Kevin Menden
0218824b86
add task.cpus to pangolin ( #263 )
...
* add task.cpus to pangolin
* bumped pangolin to v2.3.2
2021-03-10 09:02:23 +01:00
Kevin Menden
a552d97849
Exchange VCF data by sarscov2 data ( #261 )
...
* added sarscov2 vcf data; adjusted bcftools tests
* updated README.md
* deleted old VCF files; fixed mergevcfs
* fixed tabix
2021-03-09 10:04:08 +01:00
Maxime Garcia
05cbbbaded
Rename gatk/createsequencedictionary -> gatk4/createsequencedictionary ( #260 )
...
* fix: update and sort filters
* fix: rename gatk/createsequencedictionary -> gatk4/createsequencedictionary
2021-03-08 14:45:46 +01:00
Kevin Menden
4566525da2
Converge test data usage ( #249 )
...
* initial data restructuing
* fixed bedtools_complement
* fixed bedtools_genomecov
* fixed bedtools_getfasta
* fixed bedtools_intersect
* fixed bedtools maskfasta
* fixed bedtools_merge
* fixed bedtools_slop
* fixed bedtools_sort
* fixed bismark_genome_preparation
* fixed blast
* fixed bowtie data
* fixed bowtie2 data
* fixed bwa data
* fixed bwamem2 data usage
* fixed cat_fastq data
* fixed cutadapt data
* fixed dsh data
* fixed fastp data
* fixed fastqc; fixed bug with wrong fastq format
* fixed gatk
* fixed data for gffread, gunzip
* fixed ivar paths
* fixed data paths for minimap2
* fixed mosdepth
* fixed multiqc, pangolin
* fixed picard data paths
* fixed data paths for qualimap, quast
* fixed salmon data paths
* fixed samtools paths
* fixed seqwish, stringtie paths
* fixed tabix, trimgalore paths
* cleaned up data
* added first description to README
* changed test data naming again; everything up to bwa fixed
* everything up to gatk4
* fixed everything up to ivar
* fixed everything up to picard
* everything up to quast
* everything fixed up to stringtie
* switched everyting to 'test' naming scheme
* fixed samtools and ivar tests
* cleaned up README a bit
* add (simulated) methylation test data
based on SARS-CoV-2 genome; simulated with Sherman --non_dir --genome sarscov2/fasta/ --paired -n 10000 -l 100 --CG 20 --CH 90
* bwameth/align: update data paths and checksums
also, build index on the go
* bwameth/index: update data paths and checksums
* methyldackel/extract: update data paths and checksums
* methyldackel/mbias: update data paths and checksums
* bismark/deduplicate: update data paths and checksums
* remove obsolete testdata
* remove empty 'dummy_file.txt'
* update data/README.md
* methyldackel: fix test
* Revert "methyldackel: fix test"
This reverts commit f175a32d144b1b0bfa0c6885da80c51e3cfe038a.
* methyldackel: fix test
for real
* move test.genome.sizes
* changed test names
* switched genomic to genome and transcriptome
* fix bedtools, blast
* fix gtf, tabix, .paf
* fix bowtie,bwa,bwameth
* fixed: bwa, bwamem, gatk, gffread, quast
* fixed bismark and blast
* fixed remaining tests
* delete bam file
Co-authored-by: phue <patrick.huether@gmail.com>
2021-03-04 10:10:57 +00:00
JoseEspinosa
155c2a1185
Check only for vcf file to exists (includes cmd)
2021-02-26 07:14:29 +01:00
Maxime Garcia
ea6fde0193
Merge pull request #252 from MaxUlysse/master_tiddit
...
New module: tiddit
2021-02-25 09:34:33 +01:00
MaxUlysse
f62196a4a6
feat: add tiddit_sv module
2021-02-24 15:59:10 +01:00
Harshil Patel
50b98d56a1
Merge pull request #246 from drpatelh/master
...
Update iVar modules
2021-02-24 13:00:05 +00:00
FriederikeHanssen
4673c119c7
resolve merge conflicts
2021-02-24 10:03:16 +01:00
FriederikeHanssen
7627e656ee
Add all tests back in
2021-02-24 09:57:23 +01:00
FriederikeHanssen
8a7333c13b
lower case path
2021-02-24 09:53:11 +01:00
FriederikeHanssen
7f6e5d9ab5
try to make a single test pass on GHA, passes locally
2021-02-24 09:48:55 +01:00
Jose Espinosa-Carrasco
8f4363ccb5
Merge pull request #247 from JoseEspinosa/bcftools-mpileup
...
Add bcftools mpileup module
2021-02-24 09:24:43 +01:00
Harshil Patel
5287fe5f95
Merge pull request #245 from phue/bismark_deduplicate
...
add bismark/deduplicate + tests
2021-02-23 21:08:24 +00:00
Harshil Patel
4703a60443
Merge pull request #220 from phue/bwameth
...
add bwameth modules
2021-02-23 21:01:54 +00:00
drpatelh
b581bdc36c
Update test script
2021-02-23 20:43:05 +00:00
drpatelh
aaaef7df8c
Add BAM index
2021-02-23 20:42:16 +00:00
JoseEspinosa
e9d90007c5
Adding arguments to make md5 hashes stable
2021-02-23 19:39:24 +01:00
JoseEspinosa
4b3c86ed9f
Add tests for bcftools-mpileup
2021-02-23 19:05:57 +01:00
phue
e73bda26f5
add bismark/deduplicate + tests
2021-02-23 18:02:16 +01:00
FriederikeHanssen
e67515809a
try to only make paired-end test work, pass locally with conda & docker
2021-02-23 15:47:16 +01:00
FriederikeHanssen
13733b2581
Add beautiful md5sums
2021-02-23 14:57:07 +01:00
FriederikeHanssen
5e365d5eff
Make all these tests pass
2021-02-23 14:09:46 +01:00
FriederikeHanssen
25a2a16f2d
Try to make a single test pass
2021-02-23 13:34:50 +01:00
FriederikeHanssen
312bf85f70
use reasonable option params
2021-02-23 11:26:54 +01:00
FriederikeHanssen
9c51e05125
remove wrong md5 sums
2021-02-23 11:25:45 +01:00
FriederikeHanssen
c7d2bc8d43
Add tests for different options
2021-02-23 11:14:51 +01:00
FriederikeHanssen
ec63f335d5
Add split2 options
2021-02-22 22:43:32 +01:00
kevinmenden
3fee38ee2d
added gatk4 revertsam
2021-02-22 15:21:39 +01:00
kevinmenden
efd60d94ee
adding revertsam/ fix typo in mergevcfs
2021-02-22 15:10:20 +01:00
kevinmenden
69d7bb4fca
reformatted input to tuple
2021-02-22 13:31:54 +01:00
kevinmenden
43446bc37e
added sarscov2 fastq and bam files
2021-02-22 13:19:12 +01:00
phue
2d8baa8b75
bwameth/index: update test.yml
2021-02-20 12:55:09 +01:00
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
