..
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
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
amps
add Amps ( #768 )
2021-09-30 12:54:16 +02:00
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
assemblyscan
add new assembly scan module ( #971 )
2021-10-29 10:01:23 +02:00
bamaligncleaner
Add module: bamaligncleaner ( #676 )
2021-09-15 10:31:49 +02:00
bamtools /split
Update module: bamtools/split ( #885 )
2021-10-23 19:39:27 +01:00
bandage /image
Fix version commands ( #749 )
2021-09-27 22:10:37 +01:00
bbmap
Add bbmap/bbsplit module ( #771 )
2021-09-30 13:37:35 +01:00
bcftools
Add bcftools/index ( #812 )
2021-10-13 10:40:04 +02:00
bedtools
Bedtools sort add extension choice input ( #984 )
2021-10-29 13:22:17 +01:00
bismark
Fix version commands ( #749 )
2021-09-27 22:10:37 +01:00
blast
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
bowtie
Fix version commands ( #749 )
2021-09-27 22:10:37 +01:00
bowtie2
Fix version commands ( #749 )
2021-09-27 22:10:37 +01:00
bwa
Fix more version commands ( #750 )
2021-09-28 06:56:27 +01:00
bwamem2
Fix version commands ( #749 )
2021-09-27 22:10:37 +01:00
bwameth
Fix more version commands ( #750 )
2021-09-28 06:56:27 +01:00
cat
Fix flash and cat/fastq modules ( #759 )
2021-09-28 21:14:11 +01:00
cellranger /mkref
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
Chromap Module ( #659 )
2021-09-15 17:20:55 +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
csvtk /concat
add csvtk/concat module ( #785 )
2021-10-05 21:48:47 +01:00
custom /dumpsoftwareversions
Correct parsing versions with trailing zeros ( #795 )
2021-10-06 08:16:36 +02:00
cutadapt
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
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
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
delly /call
few version and test data config fixes ( #758 )
2021-09-28 20:42:04 +01:00
diamond
Diamond ( #710 )
2021-09-23 09:13:04 +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
fastani
module fastani ( #695 )
2021-09-21 20:20:26 +01:00
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
Fgbio group reads by umi ( #952 )
2021-10-29 14:00:54 +02:00
filtlong
add filtlong ( #919 )
2021-10-27 17:00:11 +02:00
flash
Fix flash and cat/fastq modules ( #759 )
2021-09-28 21:14:11 +01:00
freebayes
Check only for file being generated ( #879 )
2021-10-21 11:32:05 +02:00
gatk4
Update to allow cram + update needed to use the gatk4 modules in sarek ( #976 )
2021-10-29 13:01:05 +02:00
genmap
Fix more version commands ( #750 )
2021-09-28 06:56:27 +01:00
genrich
New module: genrich ( #877 )
2021-10-22 12:22:02 +02:00
gffread
Fix bug in gffread ( #686 )
2021-09-15 19:55:08 +01:00
glnexus
Add glnexus ( #729 )
2021-09-22 13:31:01 +01:00
graphmap2
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
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
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
hicap
add hicap module ( #772 )
2021-10-05 21:42:09 +01:00
hifiasm
few version and test data config fixes ( #758 )
2021-09-28 20:42:04 +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
Module new version reporting fixes ( #753 )
2021-09-28 10:51:19 +01:00
ismapper
add ismapper module ( #773 )
2021-10-05 21:55:41 +01:00
isoseq3
Update isoseq3/cluster ( #856 )
2021-10-14 11:07:53 +01:00
ivar
Fix more version commands ( #750 )
2021-09-28 06:56:27 +01:00
jupyternotebook
Notebook modules ( #617 )
2021-10-24 20:51:56 +02:00
kallisto /index
Fix yml ver ( #756 )
2021-09-28 18:33:07 +02:00
kallistobustools
Fix yml ver ( #756 )
2021-09-28 18:33:07 +02:00
khmer /normalizebymedian
Khmer normalizebymedian ( #985 )
2021-10-29 13:23:34 +02:00
kleborate
Add module kleborate ( #711 )
2021-09-21 20:45:42 +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
