Commit graph

463 commits

Author SHA1 Message Date
Anthony Underwood
2ed9b6ae28
Raxmlng (#443)
* new raxml module

* new raxml module

* pass in args for bootstrap and add test for support file

* remove unnecessary tag

* ensure tags meet guidleines

* Apply suggestions from code review

* Update to latest functions file

Co-authored-by: avantonder <avt@sanger.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-14 08:38:59 +01:00
Jose Espinosa-Carrasco
750bd8c3e3
Finish deeptools modules (#442)
* Adding bigWig and deeptools computeMatrix files to config

* Adding meta.yml for deeptools modules

* Add test for deeptools modules

* Fixing and reordering tags

* Fixing conda test that worked in local...

* Apply suggestions from code review

* Changing bigwig file pattern to include bigwig extension

* Saving after last change is a good practice

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-13 21:48:43 +01:00
Kevin Menden
043a7d1e3c
remove deprecated test tags (#440)
* remove deprecated test tags

* fix bowtie, gatk4/applybsqr

* fix gatk4 baserecalibrator

* fixed shovill

* fixed yara/mapper

* fixed kallistobustools/ref paths
2021-04-13 18:03:09 +01:00
Jose Espinosa-Carrasco
a9fcbd93cc
Move assembly test files from genome to illumina (#441)
* FIx plasmidid tests for new contigs.fasta file

* Fixing two md5sum hashes

* Update test path in config for illumina assembly files

* Update modules using assembly files

* Correctly setting path of assembly files

* Update tests/config/test_data.config

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-13 12:52:11 +02:00
Jose Espinosa-Carrasco
26fdebc8de
FIx plasmidid tests for new contigs.fasta file (#438)
* FIx plasmidid tests for new contigs.fasta file

* Fixing two md5sum hashes
2021-04-13 08:49:44 +01:00
Kevin Menden
1d874bb0d0
Finish rseqc modules (#439)
* 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

* added rseqc/bamstat tests

* added tests/meta.yml for rseqc/inferexperiment

* added test/meta.yml for rseqc/inner_distances

* added meta.yml and tests/main.nf for junctionannotation (test not running)

* added test/meta.yml for rseqc/readdistribution

* finished test/meta.yml for rseqc/readduplication

* added entries to pytest_software.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-13 08:49:32 +01:00
Thanh Lee
c736817598
🧸 Updated rasusa (#437)
* changed genome size input position

* fixed...😊
2021-04-12 21:47:55 +01:00
Harshil Patel
c99ab09f8d
Add kraken2 pigz multi-tool container for compressing output fastq files (#434)
* Add kraken2 pigz multi-tool container for compressing output fastq files

* Add untar to pytest config

* Add untar process to kraken2 tests

* Remove unneeded tags
2021-04-12 18:47:34 +02:00
Anthony Underwood
df8910de4e
Iqtree (#435)
* Resolve suggests after PR review

* add newline to functions

* need variable interpolation using double quotes; remove unnecessary tag

* add a more resilient link to raw github files

* remove trailing slash

* Update software/iqtree/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-12 17:01:26 +01:00
Jose Espinosa-Carrasco
3ac21ff0dc
Add abacas module (#431)
* Add abacas module

* Add test for abacas module

* Add Harshil to authorship

* Updating test with the data uploaded to nf-core/datasets

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-12 15:37:08 +01:00
Kevin Menden
0b402ffda8
Move test data to nf-core/test-datasets (#432)
* 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

* move test data directory to nf-core/test-datasets

* bump multiqc version

* remove the test data

* updated test data link

* update README

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-12 12:32:39 +01:00
Jose Espinosa-Carrasco
2c43c39ccc
Add pycoqc module (#424)
* Add pycoqc module

* Adding pycoqc module tests

* Update pycoqc wilth new functions.nf

* Update tests to check for json report content
2021-04-12 10:52:14 +01:00
Anthony Underwood
575df10781
add new iqtree module (#427)
* add new iqtree module

* Resolve suggests after PR review

* add newline to functions
2021-04-12 09:45:56 +01:00
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