Batool
f90b8ecb24
Fix the test path salmon/index and quant after switching to config data ( #385 )
...
* fix the test path in main.nf for salmon/index and quant
* fix typo
* Apply suggestions from code review
* Apply suggestions from code review
* Apply suggestions from code review
Mannnn, hopefully I finally got it right :)
* replaced /salmon/salmon/ with /index/salmon/
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-25 17:03:25 +00:00
FriederikeHanssen
555f1710e0
Update test paths in bwa mappers ( #387 )
...
* Update test paths in bwa mappers
* Fix indentation
* indices pass lcoally now
* no idea how they could ever pass before, Tests pass locally no
* Update samtools and bwamem2 versions
* Correct mulled containers + md5
2021-03-25 09:24:21 +00:00
Kevin Menden
6973df628f
Fixing vcftools and bismark tests ( #383 )
...
* fixed vcftools
* fixed genomepreparation, methylationextractor
* fixed deduplicate
2021-03-25 09:12:08 +00:00
Jose Espinosa-Carrasco
13bd67ed8a
Fix some module test after adapting test config approach ( #379 )
...
* Fix paths for bowtie2/build_test
* Fix paths for bowtie2/align
* Fix paths for bwameth/index
* Fix paths for bwameth/align
* Fix paths for multiqc tests
2021-03-24 18:29:41 +00:00
Gregor Sturm
2dba72dd14
Fix a bunch of failing tests after switching to test config ( #378 )
...
* Update test for trimgalore
* Fix picard markduplicate test
* Fix tests for picard mergesamfiles
* Fix checksum for markduplicates
* Fix multiplemetrics and wgsmetrics
* Fix checksum for mergesamfiles
2021-03-24 18:28:54 +00:00
Jose Espinosa-Carrasco
17fbdf96cb
Fix some module tests after switching to config data ( #386 )
...
* Adding tar.gz kraken2 db to test data
* Update test path files for untar module
* Update test path files for kraken2/run module
* Update test path files for cat/fastq module
2021-03-24 18:28:07 +00:00
pericsson
1e4fa57139
Update restructured paths ( #380 )
...
* dsh filterbed path updated
* dsh splitbed path updated
* adapterremoval path updated
2021-03-24 18:26:54 +00:00
Anthony Fullam
c5a5e25129
Update test data paths. ( #375 )
...
* Updata test data paths.
* Remove quote
* Revert quast
* Fix broken test
* Update md5
2021-03-24 18:18:01 +00:00
arontommi
d162f21ab3
Update samtools modules with config logic ( #381 )
...
* fixing paths for test
* fixing paths for test
* fixing pats to tests
* fixing paths to tests
* fixing paths to tests
* fixing paths for tests
* fixing paths for tests
* fixing paths for tests
* fixing paths fro tests
* fixing paths for tests
* indentation fixes
* typo
* renaming test results according to new file name
* replacing the md5sums
* fixing brackets
* replacing md5sums
* fixing md5sums
* fixing md5sums'
* Update test.yml
* Update test.yml
* Update test.yml
* Update test.yml
* Update test.yml
* Update test.yml
* Update test.yml
* Update test.yml
Co-authored-by: Ramon Rivera <ramon.rivera10@upr.edu>
Co-authored-by: Ramon Rivera <riveravicens@gmail.com>
2021-03-24 18:15:30 +00:00
Mark-S-Hill
889465cb2b
update test data paths ( #373 )
...
* update test data paths
* Update test md5sums
* gatk test fixes & update variantfiltration main
* few extra fixes after review
* fix suspected format error
* Update software/gatk4/variantfiltration/main.nf
* Update software/gatk4/variantfiltration/main.nf
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 18:14:11 +00:00
Kevin Menden
04c3684db7
Fixing a bunch of module tests ( #370 )
...
* initial 'modules create' of minia
* fixed tests
* finished meta.yml
* fixed filters.yml
* resolved issues in pytest_software.yml
* add newline
* Update software/minia/main.nf
* fixing a bunch of module tests
* remove vscode
* fixed minia
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 17:36:29 +00:00
Alexander Peltzer
0337916f8a
Add YARA module ( #353 )
...
* Initial work on yara module
* Adding in index basics
* Updated the index stuff
* Adding in proper tests
* Fix editorconfig
* Odd paths
* that should do it
* Fix tests
* Fix tests
* FFS
* Once more
* Mapping is not deterministic
2021-03-24 17:14:52 +01:00
Maxime Borry
cfc94b96dd
modify fastp tests ( #367 )
...
