..
abacas
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
adapterremoval
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
agrvate
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
allelecounter
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
amps
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
arriba
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
artic
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
assemblyscan
add new assembly scan module ( #971 )
2021-10-29 10:01:23 +02:00
bamaligncleaner
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
bamtools /split
Update module: bamtools/split ( #885 )
2021-10-23 19:39:27 +01:00
bandage /image
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
bbmap
Fix bug with SortMeRna not working on a single db file ( #788 )
2021-10-04 12:37:21 +01:00
bcftools
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
bedtools
bedtools/genomecov updated to allow for providing a per-sample scale factor ( #799 )
2021-10-28 17:50:25 +01:00
bismark
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
blast
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
bowtie
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
bowtie2
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
bwa
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
bwamem2
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
bwameth
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
cat
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
cellranger
new module cellranger mkref ( #896 )
2021-10-28 13:33:57 +02:00
checkm /lineagewf
New module: checkm/lineagewf ( #899 )
2021-10-26 21:54:10 +01:00
chromap
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
cnvkit
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
cooler
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
csvtk /concat
patch output extension in csvtk/concat ( #797 )
2021-10-05 22:15:08 +01:00
custom /dumpsoftwareversions
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
cutadapt
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
damageprofiler
fix: reduce number of required input files for damage profiler ( #612 )
2021-10-20 10:02:30 +02:00
dedup
Add module: dedup ( #907 )
2021-10-28 12:10:21 +02:00
deeptools
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
delly /call
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
diamond
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
dragonflye
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
dshbio
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
ensemblvep
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
expansionhunter
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
fastani
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
fastp
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
fastqc
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
fasttree
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
fgbio
Rewritten module fgbio/fastqtobam ( #916 )
2021-10-27 19:06:06 +02:00
filtlong
add filtlong ( #919 )
2021-10-27 17:00:11 +02:00
flash
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
freebayes
New module: freebayes ( #818 )
2021-10-20 15:19:31 +02:00
gatk4
Add gatk4/estimatelibrarycomplexity ( #965 )
2021-10-28 17:49:27 +02:00
genmap
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
genrich
New module: genrich ( #877 )
2021-10-22 12:22:02 +02:00
gffread
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
glnexus
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
graphmap2
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
gstama
New module: gstama/merge ( #813 )
2021-10-23 19:00:39 +01:00
gtdbtk /classifywf
Add gtdbtk/classifywf module ( #765 )
2021-10-05 21:23:01 +01:00
gubbins
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
gunzip
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
hicap
add hicap module ( #772 )
2021-10-05 21:42:09 +01:00
hifiasm
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
hisat2
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
hmmer /hmmalign
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
homer
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
iqtree
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
ismapper
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
isoseq3
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
ivar
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
jupyternotebook
Notebook modules ( #617 )
2021-10-24 20:51:56 +02:00
kallisto /index
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
kallistobustools
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
kleborate
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
kraken2 /kraken2
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
last
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
lib
Bulk update modules to use versions.yml ( #739 )
2021-09-27 09:41:24 +01:00
lima
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
lofreq
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
macs2 /callpeak
Remove def software lines and emit versions channel as plural ( #780 )
2021-10-01 14:04:56 +01:00
malt
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
maltextract
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
manta
adding new manta/germline + manta/tumoronly modules ( #906 )
2021-10-27 18:24:48 +02:00
mash /sketch
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
mashtree
add mashtree module ( #767 )
2021-10-05 21:27:30 +01:00
maxbin2
New module: maxbin2 ( #895 )
2021-10-26 22:07:33 +01:00
megahit
Add MEGAHIT ( #810 )
2021-10-12 16:06:06 +01:00
metaphlan3
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
methyldackel
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
minia
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
minimap2
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
mlst
added classic mlst module ( #742 )
2021-10-05 20:49:46 +01:00
mosdepth
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
msisensor
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
multiqc
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
muscle
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
nanolyse
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
nanoplot
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
nextclade
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
optitype
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
pairix
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
pairtools
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
pangolin
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
paraclu
add paraclu ( #909 )
2021-10-27 15:48:49 +02:00
pbbam /pbmerge
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
pbccs
Update of pbccs ( #835 )
2021-10-23 19:09:41 +01:00
phantompeakqualtools
Remove def software lines and emit versions channel as plural ( #780 )
2021-10-01 14:04:56 +01:00
picard
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
pirate
add pirate module ( #777 )
2021-10-05 22:28:25 +01:00
plasmidid
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
plink /vcf
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
porechop
add porechop module ( #914 )
2021-10-28 13:21:36 +02:00
preseq /lcextrap
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
prodigal
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
prokka
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
pycoqc
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
pydamage
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
qcat
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
qualimap
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
quast
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
rapidnj
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
rasusa
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
raxmlng
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
rmarkdownnotebook
Notebook modules ( #617 )
2021-10-24 20:51:56 +02:00
roary
add roary module ( #776 )
2021-10-05 22:08:47 +01:00
rsem
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
rseqc
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
salmon
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
samtools
Bam2fq ( #958 )
2021-10-29 10:46:34 +02:00
seacr /callpeak
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
seqkit /split2
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
seqtk
New module seqtk/mergepe ( #951 )
2021-10-28 16:53:33 +02:00
sequenzautils
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
seqwish /induce
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
shovill
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
snpdists
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
snpeff
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
snpsites
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
sortmerna
Fix sortmerna docker container pointer ( #791 )
2021-10-05 12:05:37 +02:00
spades
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
spatyper
add spatyper module ( #784 )
2021-10-05 22:21:35 +01:00
sratools
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
staphopiasccmec
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
star
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
strelka
Update strelka, by enabling BP if Manta candidates are present ( #923 )
2021-10-27 17:49:54 +02:00
stringtie
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
subread /featurecounts
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
tabix
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
tiddit
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
trimgalore
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
ucsc
New module: ucsc/liftover ( #868 )
2021-10-21 18:04:15 +02:00
umitools
added meta.yml for umitools ( #860 )
2021-10-23 17:30:10 +01:00
unicycler
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
untar
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
unzip
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
variantbam
Backfill software licenses meta ( #876 )
2021-10-22 15:39:54 -07:00
vcftools
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
yara
Update versions key in meta.yml for all modules ( #787 )
2021-10-03 08:20:26 +01:00
4b8c7ac7bd