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nf-core_modules/tests/modules
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Regina Hertfelder Reynolds 1b24005f07
Add bcl2fastq2 to cellranger dockerfile (#1115) 
* refactor: add bcl2fastq to cellranger dockerfile

bcl2fastq required for the cellranger mkfastq module and was therefore
added to the cellranger dockerfile. Further, cellranger was updated to
the latest version, 6.1.2., with naming and containers across
cellranger modules updated accordingly.

* chore: add bcl2fastq zip to .gitignore

* style: fix code linting error

* test(cellranger): Add tiles to mkfastq

* additional dockerfile for mkfastq

* update readme and dockerfiles

* update readme

* fix: update container for mkfastq

* docs: correct typos in readme

* test: update md5sum following cellranger update

* test: update md5sum following cellranger update

* fix: new line for external args in mkfastq

* test: update mkfastq tiles argument

* test: comment out mkfastq tests until smaller test data found

* test: stub-run mkfastq test until smaller test data found

* test: fix incorrect file path for mkfastq

Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
2022-01-25 19:58:22 +01:00
..
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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
bcftools Remove bcftools and ivar module customisations (#1217) 2022-01-18 16:04:56 +00:00
bedtools Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Bump software versions for viralrecon modules (#1198) 2022-01-07 17:52:39 +00:00
bwa Add new boolean sort_bam as input to be able to chose between sort and view in bwamem and bwamem2mem (#1125) 2021-12-08 14:31:27 +00:00
bwamem2 Add new boolean sort_bam as input to be able to chose between sort and view in bwamem and bwamem2mem (#1125) 2021-12-08 14:31:27 +00:00
bwameth Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
cat Editing the CAT/CAT module to handle single files (#1196) 2022-01-06 16:41:36 +00:00
cellranger Add bcl2fastq2 to cellranger dockerfile (#1115) 2022-01-25 19:58:22 +01:00
checkm/lineagewf Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
chromap Bump version 0.1.5 to chromap/chromap (#1223) 2022-01-20 19:00:20 +01:00
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
deepvariant Update version & add intervals usage (#1214) 2022-01-17 16:40:31 +01:00
delly/call Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
diamond Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
dragmap feat: update dragmap to follow new bwa/mem + bwamem2/mem logic (#1146) 2021-12-08 23:19:37 +01:00
dragonflye Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
dshbio Update dsh-bio to version 2.0.7, add support for compressed GFA 1.0 format (#1207) 2022-01-17 09:24:40 +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 greatly simplify syntax (#1121) 2021-12-07 11:18:12 +01:00
expansionhunter Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fargene takes gunzip out of fargene main.nf (#1090) 2021-11-29 14:32:23 +01:00
fastani Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fastp Bump software versions for viralrecon modules (#1198) 2022-01-07 17:52:39 +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 Added UMI sub-workflow (#1098) 2021-12-09 11:16:40 +01:00
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 Log4j again (#1202) 2022-01-12 13:55:54 +01:00
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 Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 hmmcopy/mapCounter (#1175) 2021-12-17 15:39:50 +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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
ivar Remove bcftools and ivar module customisations (#1217) 2022-01-18 16:04:56 +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 Fix kleborate inputs (#1172) 2021-12-22 11:39:35 +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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
leehom Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
lima Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
lissero Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
lofreq Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
macrel/contigs Add new module macrel/contigs (#1109) 2021-12-09 13:17:50 +01:00
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 add module for mash dist (#1193) 2022-01-04 17:29:49 +01:00
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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 metabat2 output channels and compression (#1111) 2021-12-09 15:00:32 +01:00
metaphlan3 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Add nextclade/datasetget and nextclade/run modules (#1210) 2022-01-17 11:46:15 +01:00
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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
pangolin Bump software versions for viralrecon modules (#1198) 2022-01-07 17:52:39 +00:00
paraclu Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pbbam/pbmerge Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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
phyloflash Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
picard Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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/bamqc 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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Provide BAI when running rseqc/tin (#1177) 2021-12-17 10:00:09 +00:00
salmon Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
samblaster Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
samtools Bump software versions for viralrecon modules (#1198) 2022-01-07 17:52:39 +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 version & prefix (#1120) 2021-12-07 10:22:32 +01:00
seqsero2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
seqtk Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
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 greatly simplify syntax (#1121) 2021-12-07 11:18:12 +01:00
snpsift/split Added new module snpsift/split (#1031) 2021-12-17 09:08:14 +01:00
snpsites 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 ucsc/wigtobigwig: add meta map (#1199) 2022-01-11 21:31:37 +00:00
ultra/pipeline Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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
vcfanno New module/vcfanno (#1204) 2022-01-20 08:46:31 +00:00
vcflib/vcfuniq Add new vcflib/vcfuniq module (#1208) 2022-01-14 18:18:11 +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