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-03-24 17:08:59 +01:00
FriederikeHanssen
86df111707
Seqkit/split2 test path update ( #372 )
...
* Update test path
* Fix bracket
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 17:05:43 +01:00
Harshil Patel
c7155d023e
Update bedtools modules with config logic ( #369 )
2021-03-24 14:14:19 +00:00
Harshil Patel
83a500e6b0
Use a config containing all test data for module tests ( #365 )
...
* Re-organise all test data
* Fix ECLint
* Fix ECLint agaaainn
* Now is not the time EClint
* Initial commit for test data config
* Rename test data
* Include test config
* Update indents
* Update test for FastQC via config
* Remove quotes of bottom-level variables
* Use underscores in key names
* Get tests working for fastp
* Remove whitespace at beginning of file
2021-03-24 13:07:37 +00:00
Gisela Gabernet
22eaefe583
Add module kallisto/index ( #357 )
...
* add kallisto index module
* update kallisto module
* add kallisto module tests
* update kallisto index test.yml
* update test data paths
* fix version
* fix kallisto index test yml
* remove TODOs
* Update software/kallisto/index/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/kallisto/index/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* output folder instead
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 12:25:39 +00:00
Harshil Patel
acb1a12a56
Re-organise all test data ( #354 )
...
* Re-organise all test data
* Fix ECLint
* Fix ECLint agaaainn
* Now is not the time EClint
2021-03-24 09:53:41 +00:00
Yuk Kei Wan
323856a9da
add nanopore 100-read test subset (fast5, fastq, and bam/bai) ( #344 )
2021-03-24 05:13:34 +00:00
arontommi
86bb832fae
Strelka germline ( #340 )
...
* nf-core template created
* boilerplate and sarek_dsl2 code merged
* adding an option to give it args
* bai got away
* seperating vcf files and vcf index files into seperate streams
* some minor spacefixes
* adding standard information about the module
* removing typos
* some basic tests based on tiddit tests
* removed the bed parameter, should be provided via options.args instead
* removing typos
* adding indexed bam file instead
* Adding changing out fasta with reference to deal with empty fasta input
* adding the correct fasta
* removing the empty test
* adding the correct data to the testoutput and removing the md5sum since
it constantly changes
* adding target_bed to input
* adding info on target bed
* adding target bed to test
* adding more files to the test
* adding meta for target bed test
* adding a test for target_bed
* typo
* fixing pytest with master
2021-03-24 05:07:29 +00:00
Erkison Ewomazino Odih
67b3e00f58
add flash module ( #341 )
...
* add flash module
* remove todo
* run tests
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 05:05:45 +00:00
Ravneet Bhuller
a70abc236b
PR for sequenzautils/gcwiggle ( #345 )
...
* added files
* edited files
* edited files
* edited file
* test(sequenzautils): Remove md5sum
Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
2021-03-24 05:03:03 +00:00
Robert A. Petit III
3f14b1fabe
Update shovill module ( #337 )
...
* add shovill module
* removed deprecated shovill module
* fix line ending in functions.nf
* fix yaml indentation
* reduce spades memory usage
* update md5sums
* remove non reproducible md5sum
* Update test.yml
Remove last non-reproducible md5sum.
* purely cosmetic order change
* proper process label, improve output readability
Co-authored-by: Florian Wuennemann <flowuenne@gmail.com>
2021-03-24 04:57:41 +00:00
Yuk Kei Wan
af3bc225c0
ucsc_bed12tobigbed (previous pull request had conflicts) ( #302 )
...
* Add files via upload
* Add files via upload
* Add files via upload
* Add files via upload
* Update pytest_software.yml
* Update main.nf
* fix linting error
* Delete test.yml
* Create functions.nf
* Update main.nf
* change test data
* revert to !>=20.11.0-edge
2021-03-24 04:55:49 +00:00
Mark-S-Hill
399b58043d
add vcftools module ( #334 )
...
* add vcftools module
* fix padding issue
* fix linting errors
2021-03-24 04:54:23 +00:00
Kevin Menden
fe8a783cef
Homer ( #330 )
...
* started with homer
* added tests for homer annotatepeaks
* fix md5
* remove md5 sum
2021-03-23 11:24:54 -07:00
Gregor Sturm
e33860a2e8
Prodigal ( #333 )
...
* WIP add prodigal
* Implement module and add tests
* Fix EC lint
2021-03-23 11:03:58 -07:00
Jose Espinosa-Carrasco
ee90e7af77
Add default output dir for modules that create indices, updated ( #336 )
...
