James A. Fellows Yates 10502399ad Replaced param with input val channel (#595) ... * Replaced param with input val channel * Apply suggestions from code review Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review (missed one) * YAML lint Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>		2021-07-21 10:00:48 +02:00
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abacas	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
adapterremoval	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
allelecounter	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
artic	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
bandage/image	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
bbmap/bbduk	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
bcftools	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
bedtools	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
bismark	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
blast	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
bowtie	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
bowtie2	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
bwa	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
bwamem2	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
bwameth	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
cat/fastq	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
cnvkit	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
cooler	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
cutadapt	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
damageprofiler	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
deeptools	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
delly/call	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
dshbio	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
ensemblvep	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
fastp	Replaced param with input val channel (#595)	2021-07-21 10:00:48 +02:00
fastqc	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
fasttree	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
fgbio	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
flash	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
gatk4	fix: update to gatk4.2.0.0 (#575)	2021-07-16 11:26:28 +02:00
genmap	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
gffread	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
graphmap2	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
gubbins	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
gunzip	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
hifiasm	Add hifiasm module (#596)	2021-07-20 21:50:22 +01:00
hisat2	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
hmmer/hmmalign	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
homer/annotatepeaks	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
iqtree	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
ivar	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
kallisto/index	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
kallistobustools	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
kraken2/kraken2	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
last	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
lib	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
lofreq	fix: lofreq/callparallel missing arg (#562) (#586)	2021-07-19 09:19:27 +01:00
macs2/callpeak	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
mash/sketch	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
metaphlan3	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
methyldackel	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
minia	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
minimap2	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
mosdepth	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
msisensor	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
multiqc	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
muscle	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
nanolyse	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
nanoplot	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
nextclade	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
optitype	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
pairix	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
pairtools	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
pangolin	Bump Pangolin to 3.1.7 (#593)	2021-07-20 12:25:36 +01:00
phantompeakqualtools	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
picard	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
plasmidid	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
preseq/lcextrap	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
prodigal	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
prokka	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
pycoqc	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
qcat	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
qualimap	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
quast	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
rapidnj	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
rasusa	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
raxmlng	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
rsem	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
rseqc	Fix tyop in output for rseqc/junctionannotation (#592)	2021-07-20 11:27:47 +01:00
salmon	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
samtools	Add samtools ampliconclip (#590)	2021-07-20 21:31:31 +01:00
seacr/callpeak	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
seqkit/split2	fix: update seqkit to 0.16.0 (#581)	2021-07-16 11:54:21 +02:00
seqtk	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
sequenzautils	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
seqwish/induce	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
shovill	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
snpeff	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
snpsites	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
sortmerna	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
spades	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
star	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
strelka/germline	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
stringtie	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
subread/featurecounts	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
tabix	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
tiddit/sv	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
trimgalore	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
ucsc	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
umitools	Add --paired flag to umitools dedup and bump to 1.1.2 (#583)	2021-07-16 14:21:08 +01:00
unicycler	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
untar	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
vcftools	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00
yara	Rename software/ directory to modules/ to re-organise module structure (#567)	2021-07-07 10:10:18 +01:00