millironx/nf-core_modules
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nf-core_modules/modules
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Harshil Patel 20d8250d9f
Update all modules to new NF DSL2 syntax (#1099) 
* Add comment line for consistency

* Remove all functions.nf

* Remove include functions.nf and publishDir options

* Replace options.args3 with task.ext.args3 - 3 modules

* Replace options.args3 with task.ext.args3 - 17 modules

* Replace {task.cpus} with task.cpus

* Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with

* Add def args = task.ext.args line to all modules in script section

* Replace options.args with args and args_list

* Initialise args2 and args3 properly

* Replace container syntax

* Revert container changes for cellranger/mkref

* Replace getProcessName in all modules

* Replace getSoftwareName in all modules

* Unify modules using VERSION variable

* Replae options.suffix with task.ext.suffix

* Remove NF version restriction for CI

* Bump NF version in README

* Replace task.process.tokenize logic with task.process

* Minor tweaks to unify syntax in tests main.nf

* Add a separate nextflow.config for each module

* Transfer remaining module options to nextflow.config

* Remove addParams from tests main.nf

* Remove TODO statements

* Use -c to import module specific config

* Bump NF version to 21.10.3

* Fix tests for artic/minion

* Fix broken publishDir syntax

* Standardise and fix obvious failing module tests

* Remove kronatools to krona

* Comment out tags in subworkflow test.yml

* Fix failing module tests

* Add consistent indentation to nextflow.config

* Comment out subworklow definitions

* Fix kallistobustools/ref

* Fix rmarkdownnotebook

* Fix jupyternotebook

* Quote task.process

* Add plink2/vcf to pytest_modules.yml

* Remove NF_CORE_MODULES_TEST from pytest CI

* Fix more tests

* Move bacteroides_fragilis to prokaryotes folder

* Fix cooler merge tests

* Fix kallistobustools/count tests

* Fix kallistobustools/ref tests

* Update test_10x_1_fastq_gz file for kallistobustools/count tests

* Fix bcftools/query tests

* Fix delly/call tests

* Fix cooler/zoomify tests

* Fix csvtk/split tests

* Fix gatk4/intervallisttools tests

* Fix gatk4/variantfiltration

* Fix pydamage/filter tests

* Fix test data for unicycler

* Fix gstama/collapse module

* Fix leehom tests

* Fix metaphlan3 tests

* Fix pairtools/select tests

* Update nextflow.config

* Update nextflow.config

* feat: update syntax

* Fix arriba tests

* Fix more failing tests

* Update test syntax

* Remove comments from tests nextflow.config

* Apply suggestions from code review

* Fix kallistobustools/count module

* Update dumpsoftwareversions module

* Update custom/dumpsoftwareversions

* Add args2 to untar module

* Update leftover modules

* Remove last remaining addParams

Co-authored-by: JoseEspinosa <kadomu@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
2021-11-26 07:58:40 +00:00
..
abacas Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
adapterremoval Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
agrvate Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
allelecounter Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
amps Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
arriba Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
artic Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
assemblyscan Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ataqv/ataqv Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bakta Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bamaligncleaner Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bamtools/split Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bamutil/trimbam Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bandage/image Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bbmap Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bcftools Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bedtools Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bismark Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
blast Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bowtie Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bowtie2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bwa Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bwamem2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bwameth Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
cat Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
cellranger Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
checkm/lineagewf Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
chromap Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
clonalframeml Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
cmseq/polymut Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
cnvkit/batch Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
cooler Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
csvtk Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
custom Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
cutadapt Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
damageprofiler Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
dastool Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
dedup Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
deeptools Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
delly/call Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
diamond Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
dragonflye Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
dshbio Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ectyper Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
emmtyper Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ensemblvep Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
expansionhunter Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fargene Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fastani Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fastp Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fastqc Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fastqscan Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fasttree Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fgbio Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
filtlong Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
flash Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
freebayes Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gatk4 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
genmap Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
genrich Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gffread Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
glnexus Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
graphmap2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gstama Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gtdbtk/classifywf Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gubbins Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gunc Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gunzip Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
hicap Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
hifiasm Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
hisat2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
hmmcopy Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
hmmer/hmmalign Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
homer Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
idr Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
imputeme/vcftoprs Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
iqtree Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ismapper Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
isoseq3 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ivar Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
jupyternotebook Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
kallisto/index Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
kallistobustools Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
khmer/normalizebymedian Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
kleborate Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
kraken2/kraken2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
krona Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
last Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
leehom Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
lima Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
lissero Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
lofreq Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
macs2/callpeak Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
malt Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
maltextract Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
manta Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mapdamage2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mash/sketch Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mashtree Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
maxbin2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
medaka Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
megahit Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
meningotype Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
metabat2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
metaphlan3 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
methyldackel Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
minia Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
miniasm Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
minimap2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mlst Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mosdepth Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
msisensor Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mtnucratio Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
multiqc Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mummer Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
muscle Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
nanolyse Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
nanoplot Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ncbigenomedownload Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
nextclade Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ngmaster Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
nucmer Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
optitype Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pairix Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pairtools Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pangolin Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
paraclu Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pbbam/pbmerge Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pbccs Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
peddy Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
phantompeakqualtools Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
phyloflash Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
picard Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pirate Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
plasmidid Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
plink Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
plink2/vcf Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pmdtools/filter Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
porechop Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
preseq/lcextrap Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
prodigal Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
prokka Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pycoqc Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pydamage Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
qcat Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
qualimap Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
quast Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
racon Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
rapidnj Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
rasusa Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
raxmlng Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
rmarkdownnotebook Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
roary Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
rsem Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
rseqc Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
salmon Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
samblaster Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
samtools Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
scoary Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
seacr/callpeak Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
seqkit/split2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
seqsero2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
seqtk Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
sequenzautils Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
seqwish/induce Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
shovill Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
snpdists Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
snpeff Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
snpsites Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
sortmerna Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
spades Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
spatyper Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
sratools Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
staphopiasccmec Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
star Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
strelka Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
stringtie Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
subread/featurecounts Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
tabix Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
tbprofiler/profile Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
tiddit Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
trimgalore Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ucsc Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ultra/pipeline Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
umitools Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
unicycler Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
untar Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
unzip Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
variantbam Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
vcftools Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
yara Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00