Commit graph

2496 commits

Author SHA1 Message Date
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
Sviatoslav Sidorov
5a270c5ba7 Removed spaced on an empty line 2021-03-16 15:55:59 +00:00
Sviatoslav Sidorov
b58233794b Add hifiasm version printing 2021-03-16 13:14:43 +00:00
Sviatoslav Sidorov
390c835f9f meta.yml init; test.yml and main.nf for printing version 2021-03-16 11:54:42 +00:00
Sviatoslav Sidorov
2f675fbe7c hifiasm tests init from fastqc 2021-03-16 11:37:06 +00:00
Sviatoslav Sidorov
38b450d0be hifiasm copied from fastqc 2021-03-16 09:54:29 +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
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
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
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
Maxime Garcia
e1f935a586
Merge pull request #256 from JoseEspinosa/fix_tiddit_sv_tests
Fix tiddit sv tests
2021-02-26 10:39:23 +01:00
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
Harshil Patel
0731b205ac
Merge pull request #251 from JoseEspinosa/fix_conda_ver_cutadapt
Fix conda version declaration of cutadapt module
2021-02-24 15:02:52 +00:00
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
278a4a5669
Merge pull request #250 from FriederikeHanssen/seqkit
Seqkit Split2
2021-02-24 10:30:01 +01:00
FriederikeHanssen
48d6d88104
Update .github/filters.yml
Co-authored-by: Kevin Menden <kevin.menden@live.com>
2021-02-24 10:29:13 +01:00
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
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
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
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
e9d90007c5 Adding arguments to make md5 hashes stable 2021-02-23 19:39:24 +01:00
JoseEspinosa
20bcb00ea0 Fix indentation 2021-02-23 19:08:56 +01:00
JoseEspinosa
4b3c86ed9f Add tests for bcftools-mpileup 2021-02-23 19:05:57 +01:00
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
e67515809a try to only make paired-end test work, pass locally with conda & docker 2021-02-23 15:47:16 +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