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nf-core_modules/tests/modules
Annick Renevey 45985ff6f0
Peddy nf core2 2dev0 ()
* Updated module to fit nf-core2.2dev0 templates

* Updated module to fit nf-core2.2dev0 templates

* Linked test files to nf-core/test-dataset branch:raredisease raw files

* Change order of input: vcf and tbi with meta, ped without

* Change order of input: vcf and tbi with meta, ped without/adapt test

* Change order of input: vcf and tbi with meta, ped without/adapt test, bugfix

* Indent and rename files

* Update modules/peddy/main.nf

Removed newline

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* Update modules/peddy/main.nf

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

* Update modules/peddy/main.nf

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

* Update modules/peddy/main.nf

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

* Update modules/peddy/meta.yml

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

* Update modules/peddy/meta.yml

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

* Update modules/peddy/main.nf

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

* Update modules/peddy/main.nf

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

* Update pytest_modules.yml

* Update main.nf

* Apply suggestions from code review

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-21 20:14:09 +00:00
..
abacas Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
adapterremoval Fix read indexing in AdapterRemoval module () 2021-11-10 12:21:12 +00:00
agrvate module for agrvate () 2021-09-16 12:42:23 +02:00
allelecounter Add cram support to Allelecounter module () 2021-11-02 17:00:25 +01:00
amps add Amps () 2021-09-30 12:54:16 +02:00
arriba Added module arriba () 2021-07-22 15:19:42 +01:00
artic Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
assemblyscan add new assembly scan module () 2021-10-29 10:01:23 +02:00
ataqv/ataqv Add new module 'ataqv/ataqv' () 2021-11-15 12:51:40 +00:00
bakta add bakta module () 2021-11-21 12:17:25 +00:00
bamaligncleaner Add module: bamaligncleaner () 2021-09-15 10:31:49 +02:00
bamtools/split Update module: bamtools/split () 2021-10-23 19:39:27 +01:00
bamutil/trimbam Add bamutil/trimbam () 2021-11-15 16:44:12 +00:00
bandage/image Fix version commands () 2021-09-27 22:10:37 +01:00
bbmap Add log to output from bbmap/align () 2021-11-10 10:27:52 +00:00
bcftools Add bcftools/index () 2021-10-13 10:40:04 +02:00
bedtools Bedtools sort add extension choice input () 2021-10-29 13:22:17 +01:00
bismark Fix version commands () 2021-09-27 22:10:37 +01:00
blast nf-core modules bump-versions for all modules () 2021-07-28 09:10:44 +01:00
bowtie Fix version commands () 2021-09-27 22:10:37 +01:00
bowtie2 Fix version commands () 2021-09-27 22:10:37 +01:00
bwa Bwa index () 2021-11-15 11:26:01 +00:00
bwamem2 Fix version commands () 2021-09-27 22:10:37 +01:00
bwameth Fix more version commands () 2021-09-28 06:56:27 +01:00
cat Fix flash and cat/fastq modules () 2021-09-28 21:14:11 +01:00
cellranger/mkref new module cellranger mkref () 2021-10-28 13:33:57 +02:00
checkm/lineagewf New module: checkm/lineagewf () 2021-10-26 21:54:10 +01:00
chromap Chromap Module () 2021-09-15 17:20:55 +01:00
clonalframeml add clonalframeml module () 2021-11-15 19:43:53 +00:00
cmseq/polymut Add new module: cmseq/polymut () 2021-11-09 16:12:51 +01:00
cnvkit/batch CNVkit: Make targets file optional when running in WGS mode () 2021-11-21 19:56:57 +00:00
cooler Cooler cload () 2021-11-15 21:43:55 +00:00
csvtk Added new module csvtk/split () 2021-11-15 18:29:55 +00:00
custom Add module get_chrom_sizes () 2021-11-15 19:22:12 +00:00
cutadapt Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
damageprofiler fix: reduce number of required input files for damage profiler () 2021-10-20 10:02:30 +02:00
dastool Add new module: Das Tool () 2021-11-19 08:33:29 +01:00
dedup Add module: dedup () 2021-10-28 12:10:21 +02:00
deeptools nf-core modules bump-versions for all modules () 2021-07-28 09:10:44 +01:00
delly/call few version and test data config fixes () 2021-09-28 20:42:04 +01:00
diamond Diamond () 2021-09-23 09:13:04 +01:00
dragonflye add module for dragonflye () 2021-08-16 11:51:30 +02:00
dshbio Add dsh-bio export-segments module () 2021-08-17 15:53:41 +02:00
ectyper add ectyper module () 2021-11-21 12:14:02 +00:00
emmtyper add emmtyper module () 2021-11-08 20:43:15 +01:00
ensemblvep Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
expansionhunter Expansionhunter () 2021-08-16 17:47:42 +02:00
fargene new module fargene () 2021-11-15 16:42:48 +00:00