* Add default output dir for modules that create indices
* Change path for index module test output
* Fix bowtie2/align tests
* Fixing bowtie/align tests
* Fix genomegenerate test
* Fixing README linting
2021-03-23 17:55:01 +00:00
suzannejin
d6850f8312
modified the samtools/fastq module ( #339 )
...
* new module: samtools/fastq
* solve conflict: pytest_software.yml
* solve linting conflicts
* solved EditorConfig linting problem
* Module samtools/fastq:
* output compressed fastq.gz file(s)
* add if conditionals for single/paired reads
* samtools/fastq: modified test.yml
* samtools/fastq: modified main.nf to avoid duplicated part of the script section
Co-authored-by: suzannejin <suzanne.jin@crg.eu>
2021-03-23 17:43:52 +00:00
yocra3
5e3c9dfbf0
Add gatk4/baserecalibrator ( #327 )
...
* Add gatk4 BaseRecalibrator
* Solve format in main.nf
* Correct functions
* Add pytest
2021-03-23 18:32:37 +01:00
Alexander Peltzer
d13e22dcbe
Add in OptiType (configbuilder, type) module(s) ( #301 )
...
* Adding in optitype prototype (To be worked on these days)
* I've tried my best 😆
* No idea
* Add in YML stuff
* Fix paths
* Ok, lets try this
* Adding proper options
* Replacec configbuilder thing
* Fix seq_type
* Adding human bam - sarscov doesnt work
* Fix a bunch of things
* -def
* Make this test run
* Fancy as fuck
* Update tests/software/optitype/test.yml
* Add proper tag
* Remove md5sums
Co-authored-by: Kevin Menden <kevin.menden@t-online.de>
2021-03-23 16:48:05 +01:00
Anthony Fullam
3d720a24fd
Add alleleCounter module ( #313 )
...
* Add allelecount module
* Add bed file input
* Added bai file
* Changed conda version
* Update main.nf
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Add allelecount module
* Add bed file input
* Added bai file
* Changed conda version
* Update main.nf
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Remove newline
* Fix pytest_software.yml
* Update pytest_software.yml
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-03-23 14:37:53 +01:00
yocra3
614d61dc13
Add gatk4/applybqsr ( #331 )
...
* Add applybqsr module
* Solve problem in functions.nf
* Add to pytest
2021-03-23 14:15:26 +01:00
suzannejin
9115c12f88
new module: samtools/fastq ( #316 )
...
* new module: samtools/fastq
* solve conflict: pytest_software.yml
* solve linting conflicts
* solved EditorConfig linting problem
2021-03-23 12:13:07 +01:00
yocra3
569ff03af9
Add readgroup to bam files ( #324 )
...
* Add readgroup to bam files
Add recalibration table
* Solve README.md issue
2021-03-23 11:59:49 +01:00
Robert A. Petit III
c2aa95cb6c
add prokka module ( #298 )
...
* add prokka module
* adjust test outputs
* fix prokka command
* adjust test outputs
* handle optional input
* update pytest
* update pytest
* adjust test outputs
* adjust test outputs
* switch to lists for optional inputs, add md5sums for non-timestamped outputs
* add optional prodigal training file
* add optional prodigal training info to meta yaml
2021-03-23 02:51:23 -07:00
Ravneet Bhuller
8a2a9f7e81
cnvkit module ( #173 )
...
