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Author SHA1 Message Date
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
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
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
JoseEspinosa
e9fc285967 Fix conda version declaration 2021-02-24 15:52:25 +01:00
Harshil Patel
50b98d56a1
Merge pull request #246 from drpatelh/master 
Update iVar modules
 2021-02-24 13:00:05 +00:00
drpatelh
1094af2206 Add missing docs 2021-02-24 12:54:45 +00:00
Harshil Patel
ca4b4eb78e
Merge pull request #248 from JoseEspinosa/fix_bcftools 
Add missing requirements to bcftools modules
 2021-02-24 12:51:39 +00:00
FriederikeHanssen
4673c119c7 resolve merge conflicts 2021-02-24 10:03:16 +01:00
JoseEspinosa
ec674bb127 Add label to bcftools processes 2021-02-24 09:47:54 +01:00
JoseEspinosa
823a631afc Fix tools entry on yml 2021-02-24 09:47:36 +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
JoseEspinosa
af7bc743bf Correct yml file, add fasta to input and correct vcf on output 2021-02-24 09:15:18 +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
JoseEspinosa
138be9f918 Adding label to the bcftools-mpileup process 2021-02-23 21:52:15 +01:00
drpatelh
89cd71309c Output log file for MultiQC 2021-02-23 20:36:23 +00:00
drpatelh
9098ba41c8 Update ivar consensus 2021-02-23 20:36:03 +00:00
JoseEspinosa
035443b6e0 Add bcftools-mpileup module 2021-02-23 19:05:26 +01:00
phue
e73bda26f5 add bismark/deduplicate + tests 2021-02-23 18:02:16 +01:00
FriederikeHanssen
bf58948dad remove todos, describe in/output 2021-02-23 15:41:11 +01:00
FriederikeHanssen
4e9d728108 allow fq.gz or gastq.gz as in/output 2021-02-23 15:40:22 +01:00
FriederikeHanssen
12137d6f3e Remove trialing whitespace 2021-02-23 15:00:21 +01:00
FriederikeHanssen
e251a3bed5 Remove todos 2021-02-23 14:58:09 +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
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
phue
bf0e0d857d bwameth/align: fix fasta name retrieval 
apparently bwameth doesn't like './' in front of the filepath? I have no idea. This works however
 2021-02-20 13:12:43 +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
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
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
phue
0606c06a25 qualimap/bamqc: remove unneeded variable definition 
can just use task.cpus directly
 2021-02-18 10:00:49 +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
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
2654c52ed1 Use list of reads as input, similar to dedup/extract 2021-02-17 17:15:02 +01:00
FriederikeHanssen
bedc2972eb Add seqkit split2 2021-02-17 17:09:24 +01:00
phue
aafc6949d3 faidx: add process label 2021-02-17 16:56:45 +01:00
phue
3b1d126a0e add samtools/faidx + tests 2021-02-17 16:46:34 +01:00
drpatelh
d47f9bb909 @kevinmenden sanity fix 2021-02-16 23:58:52 +00:00
drpatelh
dcc580e4fb Remove Conda build ids for all modules 2021-02-16 23:58:23 +00:00
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
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
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
d6d34a4b5b
Merge pull request #177 from MaxUlysse/master_gatk_createsequencedictionary 
Add gatk/createsequencedictionary
 2021-02-16 22:21:38 +00:00
Harshil Patel
a6d6c0b973
Update software/gatk/createsequencedictionary/main.nf 2021-02-16 22:08:11 +00:00
Harshil Patel
7c64e70c9e
Update software/gatk/createsequencedictionary/meta.yml 2021-02-16 22:07:51 +00:00
Harshil Patel
e558d5fb57
Merge pull request #174 from andersgs/ivar_consensus_fix 
ivar consensus: Add save mpileup as optional in output directive
 2021-02-16 22:04:38 +00:00
MaxUlysse
6a147b8aaa chores: replace bcftools/bgzip by tabix/bgzip cf #179 2021-02-16 19:11:36 +01:00
MaxUlysse
edf5fa3cf6 fix: merge bcftools/tabix and htslib/tabix into tabix/tabix 2021-02-16 18:27:13 +01:00
MaxUlysse
f660324508 chores: move file 2021-02-16 18:20:43 +01:00
MaxUlysse
274897f1fd fix: ECLint: Wrong line endings or new final newline 2021-02-16 17:11:50 +01:00
MaxUlysse
5e71dc94d6 fix: make HTSLIB_TABIX more modular 2021-02-16 17:06:55 +01:00
MaxUlysse
10524e3515 chores: add modules for htslib/tabix 2021-02-16 14:47:53 +01:00
MaxUlysse
28dc9227d7 fix: remove memory requirements and simplify URI 2021-02-16 13:54:40 +01:00
MaxUlysse
30e3f2c5f5 fix: ECLint check: trailing whitespace 2021-02-16 13:42:34 +01:00
MaxUlysse
7f35a1742d chores: add gatk/createsequencedictionary module 2021-02-16 13:40:06 +01:00
Maxime Garcia
d8706c12b3
Update meta.yml 
typo
 2021-02-16 11:22:15 +01:00
Anders Goncalves da Silva
fd854c333e
Add save mpileup as optional in output directive 2021-02-15 21:07:31 -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
7cae9b1842
Add gff to meta yaml 2021-02-15 20:49:37 -08:00
Anders Goncalves da Silva
26189f4132
Change ternary expressions back to traditional format 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:56:22 -08:00
Anders Goncalves da Silva
4f8ab8bd69
Rename gff to features 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:53:30 -08:00
Anders Goncalves da Silva
8c483d4c6a
Add gff as input for proper staging 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:53:13 -08:00
Anders Goncalves da Silva
6259b72081
Fix output format 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:52:30 -08:00
Anders Goncalves da Silva
ef1e1b2539
Fix indentation 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-15 19:51:45 -08:00
Harshil Patel
8eb3acc43f
Merge pull request #171 from JoseEspinosa/mosdepth 
Add mosdepth module
 2021-02-15 23:13:01 +00:00
Harshil Patel
f97c78b3fb
Update software/mosdepth/main.nf 2021-02-15 22:49:53 +00:00
Anders Goncalves da Silva
f841483a70
Fix URL for containers 2021-02-15 13:23:35 -08:00
Anders Goncalves da Silva
e8d1171b5d
Make gff a param and not an optional input 2021-02-15 11:50:52 -08:00
Anders Goncalves da Silva
9e3c4e598c
Add meta to ivar variants 2021-02-15 09:29:10 -08:00
Anders Goncalves da Silva
2fe3210f88
Add ivar variants 2021-02-15 09:27:59 -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
4af9417b6d
Update software/ivar/trim/main.nf 2021-02-13 08:20:06 +00:00
Harshil Patel
a5686ed14e
Update software/ivar/trim/main.nf 2021-02-13 08:19:55 +00:00
Harshil Patel
25f3d46f68
Update software/ivar/trim/meta.yml 2021-02-13 08:17:03 +00:00
Anders Goncalves da Silva
bbdca4fa76
Fix output files 2021-02-12 16:14:46 -08:00
Anders Goncalves da Silva
7c9766962d
Add ivar trim meta.yml 2021-02-12 16:02:48 -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