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602 commits

Author SHA1 Message Date
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
Edmund Miller
431c699727
Revert "ci: Test bowtie-build instead of _" 
This reverts commit 9b454416d2.
 2021-02-03 20:06:05 -06:00
drpatelh
fe3cb87f6d
Direct download Singularity containers 2021-02-03 20:03:45 -06:00
Michael L Heuer
c466255f6f Add bandage image module 2021-02-03 19:31:58 -06:00
Edmund Miller
9b454416d2
ci: Test bowtie-build instead of _ 2021-02-03 13:17:14 -06:00
Edmund Miller
7dbac4bdef
ci: Test adding another work to test name 2021-02-03 13:17:14 -06:00
Edmund Miller
b058da5856
ci: Test buil to see if build is special 2021-02-03 12:43:18 -06:00
Edmund Miller
4d58a037f6
test(bowtie_align): Fix md5sum 2021-02-03 12:37:19 -06:00
Edmund Miller
6901c7e830
ci: Fix bowtie_build names with "" 2021-02-03 12:37:14 -06:00
drpatelh
e71b3eaaa5 Rename workflows 2021-02-03 17:48:17 +00:00
drpatelh
ff6f0642d2 Fix multiqc tests 2021-02-03 17:43:14 +00:00
drpatelh
0683efc679 Fix salmon quant tests 2021-02-03 17:36:06 +00:00
drpatelh
550494cbd1 Fix picard mergesamfiles test 2021-02-03 17:31:41 +00:00
drpatelh
f079ce9d1f Fix preseq tests 2021-02-03 17:28:44 +00:00
drpatelh
f37fb66f40 Fix bwa mem tests 2021-02-03 17:26:43 +00:00
drpatelh
8a15852756 Fix salmon index tests 2021-02-03 17:13:47 +00:00
drpatelh
058d7b397c Fix fastqc test 2021-02-03 17:03:30 +00:00
drpatelh
39b8600dbb Fix trimgalore test 2021-02-03 17:02:52 +00:00
drpatelh
305d47fc87 Change path to tests 2021-02-03 16:44:56 +00:00
drpatelh
a87d584c48 Change path to bowtie tests 2021-02-03 16:39:00 +00:00
drpatelh
9b153f296d Add check to see if bowtie bam files exists 2021-02-03 16:26:10 +00:00
drpatelh
239cbe17ad Fix relative paths 2021-02-03 16:20:02 +00:00
drpatelh
38c3ecfac6 Merge branch 'master' of https://github.com/nf-core/modules into split_tests 2021-02-03 16:05:06 +00:00
drpatelh
743ba37d4b Update filters paths 2021-02-03 16:04:43 +00:00
drpatelh
ff23473e82 Restructure tests to run individually for each module 2021-02-03 16:02:58 +00:00
drpatelh
8be5e05111 Remove bam md5sum check for bowtie 2021-02-03 13:46:44 +00:00
drpatelh
1512c9af74 Unable to test BAM due to command 2021-02-03 12:26:10 +00:00
Edmund Miller
467d1595c4
test: Use docker image with singularity 2021-02-02 18:14:39 -06:00
Edmund Miller
72b4fb35aa
test: Fix profile logic order 2021-02-02 17:32:21 -06:00
Edmund Miller
67deb0d47a
ci: Add singularity tmp dir 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-02 17:25:58 -06:00
Edmund Miller
6b675eef6d
ci: Set pull docker container to false 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-02 17:00:40 -06:00
Edmund Miller
688cc05fe8
tests: Remove -profile in tests 
See ddbca7b467 for more info
 2021-02-02 15:30:59 -06:00
Edmund Miller
ddbca7b467
test: Use profile ENV variable hack 
The user will now set the env variable and pass it to pytest. You also
can't set the env variable ahead of time, it has to be run with pytest.
Example:
PROFILE=conda pytest --tag fastqc --symlink --kwd
 2021-02-02 12:44:30 -06:00
Harshil Patel
e7b1241449
Merge pull request #120 from nf-core/composite-runs 
Universal CI job
 2021-02-02 18:26:02 +00:00
drpatelh
6ac252e407 Change singularity to docker again 2021-02-02 13:38:34 +00:00
drpatelh
838defa350 Update md5sums 2021-02-02 13:37:40 +00:00
drpatelh
05b15df17e Remove file extension 2021-02-02 12:46:34 +00:00
drpatelh
d63d40827e Fix bwa index tests 2021-02-02 12:40:55 +00:00
drpatelh
ade6124a84 Change tests 2021-02-02 12:35:06 +00:00
JoseEspinosa
26829497d5 Fixing typo on path for md5 check 2021-02-02 12:19:57 +01:00
JoseEspinosa
e7f15feccf Adding --no-version to bcftools_isec for tests md5 check 2021-02-02 11:00:02 +01:00
JoseEspinosa
3a40ec5664 Adding bcftools_isec taking a path with several vcfs and its tests 2021-02-02 10:50:45 +01:00
JoseEspinosa
8e4764b8ed bcftools_filter adding argument to test to enable md5 check 2021-02-02 10:19:34 +01:00
JoseEspinosa
c25f8f0f6c Fixing tests 2021-02-02 09:57:55 +01:00
JoseEspinosa
382ea31e7e Adding bcftools test data 2021-02-02 09:18:28 +01:00
JoseEspinosa
cee37852cd Merge remote-tracking branch 'upstream/master' into bcftools_viralrecon 2021-02-02 09:15:20 +01:00
JoseEspinosa
a3ce63c79c Adding tests for bcftools 2021-02-02 09:14:00 +01:00
drpatelh
f84e5b59ca Rename bowtie_index to bowtie_build 2021-02-01 17:53:31 +00:00
Harshil Patel
0a41130276
Merge pull request #131 from KevinMenden/fastp-module 
Adding fastp module
 2021-02-01 13:43:35 +00:00