437 commits

Author	SHA1	Message	Date
phue	c67e591caf	apply suggestions from review ... thanks @drpatelh	2021-02-20 12:51:01 +01:00
kevinmenden	bb5c0ceca5	adding SplitNCigarReads	2021-02-19 14:59:29 +01:00
Kevin Menden	0202162b17	Merge branch 'master' into gatk4-mergevcfs	2021-02-19 14:11:30 +01:00
kevinmenden	02abe106ec	added optional reference dictionary as input	2021-02-19 14:09:32 +01:00
kevinmenden	3ac5c5fad6	working test	2021-02-19 13:36:42 +01:00
kevinmenden	c288e081b4	initial commit adding mergevcfs	2021-02-19 13:29:08 +01:00
Kevin Menden	5c325f2942	Merge branch 'master' into master	2021-02-19 13:08:43 +01:00
kevinmenden	908e55ee5c	fixed tag	2021-02-19 12:46:59 +01:00
kevinmenden	bd8ba42a8d	added gatk4 SamToFastq	2021-02-19 12:41:29 +01:00
kevinmenden	6dcaf5ffc8	add gatk4 bedtointervallist	2021-02-19 11:26:31 +01:00
phue	a963c67481	bwameth: pass genome index as directory ... instead of single files	2021-02-18 11:51:36 +01:00
phue	0d8f5f0572	add bismark/genome_preparation + tests	2021-02-18 10:56:36 +01:00
Patrick Hüther	dba295155e	Merge pull request #219 from phue/qualimap_bamqc ... add qualimap/bamqc + test	2021-02-18 10:09:03 +01:00
Harshil Patel	5695e4ccce	Merge pull request #222 from phue/methyldackel ... add methyldackel modules	2021-02-17 22:17:26 +00:00
Harshil Patel	ecd26b388d	Merge pull request #221 from heuermh/seqwish ... Add module for seqwish/induce	2021-02-17 22:14:49 +00:00
phue	52b00d4286	add methyldackel/mbias + tests	2021-02-17 19:27:57 +01:00
phue	5ad7c6bc51	add methyldackel/extract + tests + testdata	2021-02-17 19:18:55 +01:00
phue	1a414261c4	bwameth/align: update checksums	2021-02-17 18:35:39 +01:00
phue	84a5da0d91	add bwameth/align module + tests	2021-02-17 18:23:11 +01:00
Michael L Heuer	206b605666	Add module for seqwish/induce	2021-02-17 11:19:47 -06:00
phue	180b1cf36b	add bwameth/index module + test	2021-02-17 18:03:48 +01:00
phue	b5b259a2d9	add qualimap/bamqc + test	2021-02-17 17:34:51 +01:00
FriederikeHanssen	5f9aa7264e	Add tests	2021-02-17 17:25:41 +01:00
Patrick Hüther	0cbe0a4173	Update tests/software/samtools/faidx/main.nf ... Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>	2021-02-17 17:24:50 +01:00
phue	3b1d126a0e	add samtools/faidx + tests	2021-02-17 16:46:34 +01:00
Harshil Patel	ed573db194	Merge pull request #184 from MaxUlysse/master_fix_ci ... fix: update checksum or filename	2021-02-17 10:54:38 +00:00
Harshil Patel	4d656c8f5f	Merge pull request #181 from drpatelh/fixes ... Fix tests for iVar variants	2021-02-17 10:08:57 +00:00
MaxUlysse	28fb5e8cbd	fix: update checksum or filename	2021-02-17 01:34:50 +01:00
Harshil Patel	412172cda6	Merge pull request #180 from MaxUlysse/master_tabix_bgzip ... Replace bcftools/bgzip by tabix/bgzip	2021-02-16 23:32:23 +00:00
drpatelh	c6a0976f52	Fix tests for iVar variants	2021-02-16 23:29:15 +00:00
MaxUlysse	596bb18394	fix: rename file to input and gz, plus fix tests	2021-02-17 00:28:32 +01:00
Harshil Patel	a282ecd8c7	Merge pull request #172 from andersgs/ivar-variant ... Add ivar variants	2021-02-16 23:20:30 +00:00
Harshil Patel	cf2f0762aa	Update main.nf	2021-02-16 23:06:26 +00:00
Harshil Patel	7c276d2974	Update tests/software/ivar/variants/main.nf	2021-02-16 23:01:27 +00:00
Harshil Patel	27020105aa	Update tests/software/ivar/variants/main.nf	2021-02-16 23:00:30 +00:00
Harshil Patel	de90d371dc	Update tests/software/ivar/variants/main.nf	2021-02-16 22:58:38 +00:00
