Gisela Gabernet 22eaefe583 Add module kallisto/index (#357) ... * add kallisto index module * update kallisto module * add kallisto module tests * update kallisto index test.yml * update test data paths * fix version * fix kallisto index test yml * remove TODOs * Update software/kallisto/index/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/kallisto/index/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * output folder instead Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>		2021-03-24 12:25:39 +00:00
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adapterremoval	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
allelecounter	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
bandage/image	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
bcftools	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
bedtools	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
bismark	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
blast	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
bowtie	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
bowtie2	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
bwa	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
bwamem2	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
bwameth	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
cat/fastq	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
cnvkit	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
cutadapt	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
dsh	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
fastp	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
fastqc	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
flash	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
gatk4	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
gffread	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
gunzip	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
homer/annotatepeaks	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
ivar	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
kallisto/index	Add module kallisto/index (#357)	2021-03-24 12:25:39 +00:00
kraken2/run	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
methyldackel	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
minia	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
minimap2/align	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
mosdepth	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
multiqc	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
optitype	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
pangolin	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
picard	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
preseq/lcextrap	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
prodigal	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
prokka	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
qualimap/bamqc	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
quast	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
salmon	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
samtools	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
seacr/callpeak	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
seqkit/split2	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
sequenzautils/gcwiggle	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
seqwish/induce	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
shovill	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
spades	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
star	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
strelka/germline	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
stringtie	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
tabix	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
tiddit/sv	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
trimgalore	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
ucsc	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
unicycler	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
untar	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00
vcftools	Re-organise all test data (#354)	2021-03-24 09:53:41 +00:00