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Author SHA1 Message Date
Thanh Lee
ec15bae344
🏋️‍♀️ new submodule mash/sketch🕺 (#426) 
* new submodule mash/sketch

* fixed submodule naming

* OK, tag is diff to keyword

* OK  another round 🤣

* removed TODO comments

* updated as per review comments 🙆‍♂️

* updated functions.nf 😁

* Update software/mash/sketch/main.nf

* Update main.nf

Removed blank line at the 12th

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-04-10 16:24:23 +01:00
Harshil Patel
5e18e36895
Update and check tests are running for all modules (#420) 
* Fixes for PR 371

* Fix tags

* Add md5sum

* Add md5sums for stringtie

* Fix tests for modules where subtool = build

* Fix pytest_software name conflicts

* Change _ to / in test.yml tags

* Nope...that didnt work

* Fix sequenzautils/bam2seqz tests
 2021-04-09 13:47:05 +01:00
Thanh Lee
5a59e61052
new module: rasusa (#413) 
* new module: rasusa

* Removed blank line in software/rasusa/main

* updated code as per reviewcomments

* removed blank line as failed for lint

* updated as per review comments

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-04-09 13:10:32 +01:00
Anthony Underwood
ca776e76a2
add rapidnj module (#421) 
* add rapidnj module

* remove trailing whitespace

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-04-09 13:04:54 +01:00
Florian Wuennemann
0f53c3b96b
Added kallistobustools/ref (#408) 
* Added kallistobustools/ref. Local tests all passing with Docker. Linting passed. Test data currently in /tests/data/delete_me

* Removed trailing whitespace line 29

* Moved workflow from meta to options.

* Update main.nf

* Forgot to remove previous testing input channel for workflow.

* Apply suggestions from code review

Applied changes suggested by @drpatelh

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Added gtf to meta.yml.

* Apply suggestions from code review

Adding @drpatelh suggested changes.

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Moved workflow to input value. Fixed tests.

* Update tests/software/kallistobustools/ref/test.yml

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-04-09 09:41:41 +01:00
Yuk Kei Wan
16e8d21477
Nanoplot and sequencing_summary.txt for Nanopore test data (#364) 
* add nanoplot

* add Nanopore 100 read subset bam and fastq

* add nanoplot module and sequencing_summary.txt

* Update pytest_software.yml

* Update main.nf

* test directory path

* testing one output file

* Update main.nf

* fix typo

* remove path to test outputs (it worked locally)

* use test_data.config in test

* add meta.yml

* allowing either summary.txt or fastq.gz inputs

* fix linting and test.yml

* test whether github check can catch the output

* add summary.txt test output paths

* check Nanoplot-report.html output
 2021-04-09 08:31:38 +01:00
Anthony Underwood
6927f1d086
New Snpsites module (#416) 
* new gubbins module

* new gubbins module

* new gubbins module

* Update software/gubbins/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gubbins/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gubbins/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gubbins/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* Update tests/config/test_data.config

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update tests/software/gubbins/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* new gubbins module

* new gubbins module

* new snpsites module

* new snpsites module

* new snpsites module

* new snpsites module

* adding fasttree module

* correct trailing whitespace

* using sarscov2 as a test dir

* use sars-cov-2 alignment

* remove old test alignment

* new snpsites module

* new snpsites module

* new snpsites module

* updated test file names

* new snpsites module

* revert to gubbins test on upstream

* add new lines

* renove whitespace

* Apply suggestions from code review

Co-authored-by: avantonder <avt@sanger.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: avantonder <ajv37@cam.ac.uk>
 2021-04-09 08:00:33 +01:00
Anthony Underwood
63b3975292
Update gubbins module to use new files (#417) 
* new gubbins module

* new gubbins module

* new gubbins module

* Update software/gubbins/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gubbins/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gubbins/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gubbins/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* Update tests/config/test_data.config

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update tests/software/gubbins/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* new gubbins module

* new gubbins module

* new snpsites module

* new snpsites module

* new snpsites module

* new snpsites module

* adding fasttree module

* correct trailing whitespace

* using sarscov2 as a test dir

* use sars-cov-2 alignment

* remove old test alignment

* new snpsites module

* new snpsites module

* new snpsites module

* updated test file names

* new snpsites module

* remove snpsites from gubbins branch

* remove redundant test_fas alignment

* update md5 sums

Co-authored-by: avantonder <avt@sanger.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: avantonder <ajv37@cam.ac.uk>
 2021-04-09 07:54:11 +01:00
Jose Espinosa-Carrasco
f90dde0d88
Add plasmidid module (#410) 
* Adding plasmidid module

* Adding test for plasmidid module

* Update plasmidid version to 1.6.4

* Adding contigs.fasta file

* Update tests

* Adding output files on test.yml
 2021-04-08 22:44:30 +01:00
Anthony Underwood
be390a25e5
adding fasttree module (#412) 
* adding fasttree module

* correct trailing whitespace

* using sarscov2 as a test dir

* remove TODO

* update test data naming

* further test data naming updates

* remove options in favour of $options.args

* ensure non standard exit codes don't cause an issue

* update md5sum
 2021-04-08 18:15:23 +01:00
Edmund Miller
a3684d9594
Lint modules ci (#389) 
* ci: Add modules lint step

Moved it ahead of the nextflow install so ideally it'll fail before we
bother doing any more setup

* ci: _ => /

* Update tests/config/pytest_software.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-04-08 09:10:52 +01:00
avantonder
710ab76b90
new module: gubbins (#377) 
* new gubbins module