fastani module fastani () 2021-09-21 20:20:26 +01:00
fastp enhance module fastp: add save_merged () () 2021-07-23 10:44:00 +01:00
fastqc Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
fastqscan add module for fastq-scan () 2021-11-15 15:41:36 +01:00
fasttree Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
fgbio Fgbio group reads by umi () 2021-10-29 14:00:54 +02:00
filtlong add filtlong () 2021-10-27 17:00:11 +02:00
flash Fix flash and cat/fastq modules () 2021-09-28 21:14:11 +01:00
freebayes fix remove md5sum check () 2021-11-03 11:41:12 +01:00
gatk4 Update in GATK4 variantfiltration: Added vcf_index to vcf tuple; output to vcf.gz format. () 2021-11-18 21:47:40 +01:00
genmap Fix more version commands () 2021-09-28 06:56:27 +01:00
genrich Refactor genrich to avoid params in main () 2021-10-29 16:37:39 +02:00
gffread Fix bug in gffread () 2021-09-15 19:55:08 +01:00
glnexus Add glnexus () 2021-09-22 13:31:01 +01:00
graphmap2 Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
gstama Update: gstama/collapse () 2021-11-11 14:57:55 +00:00
gtdbtk/classifywf Add gtdbtk/classifywf module () 2021-10-05 21:23:01 +01:00
gubbins nf-core modules bump-versions for all modules () 2021-07-28 09:10:44 +01:00
gunc New module: gunc run (+ gunc downloaddb) () 2021-11-03 17:01:23 +01:00
gunzip update: gunzip to include meta input tuple () 2021-11-21 12:41:03 +00:00
hicap [fix] hicap module allow optional outputs () 2021-11-16 09:23:07 +00:00
hifiasm few version and test data config fixes () 2021-09-28 20:42:04 +01:00
hisat2 nf-core modules bump-versions for all modules () 2021-07-28 09:10:44 +01:00
hmmcopy readcounter module for hmmcopy () 2021-11-02 11:01:13 +00:00
hmmer/hmmalign Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
homer Homer Modules () 2021-09-08 15:40:34 +00:00
idr Add IDR module () 2021-10-30 10:52:13 +02:00
imputeme/vcftoprs Imputeme () 2021-11-05 10:25:54 +01:00
iqtree Module new version reporting fixes () 2021-09-28 10:51:19 +01:00
ismapper add ismapper module () 2021-10-05 21:55:41 +01:00
isoseq3 Update isoseq3/cluster () 2021-10-14 11:07:53 +01:00
ivar Fix more version commands () 2021-09-28 06:56:27 +01:00
jupyternotebook Notebook modules () 2021-10-24 20:51:56 +02:00
kallisto/index Fix yml ver () 2021-09-28 18:33:07 +02:00
kallistobustools Fix yml ver () 2021-09-28 18:33:07 +02:00
khmer/normalizebymedian Khmer normalizebymedian () 2021-10-29 13:23:34 +02:00
kleborate Add module kleborate () 2021-09-21 20:45:42 +01:00
kraken2/kraken2 Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
kronatools add Kronatools KTImportTaxonomy () 2021-11-15 17:40:46 +00:00
last nf-core modules bump-versions for all modules () 2021-07-28 09:10:44 +01:00
leehom Add leehom module () 2021-11-15 15:26:06 +01:00
lima New module: LIMA () 2021-09-27 16:14:35 +01:00
lissero add lissero module () 2021-11-08 20:52:07 +01:00
lofreq fix: lofreq/callparallel missing arg () () 2021-07-19 09:19:27 +01:00
macs2/callpeak Macs2 calllpeak () 2021-11-15 18:17:40 +01:00
malt update: MALT build version bump () 2021-09-15 16:46:29 +01:00
maltextract add: MALTEXTRACT () 2021-09-21 19:57:27 +01:00
manta adding new manta/germline + manta/tumoronly modules () 2021-10-27 18:24:48 +02:00
mapdamage2 Add new module Mapdamage2 () 2021-11-09 14:05:23 +01:00
mash/sketch Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
mashtree add mashtree module () 2021-10-05 21:27:30 +01:00
maxbin2 New module: maxbin2 () 2021-10-26 22:07:33 +01:00
medaka Add Medaka module () 2021-11-15 17:26:37 +00:00
megahit Add MEGAHIT () 2021-10-12 16:06:06 +01:00
meningotype add meningotype module () 2021-11-06 16:44:26 +01:00
metabat2 New module: metabat2 () 2021-11-08 21:08:26 +01:00
metaphlan3 Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
methyldackel Fix version commands () 2021-09-27 22:10:37 +01:00
minia Fix version commands () 2021-09-27 22:10:37 +01:00
miniasm Add Miniasm module () 2021-11-15 17:50:56 +00:00
minimap2 Add Racon module to nf-core/modules () 2021-10-29 13:33:38 +01:00
mlst added classic mlst module () 2021-10-05 20:49:46 +01:00
mosdepth Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
msisensor Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
mtnucratio Mtnucratio () 2021-10-29 15:02:02 +02:00
multiqc Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
mummer Initial commit mummer module () 2021-11-15 16:53:41 +01:00
muscle Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
nanolyse Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
nanoplot Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