* Normal bam file added
* Normal bam.bai file added
* Tumour bam bai files added
* human dir added
* annotation dir added
* cnvkit dir added
* cnvkit dir added
* Update software/cnvkit/main.nf
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
* Update software/cnvkit/main.nf
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
* Update software/cnvkit/main.nf
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
* changed input filenames
* edited main.nf
* edited main.nf
* edited meta.nf
* edited test.yml
* filters.yml
* edited main
* edited main
* edited meta
* edited meta
* edited main
* removed unwanted lines
* edited the path to the main.nf
* removed function.nf
* added functions.nf
* deleted 2 workflows and craeted a common workflow
* deleted paths for 2 workflows and created paths for a common workflow
* Deleted annotation dir
* deleted params.modules
* Edited meta.with_normal
* deleted normal_280_sub_chr21.bam
* deleted normal_280_sub_chr21.bam.bai
* deleted tumour_278_sub_chr21.bam
* deleted tumour_278_sub_chr21.bam.bai
* Edited input and script parts
* Edited input part
* Added
* Edited args
* Edited script
* Edited input
* Changed annotation to annotationfile
* Changed description of the tool
* edited singularuty container
* edited input
* line 44 removed trailing whitespace
* Edited addParams
* Deleted pdf output
* Deleted pdf output
* edited the path to main.nf
* edited path to the main.nf
* Added docker image version
* Removed extra ../
* added md5sums
* added md5sums
* Update software/cnvkit/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/cnvkit/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Edited the script
* Edited the input
* Edited main.nf
* Edited main.nf
* edited md5sum for reference.cnn
* removed human fasta
* removed human fasta.fai
* added GRCh38 fasta
* added GRCh38 fasta.fai
* added hg19 fasta.fai
* added hg19 fasta
* Edited fasta file name
* Edited bed file names and md5sums
* Edited md5sums
* edited the input and script section
* edited input section
* added targetfile
* changed the files
* changed the output files
* added bam files
* added bam files
* remove files
* added md5sums
* replace file
* added files
* edited tests/software/cnvkit files
* edited tests/software/cnvkit files
* edited authors list
* removed files
* added files
* added files
* added files
* added files
* added file
* added file
* added file
* added file
* edited files
* edited files
* edited files
* edited files
* edited files
* edited files
* added new module
* added new module
* edited files
* edited file
* edited file
* edited file
* removed files
Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 15:27:30 -07:00
Nicholas Toda
53109d53c0
add gatk4/fastqtosam #198 ( #311 )
...
* Inital nf-core create
* remove TODO comments, input and output files defined
* add get version in script
* added flow control for single/paired end data
* added script main commands
* removed completed TODO messages
* removed completed TODO messages
* added software info
* added input reads description
* added output description
* added description and keywords
* added single end test
* added paired end test
* fixed sample name flag
* fixed reverse read variable
* added test yaml
* update for pytest_software
* order in pytest_software was different
* replaced functions.nf with copy from another module
* simplify read command line
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 18:26:02 +00:00
Maxime Garcia
0a4fa5050a
Update main.nf ( #314 )
2021-03-22 17:16:43 +00:00
Maxime Borry
aa76c6d870
new module: AdapterRemoval ( #309 )
...
* add adapterremoval module
* fix indentations
* switch to process_medium
* update docker tests
* remove duplicated entry
* fix line ending
* Update software/adapterremoval/main.nf
* Update software/adapterremoval/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 17:16:04 +00:00
Jose Espinosa-Carrasco
cfa8f64c4f
Adding unicycler module ( #307 )
...
* Adding unicycler module
* Do not forget to change default keywords on meta.yml
2021-03-22 18:14:24 +01:00
Patrick Hüther
7fe6f9fab2
bismark: remove underscores from process names ( #303 )
...
* sanitize process names
no underscores allowed
* remove underscores from process names
2021-03-22 17:46:11 +01:00
Florian Wuennemann
592002aa23
add picard_collectwgsmetrics ( #304 )
...
* Added new module picard/collectwgsmetrics.
* Removed unused outputs from meta.yml
* Added version.txt file back to meta.yml
* Updated test.yml
* Removed md5sum from test.yaml and added contain tests.
* Update functions.nf
Fixed missing newline formatting.
* Update main.nf
Fixed missing newline formatting.
* style(picard): Remove trailing whitespace
Co-authored-by: Kevin Menden <kevin.menden@t-online.de>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
2021-03-22 17:05:59 +01:00
Patrick Hüther
eb9178970f
add bismark/summary ( #295 )
...
* add bismark/align module
* bismark/align: add tests
* bismark/align: update meta.yml
* bismark/align: skip checksum for alignment logs
they contain timestamps
* bismark/align: restore correct checksum
caused some mixup in the last commit
* bismark/align: add genome_preparation to filters
* Fix conda version pin
* change options to be a global var
* remove params from meta.yml
* add bismark/summary
* remove md5sum check for bismark_summary_report.html
it contains a timestamp
* fix tests
* update meta.yml
* remove mysterious index files
2021-03-22 14:58:54 +01:00
Yuk Kei Wan
134c8ef6ce
add samtools merge ( #296 )
...
* add samtools merge
* Update pytest_software.yml
* get it back to 20.11.0-edge
* Update test.yml
* Update test.yml
* Update test.yml
* Update test.yml
2021-03-22 13:48:23 +01:00
Patrick Hüther
f9ce8664ba
add bismark/report ( #297 )
...
* add bismark/align module
* bismark/align: add tests
* bismark/align: update meta.yml
* bismark/align: skip checksum for alignment logs
they contain timestamps
* bismark/align: restore correct checksum
caused some mixup in the last commit
* bismark/align: add genome_preparation to filters
* Fix conda version pin
* change options to be a global var
* remove params from meta.yml
* add bismark/report
* fix test filepaths
* remove mysterious index files
2021-03-22 13:38:08 +01:00
Patrick Hüther
04704c2034
add bismark/methylation_extractor ( #274 )
...
