kevbrick
fead37d57a
Add module: nf-core hackathon #207 : new module: msisensor/msi ( #343 )
...
* Add module: nf-core hackathon #207 : new module: msisensor/msi
* Add module: nf-core hackathon #207 : new module: msisensor/msi
* Fix 4-spacing issues (caught in PR linting)
* Code review fixes & update configs
* Code review: remove stray echo
* Code review: Add msisensor modules
* Slashes to underscores to get tests to run on github
* Update software/msisensor/scan/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/msisensor/scan/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/msisensor/msi/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/msisensor/msi/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Add all outputs to meta.ymls
* Fixes from code review
* Fixes from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-25 16:46:00 -04:00
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
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
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
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
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
Robert A. Petit III
a13d859c87
Add process label to prokka ( #350 )
2021-03-24 04:54:52 +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
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 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
c736022942
methyldackel: bump version to 0.5.2 ( #305 )
2021-03-22 17:46:28 +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
Patrick Hüther
8a44258548
remove params section from meta.yml ( #282 )
2021-03-19 13:16:50 +01:00
Edmund Miller
36593aa43e
chore: Remove stray functions file ( #279 )
2021-03-19 05:49:02 +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
Michael L Heuer
1845db4043
Update dsh-bio to 2.0.3 ( #276 )
2021-03-18 13:06:56 +00:00
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
Harshil Patel
3df3d671f2
Fix nf-core modules lint tests ( #275 )
...
* Fix Conda definition bug
* Add process label
2021-03-16 17:16:47 +00:00
Jose Espinosa-Carrasco
74ff11b07b
Fix bowtie builds ( #273 )
...
* 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
Harshil Patel
9b99b33401
Rename .github/filters.yml -> tests/config/pytest_software.yml ( #271 )
...
* Rename pytest filters.yml
* Change filters.yml name
* Update resoures for ivar trim
2021-03-15 12:51:30 +00:00
Harshil Patel
d9396adbdf
Update software version command ( #269 )
2021-03-15 12:21:21 +00:00
Jose Espinosa-Carrasco
572abb00b3
Remove def from module options definition in main ( #270 )
...
* 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 )
...
* 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
