow up fixes for bedtools modules added in #79	2021-02-09 01:54:31 +00:00
Harshil Patel	84cf5ea2ef	Merge pull request #153 from JoseEspinosa/bedtools_maskfasta ... Add bedtools maskfasta module	2021-02-08 23:11:00 +00:00
Harshil Patel	132dabbbb6	Update tests/data/bed/C.bed	2021-02-08 23:03:26 +00:00
JoseEspinosa	1b3e5e0283	Fixing module name in test.yml	2021-02-08 23:45:01 +01:00
JoseEspinosa	02d10c25a3	Add bedtools maskfasta module	2021-02-08 23:41:10 +01:00
drpatelh	0b9e32e32d	Remove complement suffix from tests	2021-02-08 22:25:13 +00:00
Harshil Patel	0f6830f7cc	Update tests/software/bcftools/consensus/main.nf	2021-02-08 21:41:24 +00:00
JoseEspinosa	f8882de456	Renaming test ymls just to: software tool	2021-02-08 21:56:53 +01:00
JoseEspinosa	f4e322f88d	Merging upstream changes ... # Conflicts: # .github/filters.yml	2021-02-08 18:09:41 +01:00
JoseEspinosa	4fa38ebb7a	Separate test data to break dependencies between bcftools modules tests	2021-02-08 16:51:21 +01:00
JoseEspinosa	83cc25860d	Rearranging tests to test each module separately	2021-02-08 15:16:51 +01:00
JoseEspinosa	5071bf5914	Merge remote-tracking branch 'upstream/master' into bcftools_viralrecon	2021-02-08 10:45:57 +01:00
drpatelh	83a50d8ae0	Rename SOFTWARE_TOOL to TOOL_SUBTOOL	2021-02-07 23:20:53 +00:00
drpatelh	5779b180da	Fix bedtools sort module	2021-02-07 21:32:43 +00:00
drpatelh	f3b5af4ed5	Fix bedtools slip module	2021-02-07 21:32:20 +00:00
drpatelh	38964ecfc0	Fix bedtools intersect module	2021-02-07 21:32:01 +00:00
drpatelh	a37b116186	Fix bedtools merge module	2021-02-07 21:31:39 +00:00
drpatelh	4564ef0e54	Fix bedtools genomecov module	2021-02-07 21:31:21 +00:00
drpatelh	a0c08e0c06	Fix bedtools complement module	2021-02-07 21:31:02 +00:00
Harshil Patel	0393d39105	Update tests/software/bedtools/complement/main.nf	2021-02-07 20:35:51 +00:00
Harshil Patel	5269c1ec60	Update tests/software/bedtools/intersect/main.nf	2021-02-07 20:35:12 +00:00
Harshil Patel	8841af1267	Update tests/software/bedtools/merge/main.nf	2021-02-07 20:34:30 +00:00
Harshil Patel	b068f2fc53	Update tests/software/bedtools/sort/main.nf	2021-02-07 20:33:02 +00:00
drpatelh	137d00b523	Fix tests	2021-02-05 10:44:08 +00:00
drpatelh	81ae0089bc	Fix merge conflicts	2021-02-05 10:06:39 +00:00
Kevin Menden	17dd0415f2	Merge pull request #146 from heuermh/bandage ... Add bandage image module	2021-02-05 08:00:44 +01:00
Michael L Heuer	37a9f6f456	Address review comments	2021-02-04 12:10:54 -06:00
Harshil Patel	5aa920eb53	Update tests/software/bowtie/align/test.yml	2021-02-04 10:19:28 +00:00
Harshil Patel	68f9a0b711	Update tests/software/bowtie/build/test.yml	2021-02-04 10:08:01 +00:00
Harshil Patel	eb45368a35	Update tests/software/bowtie2/build/test.yml	2021-02-04 10:07:44 +00:00
Edmund Miller	431c699727	Revert "ci: Test bowtie-build instead of _" ... This reverts commit 9b454416d2.	2021-02-03 20:06:05 -06:00
drpatelh	fe3cb87f6d	Direct download Singularity containers	2021-02-03 20:03:45 -06:00
Michael L Heuer	c466255f6f	Add bandage image module	2021-02-03 19:31:58 -06:00
Edmund Miller	9b454416d2	ci: Test bowtie-build instead of _	2021-02-03 13:17:14 -06:00
Edmund Miller	7dbac4bdef	ci: Test adding another work to test name	2021-02-03 13:17:14 -06:00
Edmund Miller	b058da5856	ci: Test buil to see if build is special	2021-02-03 12:43:18 -06:00
Edmund Miller	4d58a037f6	test(bowtie_align): Fix md5sum	2021-02-03 12:37:19 -06:00
Edmund Miller	6901c7e830	ci: Fix bowtie_build names with ""	2021-02-03 12:37:14 -06:00
drpatelh	e71b3eaaa5	Rename workflows	2021-02-03 17:48:17 +00:00
drpatelh	ff6f0642d2	Fix multiqc tests	2021-02-03 17:43:14 +00:00
drpatelh	0683efc679	Fix salmon quant tests	2021-02-03 17:36:06 +00:00
drpatelh	550494cbd1	Fix picard mergesamfiles test	2021-02-03 17:31:41 +00:00
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	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