lima
New module: LIMA ( #719 )
2021-09-27 16:14:35 +01:00
lofreq
fix: lofreq/callparallel missing arg ( #562 ) ( #586 )
2021-07-19 09:19:27 +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
manta
adding new manta/germline + manta/tumoronly modules ( #906 )
2021-10-27 18:24:48 +02:00
mash /sketch
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +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
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
methyldackel
Fix version commands ( #749 )
2021-09-27 22:10:37 +01:00
minia
Fix version commands ( #749 )
2021-09-27 22:10:37 +01:00
minimap2
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
mlst
added classic mlst module ( #742 )
2021-10-05 20:49:46 +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
Update Nextclade to output all files by default ( #638 )
2021-07-28 19:49:50 +01:00
optitype
Updating test file for optitype ( #782 )
2021-10-28 14:24:52 +02:00
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
paraclu
add paraclu ( #909 )
2021-10-27 15:48:49 +02:00
pbbam /pbmerge
New module: pbbam/pbmerge ( #752 )
2021-10-05 23:16:45 +01:00
pbccs
Update of pbccs ( #835 )
2021-10-23 19:09:41 +01:00
picard
Module new version reporting fixes ( #753 )
2021-09-28 10:51:19 +01:00
pirate
add pirate module ( #777 )
2021-10-05 22:28:25 +01:00
plasmidid
Fix yml ver ( #756 )
2021-09-28 18:33:07 +02:00
plink /vcf
Adding plink/vcf module ( #656 )
2021-09-14 08:51:40 +02:00
porechop
add porechop module ( #914 )
2021-10-28 13:21:36 +02:00
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
pydamage
Pydamage analyzer update ( #863 )
2021-10-18 15:24:49 +02:00
qcat
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
qualimap /bamqc
Fix more version commands ( #750 )
2021-09-28 06:56:27 +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
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
Update checksum modules using human GTF ( #900 )
2021-10-26 23:09:04 +01:00
rseqc
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
salmon
Fix version commands ( #749 )
2021-09-27 22:10:37 +01:00
samtools
Update to allow cram + update needed to use the gatk4 modules in sarek ( #976 )
2021-10-29 13:01:05 +02:00
seacr /callpeak
I accidently deleted a branch before the PR merged for PR 800 ( #881 )
2021-10-21 12:28:59 +01:00
seqkit /split2
Fix version commands: round 3 ( #754 )
2021-09-28 14:37:47 +01:00
seqtk
New module seqtk/mergepe ( #951 )
2021-10-28 16:53:33 +02:00
sequenzautils
Fix version commands: round 3 ( #754 )
2021-09-28 14:37:47 +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
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
spades
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
spatyper
add spatyper module ( #784 )
2021-10-05 22:21:35 +01:00
sratools
Add a new module for fasterq-dump ( #807 )
2021-10-12 14:20:58 +01:00
staphopiasccmec
add staphopia-sccmec module ( #702 )
2021-09-15 17:24:11 +01:00
star
Update checksum modules using human GTF ( #900 )
2021-10-26 23:09:04 +01:00
strelka
Update strelka, by enabling BP if Manta candidates are present ( #923 )
2021-10-27 17:49:54 +02:00
stringtie
Update checksum modules using human GTF ( #900 )
2021-10-26 23:09:04 +01:00
subread /featurecounts
fix more ver yml ( #757 )
2021-09-28 20:25:10 +01:00
tabix
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
tiddit
Add TIDDIT cov ( #822 )
2021-10-13 12:59:35 +02:00
trimgalore
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
ucsc
New module: ucsc/liftover ( #868 )
2021-10-21 18:04:15 +02:00
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
Unzip update ( #730 )
2021-09-22 11:02:32 +01:00
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
fix more ver yml ( #757 )
2021-09-28 20:25:10 +01:00
2959b4ba07