* add bismark/methylation_extractor
* add tests for bismark/methylation_extractor
* bismark/methylation_extractor: add genome_preparation to filters
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* remove params from meta.yml
* pytest: remove md5sum checks for gzipped output
gzip stores timestamps in the file header, so the checksum will be different each time
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-20 23:54:42 +00:00
Jose Espinosa-Carrasco
72e81d6e90
Add spades module ( #277 )
...
* Add spades module
* Reorder gatk4 modules alphabetically
* Update software/spades/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-18 13:48:38 +00:00
Jose Espinosa-Carrasco
313241749c
Add kraken2 run module ( #266 )
...
* Add kraken2 run module
* Add kraken2 run module
* Add coronavirus kraken2 db
* Adding kraken2 run tests
* Update software/kraken2/run/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Fixing files commited by mistake
* Remove params for meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-18 13:08:06 +00:00
Harshil Patel
d1cb9a845f
Check for minimum NF version ( #278 )
2021-03-18 12:00:32 +01:00
Kevin Menden
a90332906b
add mergebamalignment ( #259 )
...
* add mergebamalignment
* fix test.yml
* update to latest gatk4 version
* Update software/gatk4/mergebamalignment/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/data/README.md
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gatk4/mergebamalignment/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/gatk4/mergebamalignment/meta.yml
* fixed unmapped/unaligned
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-17 15:56:56 +01:00
Kevin Menden
3c4d9466f4
Adding minia for viralrecon ( #267 )
...
* initial 'modules create' of minia
* fixed tests
* finished meta.yml
* fixed filters.yml
* resolved issues in pytest_software.yml
* add newline
* Update software/minia/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-17 12:54:15 +01:00
Kevin Menden
17dbff52f4
added gatk4 variantfiltration ( #265 )
...
* added gatk4 variantfiltration
* replace merge with filter
* Update software/gatk4/variantfiltration/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* updated input
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-17 09:42:35 +01:00
Jose Espinosa-Carrasco
74ff11b07b
Fix bowtie builds ( #273 )
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* Fix bowtie build test
* Forgot to delete old bowtie_build
* Fix bowtie2 build tests
* Add initOptions include on hisat2 extractsplicesites
2021-03-15 15:39:42 +01:00
Maxime Garcia
66fd57a8bc
fix: update tiddit_sv tests ( #272 )
2021-03-15 14:02:20 +00:00
Harshil Patel
9b99b33401
Rename .github/filters.yml -> tests/config/pytest_software.yml ( #271 )
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* Rename pytest filters.yml
* Change filters.yml name
* Update resoures for ivar trim
2021-03-15 12:51:30 +00:00
Jose Espinosa-Carrasco
572abb00b3
Remove def from module options definition in main ( #270 )
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* Remove def from module options definition in main
* Fix bismark_deduplicate tests
* Fix bwameth_align tests
* Fixing gatk4 conda tests ("=" instead of ':' in build id)
* Same as previous commit (Fix gatk4 test)
* Fix qualimap bamqc test (no md5 check for pngs)
* Fix seqkit split2 tests. Changed to new test data
* Fix samtools tests. Some were missing initOptions include
* Removing TOOL SUBTOOL template module since now it is included on tools repo
2021-03-15 12:16:43 +00:00
Kevin Menden
0218824b86
add task.cpus to pangolin ( #263 )
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* 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 )
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* 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 )
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* 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 )
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* 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
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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
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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
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Add bcftools mpileup module
2021-02-24 09:24:43 +01:00
Harshil Patel
5287fe5f95
Merge pull request #245 from phue/bismark_deduplicate
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add bismark/deduplicate + tests
2021-02-23 21:08:24 +00:00
Harshil Patel
4703a60443
Merge pull request #220 from phue/bwameth
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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
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add qualimap/bamqc + test
2021-02-18 10:09:03 +01:00
Harshil Patel
5695e4ccce
Merge pull request #222 from phue/methyldackel
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add methyldackel modules
2021-02-17 22:17:26 +00:00
Harshil Patel
ecd26b388d
Merge pull request #221 from heuermh/seqwish
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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
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fix: update checksum or filename
2021-02-17 10:54:38 +00:00
Harshil Patel
4d656c8f5f
Merge pull request #181 from drpatelh/fixes
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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
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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
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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
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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
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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
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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
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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
