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nf-core_modules/software
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Jose Espinosa-Carrasco e621f78757
Update salmon/quant to provide '--libType A' option (#536) 
* Update salmon/quant to provide '--libType A' option

* Modify lib_type description to  be a string

* Update tests

* lyb_type can be explicitly overwrite

* Update main.nf

* Update main.nf

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-06-17 15:13:47 +02:00
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abacas Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
adapterremoval Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
allelecounter Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
artic Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
bandage/image Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
bbmap/bbduk Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
bcftools Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
bedtools Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
bismark Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
blast Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
bowtie Fix number of cpus for modules with piped tools (#499) 2021-05-18 09:52:00 +02:00
bowtie2 Fix number of cpus for modules with piped tools (#499) 2021-05-18 09:52:00 +02:00
bwa Fix number of cpus for modules with piped tools (#499) 2021-05-18 09:52:00 +02:00
bwamem2 Fix number of cpus for modules with piped tools (#499) 2021-05-18 09:52:00 +02:00
bwameth Fix number of cpus for modules with piped tools (#499) 2021-05-18 09:52:00 +02:00
cat/fastq Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
cnvkit Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
cooler Cooler digest (#517) 2021-06-09 11:39:22 +02:00
cutadapt Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
deeptools Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
dshbio Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
fastp Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
fastqc Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
fasttree Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
fgbio Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
flash Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
gatk4 Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
genmap add genmap/mappability (#509) 2021-05-25 22:12:10 +01:00
gffread Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
graphmap2 Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
gubbins Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
gunzip Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
hisat2 Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
hmmer/hmmalign Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
homer/annotatepeaks Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
iqtree Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
ivar Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
kallisto/index Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
kallistobustools Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
kraken2/run Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
last Update last module (#533) 2021-06-14 12:27:27 +01:00
lib Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
macs2/callpeak Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
mash/sketch Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
methyldackel Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
minia Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
minimap2 Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
mosdepth Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
msisensor Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
multiqc Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
nanolyse Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
nanoplot Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
nextclade Bump new nextclade version (0.14.4) (#532) 2021-06-09 14:12:21 +01:00
optitype Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
pairix add software/pairix (#508) 2021-05-25 21:22:57 +01:00
pairtools Pairtools restrict (#522) 2021-06-10 19:39:35 +02:00
pangolin Pangolin bump new version (3.0.5) (#531) 2021-06-09 14:11:59 +01:00
phantompeakqualtools Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
picard Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
plasmidid Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
preseq/lcextrap Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
prodigal Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
prokka Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
pycoqc Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
qcat Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
qualimap Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
quast Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
rapidnj Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
rasusa Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
raxmlng Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
rsem Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
rseqc Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
salmon Update salmon/quant to provide '--libType A' option (#536) 2021-06-17 15:13:47 +02:00
samtools Update samtools from 1.10 to 1.12 (#530) 2021-06-07 13:07:32 +02:00
seacr/callpeak Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
seqkit/split2 Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
seqtk Feat seqtk update (#503) 2021-06-14 12:23:15 +01:00
sequenzautils Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
seqwish/induce Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
shovill Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
snpsites Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
sortmerna Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
spades Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
star Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
strelka/germline Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
stringtie Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
subread/featurecounts Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
tabix Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
tiddit/sv Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
trimgalore Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
ucsc add additional ucsc tools (#506) 2021-05-20 15:39:33 -04:00
umitools Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
unicycler Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
untar Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
vcftools Update comments with new style (#497) 2021-05-12 14:56:46 +01:00
yara Update comments with new style (#497) 2021-05-12 14:56:46 +01:00