ncbigenomedownload add ncbi-genome-download module () 2021-11-15 18:32:53 +00:00
nextclade Update Nextclade to output all files by default () 2021-07-28 19:49:50 +01:00
ngmaster add ngmaster module () 2021-11-10 11:25:50 -07:00
nucmer add new nucmer module () 2021-11-15 22:05:34 +00:00
optitype Updating test file for optitype () 2021-10-28 14:24:52 +02:00
pairix Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
pairtools Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
pangolin Update pangolin to 3.1.11 () 2021-09-20 19:59:05 +01:00
paraclu add paraclu () 2021-10-27 15:48:49 +02:00
pbbam/pbmerge New module: pbbam/pbmerge () 2021-10-05 23:16:45 +01:00
pbccs Update module: pbccs () 2021-11-11 14:19:26 +00:00
peddy Peddy nf core2 2dev0 () 2021-11-21 20:14:09 +00:00
phyloflash Add phyloflash module () 2021-11-21 19:43:58 +00:00
picard Fix picard markduplicates () 2021-11-18 21:54:14 +01:00
pirate add pirate module () 2021-10-05 22:28:25 +01:00
plasmidid Fix yml ver () 2021-09-28 18:33:07 +02:00
plink Implement plink/extract module () 2021-11-09 14:03:13 +00:00
plink2/vcf New module: plink2/vcf () 2021-11-15 13:55:18 +00:00
pmdtools/filter add new module pmdtools/filter () 2021-11-13 15:09:14 +00:00
porechop add porechop module () 2021-10-28 13:21:36 +02:00
preseq/lcextrap Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
prodigal Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
prokka Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
pycoqc Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
pydamage Pydamage analyzer update () 2021-10-18 15:24:49 +02:00
qcat Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
qualimap/bamqc Fix more version commands () 2021-09-28 06:56:27 +01:00
quast Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
racon Add Racon module to nf-core/modules () 2021-10-29 13:33:38 +01:00
rapidnj Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
rasusa Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
raxmlng Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
rmarkdownnotebook Notebook modules () 2021-10-24 20:51:56 +02:00
roary add roary module () 2021-10-05 22:08:47 +01:00
rsem Update checksum modules using human GTF () 2021-10-26 23:09:04 +01:00
rseqc Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
salmon Fix version commands () 2021-09-27 22:10:37 +01:00
samblaster New module: Samblaster () 2021-11-04 18:18:56 +01:00
samtools Add thread option to samtools modules () 2021-11-18 22:24:47 +01:00
scoary add scoary module () 2021-11-06 16:34:39 +01:00
seacr/callpeak I accidently deleted a branch before the PR merged for PR 800 () 2021-10-21 12:28:59 +01:00
seqkit/split2 Fix version commands: round 3 () 2021-09-28 14:37:47 +01:00
seqsero2 add seqsero2 module () 2021-11-04 07:49:30 +00:00
seqtk New module seqtk/mergepe () 2021-10-28 16:53:33 +02:00
sequenzautils Fix version commands: round 3 () 2021-09-28 14:37:47 +01:00
seqwish/induce Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
shovill Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
snpdists module: snp-dists () 2021-09-15 16:36:49 +01:00
snpeff Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
snpsites Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
spades Change Spades input () 2021-11-15 11:53:07 +00:00
spatyper add spatyper module () 2021-10-05 22:21:35 +01:00
sratools Fix subworkflows seperate from modules () 2021-11-15 18:18:46 +00:00
staphopiasccmec add staphopia-sccmec module () 2021-09-15 17:24:11 +01:00
star Update checksum modules using human GTF () 2021-10-26 23:09:04 +01:00
strelka Update strelka, by enabling BP if Manta candidates are present () 2021-10-27 17:49:54 +02:00
stringtie Update checksum modules using human GTF () 2021-10-26 23:09:04 +01:00
subread/featurecounts fix more ver yml () 2021-09-28 20:25:10 +01:00
tabix nf-core modules bump-versions for all modules () 2021-07-28 09:10:44 +01:00
tbprofiler/profile add module for tbprofiler () 2021-11-15 15:35:55 +01:00
tiddit Add TIDDIT cov () 2021-10-13 12:59:35 +02:00
trimgalore Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
ucsc New module: ucsc/liftover () 2021-10-21 18:04:15 +02:00
ultra/pipeline Update: uLTRA () 2021-11-21 13:00:53 +00:00
unicycler Unicycler with long read input () 2021-11-15 11:48:56 +00:00
untar Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
unzip Unzip update () 2021-09-22 11:02:32 +01:00
variantbam Add variantbam () 2021-07-26 19:07:29 +01:00
vcftools Rename software/ directory to modules/ to re-organise module structure () 2021-07-07 10:10:18 +01:00
yara fix more ver yml () 2021-09-28 20:25:10 +01:00