* new gubbins module

* new gubbins module

* Update software/gubbins/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gubbins/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gubbins/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gubbins/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* Update tests/config/test_data.config

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update tests/software/gubbins/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* new gubbins module

* new gubbins module

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-04-07 16:31:24 +01:00
Harshil Patel
242fdb2f73
Version bumps and minor module updates (#406) 
* Version bumps and minor module updates

* Fix Pangolin tests

* Fix SPAdes tests

* stageAs @phue
 2021-04-06 13:38:41 +01:00
Patrick Hüther
3b1dcc9cc0
MethylDackel: fix version scraping (#401) 
* methyldackel: fix version scraping

* fix output file path
 2021-04-06 10:59:33 +01:00
Jose Espinosa-Carrasco
f8e428d690
Restructuring spades tests whith new test data sets + fixing spades tests (#396) 
* Restructuring with new test data sets + fixing tests

* Remove checkings for warning files

* Remove md5 check for test.gene_clusters.fa

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-04-01 20:31:23 +01:00
Robert A. Petit III
c9256616b9
update tests for new config (#384) 
* update tests for new config

* fix quast, update more

* more updates!

* more tests updated

* fix tests, added tabix gff3.gz

* Delete main.nf

Removing SPAdes from PR to avoid merge conflicts with https://github.com/nf-core/modules/pull/396

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-04-01 20:22:06 +01:00
Nicholas Toda
f126d980d7
Add tests for subread #106 (#393) 
* inital commit

* added meta.yaml info

* add initial logic for featurecounts test

* add args and change SE/PE to strandedness for featurecounts test

* added tests to pytest

* added test.yml

* removed GTF flag in options

* corrected test meta params

* meta yaml corrected tool info

* update test.yml

* fix lint errors meta.yml

Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr>
 2021-04-01 20:02:36 +01:00
Ravneet Bhuller
c5c59d44a1
PR for sequenzautils/bam2seqz (#395) 
* added files

* edited files

* removed file

* README.md edited

Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
 2021-04-01 07:08:27 +02:00
sruthipsuresh
983ba000c1
New modules: Fgbio callmolecularconsensusreads and sortbam (#352) 
* Added fgbio callmolecularconsensusreads and sortbam modules

* Fixed naming issue in meta.yml

* fix: test.yml and config lint

* Revert "fix: test.yml and config lint"

This reverts commit 0453bc3a8dc3dab6997442a4349ee2241adcc380, which caused the sortbam tests to fail.

* style: Fix test names

* style: Remove trailing whitespace

* fixed test.yml

* fix: test data in sortbam

* fix: data format

* fix: test data for callmolecularconsensusreads

* Corrected with updated test data

* Apply suggestions from code review

Applied changes from code review, mainly syntactical changes

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

Co-authored-by: Sruthi Suresh <sps180004@ganymede.utdallas.edu>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-03-28 20:38:50 +01:00
JJ
e50a525715
gatk4 markduplicates (#356) 
* new module gatk4/markduplicates

* add tests

* add gatk4_markduplicates entry in pytest_software.yml

* Update software/gatk4/markduplicates/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gatk4/markduplicates/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gatk4/markduplicates/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gatk4/markduplicates/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update tests/software/gatk4/markduplicates/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update tests/software/gatk4/markduplicates/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Apply suggestions from code review

* Fix EC lint

* Update md5sum

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-03-26 23:25:40 +00:00
suzannejin
989fb7d5b7
modify test path - module gatk4 + added new module gatk4/haplotypecaller (#382) 
* 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

* fix README.md

* modify test path gatk4

* fix config

* Add new module gatk4/haplotypecaller

* solve check issues

* fix test.yml file

* fix test.yml gz.tbi

* Update software/gatk4/haplotypecaller/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gatk4/haplotypecaller/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gatk4/haplotypecaller/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gatk4/haplotypecaller/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/gatk4/haplotypecaller/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update tests/software/gatk4/haplotypecaller/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Apply suggestions from code review

Co-authored-by: suzannejin <suzanne.jin@crg.eu>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-03-26 12:46:46 +01:00
Nicholas Toda
e526eae472
Add tests for hisat2 (#366) 
* initial commit hisat2/build

* initial commit hisat2/build

* changed names for hisat2

* fixed directory structure and args

* added splice site test data

* added splice site inputs

* replaced list with individual args

* fixed removed commas

* added test yml file

* updated hisat2 conda version

* added meta.yml

* added meta.yml description

* added meta.yml inputs

* added meta.yml outputs

* update conda version for hisat2

* removed trailing whitespace meta.yml

* fixed version number for containers

* added test data to test config

* updated for new test logic

* fix pytest issue?

* fix pytest issue

* fixed wrong tool in meta.yaml

* updated tets.yaml name

* handle build bug for testing

* handle build bug for testing in yaml

* moved test folder to fix build bug

* use old hisat2 version to avoid conda giving inconsistent md5sum

* initial commit

* removed temp file

* added meta yaml

* add to pytest

* added tests

* added test yml

* add align meta yaml

* add hisat2 align to pytest

* remove need for splice data by calling process

* add hisat2 align se test

* add hisat2 align pe test

* update names hisat2 align

* update software pytest for using mutiple modules

* remove splice site test data since using module instead

* remove splice site from config since using module instead

* fixed extra brace

* added hisat2 align test.yml

* removed md5sum for bam files

* updated build md5sums

* Apply suggestions from code review

Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-03-25 21:08:46 +00:00
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
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) 
* 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) 
* 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) 
* 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
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
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