..
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
agrvate
module for agrvate ( #693 )
2021-09-16 12:42:23 +02:00
allelecounter
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
arriba
Added module arriba ( #611 )
2021-07-22 15:19:42 +01:00
artic
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
bamaligncleaner
Add module: bamaligncleaner ( #676 )
2021-09-15 10:31:49 +02:00
bandage /image
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
bbmap
Module to map reads with BBMap ( #717 )
2021-09-20 11:27:34 +02:00
bcftools
Add bcftools/query module ( #670 )
2021-09-14 09:19:01 +02:00
bedtools
Add bedtools/makewindows module ( #658 )
2021-09-07 14:36:06 -04:00
bismark
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
blast
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
bowtie
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
bowtie2
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
bwa
update: BWA/ALN ( #653 )
2021-08-17 15:55:54 +02:00
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
Refactor cat/cat module ( #723 )
2021-09-21 11:17:00 +01:00
chromap
Chromap patch ( #712 )
2021-09-16 09:23:07 +01:00
cnvkit
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
cooler
update typos. change quote from ' to ". ( #652 )
2021-08-16 11:57:22 +02:00
cutadapt
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
damageprofiler
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
deeptools
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
delly /call
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
dragonflye
add module for dragonflye ( #633 )
2021-08-16 11:51:30 +02:00
dshbio
Add dsh-bio export-segments module ( #631 )
2021-08-17 15:53:41 +02:00
ensemblvep
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
expansionhunter
Expansionhunter ( #666 )
2021-08-16 17:47:42 +02:00
fastp
enhance module fastp: add save_merged ( #598 ) ( #614 )
2021-07-23 10:44:00 +01:00
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
Update for mutect2: add output channel for stats file ( #716 )
2021-09-17 09:56:56 +01:00
genmap
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
gffread
Fix bug in gffread ( #686 )
2021-09-15 19:55:08 +01:00
graphmap2
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
gubbins
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +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
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
hmmer /hmmalign
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
homer
Homer Modules ( #75 )
2021-09-08 15:40:34 +00:00
iqtree
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +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
Fix kallistobustools version extraction ( #691 )
2021-09-15 17:56:12 +01:00
kraken2 /kraken2
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
last
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +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
malt
update: MALT build version bump ( #699 )
2021-09-15 16:46:29 +01:00
maltextract
add: MALTEXTRACT ( #725 )
2021-09-21 19:57:27 +01:00
mash /sketch
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
metaphlan3
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
methyldackel
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
minia
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
minimap2
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
mosdepth
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
msisensor
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
multiqc
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +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
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
nextclade
Update Nextclade to output all files by default ( #638 )
2021-07-28 19:49:50 +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
Update pangolin to 3.1.11 ( #721 )
2021-09-20 19:59:05 +01:00
pbccs
new module: pbccs ( #688 )
2021-09-16 11:48:18 +01:00
phantompeakqualtools
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
picard
modify markduplicates module ( #681 )
2021-09-15 11:02:28 +02:00
plasmidid
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
plink /vcf
Adding plink/vcf module ( #656 )
2021-09-14 08:51:40 +02:00
preseq /lcextrap
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
prodigal
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +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
pydamage
Add PyDamage filter ( #713 )
2021-09-16 15:05:49 +02:00
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
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
rsem
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
rseqc
Require r-base>=3.5 for RSeqC Conda envs ( #654 )
2021-08-05 18:59:56 +01:00
salmon
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
samtools
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +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
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
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
Update seqwish reported version to match bioconda version. ( #678 )
2021-08-26 15:33:38 -05:00
shovill
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
snpdists
module: snp-dists ( #697 )
2021-09-15 16:36:49 +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
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
staphopiasccmec
add staphopia-sccmec module ( #702 )
2021-09-15 17:24:11 +01:00
star
Added PL tag in read group information for downstream analysis ( #649 )
2021-08-04 11:16:51 +02:00
strelka /germline
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
stringtie
Add option -p to set the # of cpus on stringtie ( #601 )
2021-07-21 15:38:40 +02:00
subread /featurecounts
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
tabix
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
tiddit /sv
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
trimgalore
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +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
unzip
module: unzip ( #642 )
2021-08-02 09:40:57 +02:00
variantbam
Add variantbam ( #618 )
2021-07-26 19:07:29 +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
7830a4a80c