millironx/nf-core_modules
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GCJMackenzie 61376425fb
BugFix: add missing tbi output channel to genotypeGVCFs (#1153) 
* initial commit to setup branch

* workflow finished

* Update nextflow.config

* tumour to tumor, getpileup passed as nomral and tumor

* paired_somatic renamed to tumor_normal_somatic

* Apply suggestions from code review

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* updated index names in meta.yml

* changed index file names in main script and test

* Apply suggestions from code review

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* Apply suggestions from code review

* fixed bug from changes

* Apply suggestions from code review

* modified yml to allow new subworkflow testing

* Update test.yml

* Update test.yml

* added output channel for tbi files, tweaked method of adding blank inputs for gendb tests

* Update main.nf

* Update main.nf

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-12-14 16:10:08 +00:00
..
abacas Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
adapterremoval Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
agrvate Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
allelecounter Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
amps Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
arriba Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
artic Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
assemblyscan Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
ataqv/ataqv Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
bakta Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
bamaligncleaner Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
bamtools/split Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
bamutil/trimbam Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
bandage/image Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
bedtools Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
bismark Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
blast Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
bowtie Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
bowtie2 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
cat Stage fastq for concat in subfolders to avoid name collision issue (#1107) 2021-12-13 19:18:27 +00:00
cellranger Add Cell Ranger mkfastq, mkgtf, and count (#979) 2021-12-02 14:27:20 +00:00
checkm/lineagewf Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
chromap Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
clonalframeml Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
cmseq/polymut Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
cnvkit/batch Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
cooler Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
csvtk Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
custom Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
cutadapt Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
damageprofiler Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
dastool Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
dedup Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
deeptools Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
delly/call Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
ectyper Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
emmtyper Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
ensemblvep greatly simplify syntax (#1121) 2021-12-07 11:18:12 +01:00
expansionhunter Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
fargene Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
fastani Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
fastp Update meta.yml by fixing html pattern expected (#1113) 2021-12-05 21:45:09 +00:00
fastqc Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
fastqscan Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
fasttree Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fgbio Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
filtlong Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
flash Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
freebayes Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
gatk4 BugFix: add missing tbi output channel to genotypeGVCFs (#1153) 2021-12-14 16:10:08 +00:00
genmap Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
genrich Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
gffread Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
glnexus Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
graphmap2 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
gunzip Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
hicap Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
hifiasm Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
hisat2 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
hmmcopy Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
hmmer/hmmalign Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
homer Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
idr Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
imputeme/vcftoprs Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
iqtree Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ismapper Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
jupyternotebook Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
kallisto/index Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
kallistobustools Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
khmer/normalizebymedian Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
kleborate Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
kraken2/kraken2 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
lima Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
lissero Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
mapdamage2 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
mash/sketch Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
mashtree Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
maxbin2 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
meningotype Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
minia Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
mlst Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
mosdepth Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
msisensor Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
mtnucratio Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
multiqc Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mummer Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
muscle Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
nextclade Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
ngmaster Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
nucmer Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
optitype Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
paraclu Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
peddy Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
phantompeakqualtools Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
phyloflash Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
plasmidid Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
pmdtools/filter Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
prodigal Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
prokka Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
pycoqc Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pydamage Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
qcat Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
qualimap Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
quast Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
racon Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
roary Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
rsem Fix transcriptome staging issues on DNAnexus for rsem/prepareference (#1163) 2021-12-13 14:10:29 +00:00
rseqc Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
salmon Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
samblaster Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
samtools Revert PR #1147 (#1166) 2021-12-13 16:15:20 +00:00
scoary Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
seacr/callpeak Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
seqkit/split2 Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
seqsero2 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
seqtk Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
sequenzautils Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
seqwish/induce Update seqwish to version 0.7.2 (#1144) 2021-12-09 11:07:47 -06:00
shovill Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
snpdists Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
snpeff greatly simplify syntax (#1121) 2021-12-07 11:18:12 +01:00
snpsites Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
sortmerna Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
spades Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
spatyper Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
sratools Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
staphopiasccmec Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
star Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
strelka Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
stringtie Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
subread/featurecounts Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
tabix feat: emited channel should be gz_tbi and not only tbi (#1118) 2021-12-07 10:12:58 +01:00
tbprofiler/profile Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
tiddit Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
trimgalore Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
ucsc Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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
umitools Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
unicycler Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +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 Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
vcftools Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
yara Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00