..
abacas
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
adapterremoval
Fix read indexing in AdapterRemoval module ( #1051 )
2021-11-10 12:21:12 +00:00
agrvate
module for agrvate ( #693 )
2021-09-16 12:42:23 +02:00
allelecounter
Add cram support to Allelecounter module ( #1013 )
2021-11-02 17:00:25 +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
ataqv /ataqv
Add new module 'ataqv/ataqv' ( #998 )
2021-11-15 12:51:40 +00:00
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
bamutil /trimbam
Add bamutil/trimbam ( #1060 )
2021-11-15 16:44:12 +00:00
bandage /image
Fix version commands ( #749 )
2021-09-27 22:10:37 +01:00
bbmap
Add log to output from bbmap/align ( #1050 )
2021-11-10 10:27:52 +00:00
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
Bwa index ( #1040 )
2021-11-15 11:26:01 +00:00
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
clonalframeml
add clonalframeml module ( #974 )
2021-11-15 19:43:53 +00:00
cmseq /polymut
Add new module: cmseq/polymut ( #918 )
2021-11-09 16:12:51 +01:00
cnvkit
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
cooler
Cooler cload ( #634 )
2021-11-15 21:43:55 +00:00
csvtk
Added new module csvtk/split ( #1014 )
2021-11-15 18:29:55 +00:00
custom
Add module get_chrom_sizes ( #1063 )
2021-11-15 19:22:12 +00:00
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
emmtyper
add emmtyper module ( #1028 )
2021-11-08 20:43:15 +01:00
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
fargene
new module fargene ( #1068 )
2021-11-15 16:42:48 +00:00
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
fastqscan
add module for fastq-scan ( #935 )
2021-11-15 15:41:36 +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
fix remove md5sum check ( #1017 )
2021-11-03 11:41:12 +01:00
gatk4
Update in GATK4 variantfiltration: Added vcf_index to vcf tuple; output to vcf.gz format. ( #1083 )
2021-11-18 21:47:40 +01:00
genmap
Fix more version commands ( #750 )
2021-09-28 06:56:27 +01:00
genrich
Refactor genrich to avoid params in main ( #981 )
2021-10-29 16:37:39 +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
Update: gstama/collapse ( #1057 )
2021-11-11 14:57:55 +00:00
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
gunc
New module: gunc run (+ gunc downloaddb) ( #880 )
2021-11-03 17:01:23 +01:00
gunzip
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
hicap
[fix] hicap module allow optional outputs ( #937 )
2021-11-16 09:23:07 +00:00
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
hmmcopy
readcounter module for hmmcopy ( #1001 )
2021-11-02 11:01:13 +00:00
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
idr
Add IDR module ( #908 )
2021-10-30 10:52:13 +02:00
imputeme /vcftoprs
Imputeme ( #882 )
2021-11-05 10:25:54 +01:00
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
kronatools
add Kronatools KTImportTaxonomy ( #928 )
2021-11-15 17:40:46 +00:00
last
nf-core modules bump-versions for all modules ( #630 )
2021-07-28 09:10:44 +01:00
leehom
Add leehom module ( #1052 )
2021-11-15 15:26:06 +01:00
lima
New module: LIMA ( #719 )
2021-09-27 16:14:35 +01:00
lissero
add lissero module ( #1026 )
2021-11-08 20:52:07 +01:00
lofreq
fix: lofreq/callparallel missing arg ( #562 ) ( #586 )
2021-07-19 09:19:27 +01:00
macs2 /callpeak
Macs2 calllpeak ( #1038 )
2021-11-15 18:17:40 +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
mapdamage2
Add new module Mapdamage2 ( #975 )
2021-11-09 14:05:23 +01:00
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
medaka
Add Medaka module ( #992 )
2021-11-15 17:26:37 +00:00
megahit
Add MEGAHIT ( #810 )
2021-10-12 16:06:06 +01:00
meningotype
add meningotype module ( #1022 )
2021-11-06 16:44:26 +01:00
metabat2
New module: metabat2 ( #875 )
2021-11-08 21:08:26 +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
miniasm
Add Miniasm module ( #962 )
2021-11-15 17:50:56 +00:00
minimap2
Add Racon module to nf-core/modules ( #949 )
2021-10-29 13:33:38 +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
mtnucratio
Mtnucratio ( #986 )
2021-10-29 15:02:02 +02:00
multiqc
Rename software/ directory to modules/ to re-organise module structure ( #567 )
2021-07-07 10:10:18 +01:00
mummer
Initial commit mummer module ( #940 )
2021-11-15 16:53:41 +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
ncbigenomedownload
add ncbi-genome-download module ( #980 )
2021-11-15 18:32:53 +00:00
nextclade
Update Nextclade to output all files by default ( #638 )
2021-07-28 19:49:50 +01:00
ngmaster
add ngmaster module ( #1024 )
2021-11-10 11:25:50 -07:00
nucmer
add new nucmer module ( #945 )
2021-11-15 22:05:34 +00:00
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 module: pbccs ( #1018 )
2021-11-11 14:19:26 +00:00
picard
Fix picard markduplicates ( #1084 )
2021-11-18 21:54:14 +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
Implement plink/extract module ( #901 )
2021-11-09 14:03:13 +00:00
plink2 /vcf
New module: plink2/vcf ( #1006 )
2021-11-15 13:55:18 +00:00
pmdtools /filter
add new module pmdtools/filter #847 ( #963 )
2021-11-13 15:09:14 +00:00
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
racon
Add Racon module to nf-core/modules ( #949 )
2021-10-29 13:33:38 +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
samblaster
New module: Samblaster ( #954 )
2021-11-04 18:18:56 +01:00
samtools
Add CRAM to samtools/index ( #1049 )
2021-11-10 10:30:48 +01:00
scoary
add scoary module ( #1034 )
2021-11-06 16:34:39 +01:00
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
seqsero2
add seqsero2 module ( #1016 )
2021-11-04 07:49:30 +00:00
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
Change Spades input ( #1039 )
2021-11-15 11:53:07 +00:00
spatyper
add spatyper module ( #784 )
2021-10-05 22:21:35 +01:00
sratools
Fix subworkflows seperate from modules ( #933 )
2021-11-15 18:18:46 +00:00
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
tbprofiler /profile
add module for tbprofiler ( #947 )
2021-11-15 15:35:55 +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
ultra /pipeline
New module: Ultra ( #871 )
2021-11-15 15:57:58 +00:00
unicycler
Unicycler with long read input ( #1041 )
2021-11-15 11:48:56 +00:00
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
4e5b6ed843