Harshil Patel	23987bdad0	Update tests/software/ivar/variants/main.nf	2021-02-16 22:57:47 +00:00
Harshil Patel	b07ad23efa	Merge pull request #179 from MaxUlysse/master_htslib_tabix ... Replace bcftools/tabix by tabix/tabix	2021-02-16 22:30:45 +00:00
Harshil Patel	4f11064ae2	Update tests/software/tabix/bgzip/main.nf	2021-02-16 22:30:06 +00:00
Harshil Patel	8dd6d1d38a	Update tests/software/tabix/bgzip/main.nf	2021-02-16 22:29:13 +00:00
Harshil Patel	d6d34a4b5b	Merge pull request #177 from MaxUlysse/master_gatk_createsequencedictionary ... Add gatk/createsequencedictionary	2021-02-16 22:21:38 +00:00
MaxUlysse	6a147b8aaa	chores: replace bcftools/bgzip by tabix/bgzip cf #179	2021-02-16 19:11:36 +01:00
MaxUlysse	5a144d6213	fix: merge bcftools/tabix and htslib/tabix tests into tabix/tabix	2021-02-16 18:35:32 +01:00
MaxUlysse	f660324508	chores: move file	2021-02-16 18:20:43 +01:00
MaxUlysse	5e71dc94d6	fix: make HTSLIB_TABIX more modular	2021-02-16 17:06:55 +01:00
MaxUlysse	fa34f806d2	chores: add bgzip files for tests	2021-02-16 17:06:09 +01:00
MaxUlysse	10524e3515	chores: add modules for htslib/tabix	2021-02-16 14:47:53 +01:00
MaxUlysse	4968458b6c	chores: add cpus, memory and time requirements to limit resource consumption	2021-02-16 14:18:29 +01:00
MaxUlysse	763800a0e2	fix: correct md5sum	2021-02-16 13:54:54 +01:00
MaxUlysse	28dc9227d7	fix: remove memory requirements and simplify URI	2021-02-16 13:54:40 +01:00
MaxUlysse	053dd6ee1b	add minimal cpu,memory and time requirements	2021-02-16 13:40:22 +01:00
MaxUlysse	7f35a1742d	chores: add gatk/createsequencedictionary module	2021-02-16 13:40:06 +01:00
Anders Goncalves da Silva	eeedb959c9	Clean out comments	2021-02-15 21:04:17 -08:00
Anders Goncalves da Silva	b99972f3a0	Move params to nextflow invocation	2021-02-15 20:59:45 -08:00
Anders Goncalves da Silva	89f65e0875	Merge branch 'master' into ivar-variant	2021-02-15 20:50:35 -08:00
Anders Goncalves da Silva	c12a558f15	Add tests without mpileup	2021-02-15 20:49:27 -08:00
Anders Goncalves da Silva	3188b8e30e	Add explicit gff is false param ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:55:34 -08:00
Anders Goncalves da Silva	ee4c2828a0	Update gff assignment to string ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:55:12 -08:00
Anders Goncalves da Silva	39401ccd07	Add gff as input ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:54:36 -08:00
Anders Goncalves da Silva	8b6989f2d7	Add gff as input ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:54:19 -08:00
Harshil Patel	8eb3acc43f	Merge pull request #171 from JoseEspinosa/mosdepth ... Add mosdepth module	2021-02-15 23:13:01 +00:00
Anders Goncalves da Silva	9a5aa0f145	Fix tests to work with gff param	2021-02-15 11:51:04 -08:00
Anders Goncalves da Silva	4af7414419	Add tests for ivar variants	2021-02-15 09:29:40 -08:00
JoseEspinosa	6e92a6a080	Adding mosdepth module	2021-02-15 14:33:44 +01:00
Maxime Garcia	ec0bf0145e	Merge branch 'master' into master_bwa-mem2	2021-02-15 13:08:52 +01:00
Harshil Patel	f51f8c6400	Update tests/software/ivar/trim/main.nf	2021-02-13 08:18:32 +00:00
Harshil Patel	9d6f29fc61	Update tests/software/ivar/trim/main.nf	2021-02-13 08:17:15 +00:00
Harshil Patel	cdd9be0a2d	Update tests/software/ivar/trim/main.nf	2021-02-13 08:16:44 +00:00
Anders Goncalves da Silva	47670a12ad	Fix ivar trim test.yml	2021-02-12 16:03:18 -08:00
