168 commits

Author	SHA1	Message	Date
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
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	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