Anders Goncalves da Silva	ed74d366bf	Clean up ivar trim main.nf	2021-02-12 16:03:07 -08:00
Anders Goncalves da Silva	6dca7799e6	Add ivar trim	2021-02-12 16:02:10 -08:00
Harshil Patel	63a20e7b5c	Merge pull request #168 from JoseEspinosa/bcftools_merge ... Add bcftools merge module	2021-02-12 23:20:30 +00:00
JoseEspinosa	5313698705	Add bcftools merge module	2021-02-13 00:08:57 +01:00
Harshil Patel	96d3b0a18b	Update tests/software/ivar/consensus/main.nf	2021-02-12 23:02:25 +00:00
Harshil Patel	f8916060f8	Update tests/software/ivar/consensus/main.nf	2021-02-12 23:02:19 +00:00
Anders Goncalves da Silva	ffc849761d	Edit test to output mpileup and passing args to samtools	2021-02-12 14:43:19 -08:00
Anders Goncalves da Silva	487ec7b793	Fix test.yml	2021-02-12 14:42:42 -08:00
Anders Goncalves da Silva	24b212318b	Merge branch 'master' into ivar-consensus	2021-02-12 11:51:24 -08:00
Anders Goncalves da Silva	8b3c16a518	Add ref FASTA to test main.nf	2021-02-12 11:29:16 -08:00
Anders Goncalves da Silva	0a6e8400ac	Add reference SC2 genome to test data	2021-02-12 11:27:12 -08:00
JoseEspinosa	fafe068192	Fixing test tags	2021-02-12 18:49:57 +01:00
JoseEspinosa	0688230863	Revert since fixes to test were not working ... This reverts commit d7a219e88d.	2021-02-12 18:02:32 +01:00
JoseEspinosa	8e23e1839d	Trying to fix tests	2021-02-12 17:56:51 +01:00
JoseEspinosa	d7a219e88d	Fix test.yml	2021-02-12 17:37:49 +01:00
JoseEspinosa	6e8b63fc26	Add cat fastq module	2021-02-12 17:22:07 +01:00
MaxUlysse	9c98194d3c	chores: remove fasta file from bwamem2 mem process	2021-02-12 16:00:59 +01:00
MaxUlysse	0afddf6ca4	fix: CI is working	2021-02-12 15:24:09 +01:00
Maxime Garcia	27be87ac72	Merge pull request #135 from drpatelh/bwa ... Update indices syntax for BWA index and mem modules	2021-02-12 12:45:38 +01:00
Anders Goncalves da Silva	df9125b46a	Fix test name ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 12:05:01 -08:00
Anders Goncalves da Silva	40bbf94ef9	Update filename for outputted mpileup file in test ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 12:04:46 -08:00
Anders Goncalves da Silva	68de6fef0d	Fix indentation ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 12:04:15 -08:00
Anders Goncalves da Silva	ffa9cf85b1	Clean up header params ... I used these for testing and forgot to remove them Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 12:03:50 -08:00
Anders Goncalves da Silva	1f6419f8f5	Fix indentation ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 10:55:24 -08:00
drpatelh	1d00a4a11c	Update md5sum	2021-02-09 23:31:39 +00:00
drpatelh	79d730f2c3	Change output name	2021-02-09 23:27:08 +00:00
drpatelh	7f629bca45	OCDness	2021-02-09 23:26:55 +00:00
Harshil Patel	28866f3dc7	Update tests/software/bedtools/maskfasta/main.nf	2021-02-09 21:36:38 +00:00
Harshil Patel	aaa088dba8	Update tests/software/bedtools/getfasta/main.nf	2021-02-09 21:34:29 +00:00
Anders Goncalves da Silva	8f546a1f95	Add ivar consensus	2021-02-09 10:26:35 -08:00
JoseEspinosa	68b85d9191	Merge remote-tracking branch 'upstream/master' into bedtools_getfasta	2021-02-09 18:23:24 +01:00
JoseEspinosa	e118bc049a	Add bedtools getfasta module	2021-02-09 17:56:51 +01:00
JoseEspinosa	7536b386a5	Correct channel declaration on bedtools_maskfasta	2021-02-09 17:56:01 +01:00
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