Matt Olm 031fbd37aa Instrain profile (#1822) ... * add instrain profile * module instrain/profile * add instrain profile * module instrain/profile * instrain profile * Update modules/instrain/profile/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/instrain/profile/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/instrain/profile/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/instrain/profile/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/instrain/profile/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/instrain/profile/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/instrain/profile/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * update * linting * Apply suggestions from code review * Update modules/instrain/profile/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>		2022-06-30 18:44:41 +02:00
..
abacas
abricate
adapterremoval	Refactor adapterremoval (#1491)	2022-04-04 21:40:35 +02:00
adapterremovalfixprefix
agrvate
allelecounter
ampir	Add file name collision check + TSV output	2022-06-10 12:54:39 +02:00
amplify/predict	add module AMPlify (#1498)	2022-04-20 11:53:26 +02:00
amps
amrfinderplus
antismash	Apply suggestions from code review	2022-05-12 15:28:19 +02:00
ariba	add module for ariba (#1731)	2022-06-15 10:18:31 -06:00
arriba	Update Arriba to 2.3.0 (#1827)	2022-06-29 14:39:13 +02:00
artic
ascat	Added output files to ASCAT (#1820)	2022-06-28 14:45:57 +02:00
assemblyscan
ataqv/ataqv
atlas	Add Atlas/PMD (#1810)	2022-06-24 16:53:51 +02:00
bakta
bamaligncleaner
bamcmp	bamcmp (#1244)	2022-02-02 16:38:41 +00:00
bamtools	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
bamutil/trimbam
bandage/image
bbmap	Samtools version update (#1507)	2022-04-11 14:26:28 +02:00
bcftools	added an optional vcf index to bcftools/norm (#1821)	2022-06-28 16:18:12 +02:00
bclconvert	bump bclconvert version (#1806)	2022-06-24 07:14:42 +02:00
bedtools	added bedtools split	2022-05-17 14:24:32 +02:00
biobambam	fix config	2022-05-17 09:09:19 +02:00
biscuit
bismark
blast
bowtie
bowtie2	add PE sorted test	2022-05-13 19:16:50 +02:00
bracken/bracken
busco	Change busco multi-fasta test md5sum to contains	2022-06-13 08:51:41 +00:00
bwa	Samtools version update (#1507)	2022-04-11 14:26:28 +02:00
bwamem2
bwameth	Fix formatting in yaml files, add yamllint config (#1279)	2022-02-15 11:15:27 +00:00
cat	Update cat module (#1469)	2022-03-31 13:42:44 +02:00
cellranger	Remove empty file md5sum	2022-06-10 11:53:28 +02:00
centrifuge	Add centrifuge_kreport module (#1514)	2022-04-13 15:33:51 +02:00
checkm/lineagewf
chromap	Samtools version update (#1507)	2022-04-11 14:26:28 +02:00
clonalframeml
cmseq/polymut
cnvkit	added fasta_fai as input + changed if statements	2022-06-02 12:57:50 +02:00
cnvpytor	combine multiple pytor	2022-05-05 23:59:12 +02:00
controlfreec	Fix Controlfreec: Add stub runs to test single sample input & make conda work with R scripts (#1504)	2022-04-08 11:43:40 +02:00
cooler
csvtk
custom	tests: add missing paths to config	2022-05-11 18:17:27 +02:00
cutadapt
damageprofiler
dastool	Update DASTool to 1.1.4 (#1471)	2022-04-01 11:33:07 +02:00
dedup
deeparg
deeptools	changed container + add cram2bam conversion	2022-06-02 10:38:05 +02:00
deepvariant
delly/call
diamond	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
dragmap
dragonflye
dshbio
ectyper
elprep	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
emmtyper
ensemblvep	Optional output from the VEP-moduel (#1775)	2022-06-15 13:52:12 +02:00
expansionhunter	add stub to modules used in raredisease pipeline (#1206)	2022-03-28 17:48:39 +02:00
faqcs
fargene
fastani
fastk	Add FastK/Merge (#1828)	2022-06-29 18:04:36 +02:00
fastp	Proposal: Rename output from fastp module (#1802)	2022-06-24 10:01:14 +02:00
fastqc
fastqscan
fasttree
fgbio
filtlong	Fix config for tests	2022-05-31 20:07:52 +02:00
flash
freebayes
gamma/gamma	fixed test.yml	2022-05-24 19:27:09 -04:00
gatk	Add GATK indelrealigner tests	2022-06-08 21:14:08 +02:00
gatk4	Add module: gatk4/leftalignandtrimvariants (#1808)	2022-06-28 10:44:08 +02:00
gecco/run	Add gecco/run module (#1790)	2022-06-22 13:43:45 +02:00
genescopefk	Add GeneScopeFK (#1781)	2022-06-14 20:49:06 +02:00
genmap
genomescope2	Update tests/modules/genomescope2/test.yml	2022-05-13 11:27:42 +02:00
genrich
gffread
glnexus
graphmap2	Update all modules to new NF DSL2 syntax (#1099)	2021-11-26 07:58:40 +00:00
gstama	New Module: gstama/polyacleanup (#1468)	2022-03-31 09:11:51 -04:00
gtdbtk/classifywf
gubbins
gunc
gunzip
hamronization
haplocheck	fix: string interpolation and test input access	2022-06-08 09:08:59 -03:00
happy	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
hicap
hifiasm
hisat2
hmmcopy
hmmer
hmtnote	Update main.nf	2022-05-16 15:20:15 +00:00
homer	Fix homer/maketagdirectory output collision (#1456)	2022-03-27 03:17:42 +00:00
hpsuissero
ichorcna
idr
imputeme/vcftoprs
instrain/profile	Instrain profile (#1822)	2022-06-30 18:44:41 +02:00
iqtree
ismapper
isoseq3
ivar
jupyternotebook
kaiju	Add KAIJU2KRONA module (#1800)	2022-06-23 16:38:50 +00:00
kallisto/index
kallistobustools
kat/hist	Update tests/modules/kat/hist/test.yml	2022-05-23 08:51:49 +02:00
khmer	Add khmer unique-kmers.py module (#1838)	2022-06-30 16:23:30 +01:00
kleborate
kraken2/kraken2	update to kraken2: breaking change - output channels renamed (#1525)	2022-04-21 14:33:59 +02:00
krakentools/kreport2krona	New module: krakentools/kreport2krona (#1746)	2022-06-13 20:14:44 +02:00
krona	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
last
leehom
legsta
lima
lissero
lofreq
macrel/contigs
macs2/callpeak
mafft
malt	Update MALT to older version due to major bug in most recent version (#1796)	2022-06-20 08:20:22 +02:00
maltextract
manta	Update tests/modules/manta/convertinversion/main.nf	2022-06-13 09:26:35 +02:00
mapdamage2
mash	Patch mash screen	2022-05-25 12:29:14 +00:00
mashtree
maxbin2
maxquant/lfq
mcroni	add module for mcroni (#1750)	2022-06-13 15:04:01 +02:00
md5sum	new module: md5sum	2022-05-06 09:20:40 +02:00
medaka
megahit
megan/rma2info	Add MEGAN/RMA2INFO (#1513)	2022-04-12 08:35:36 +02:00
meningotype
merquryfk	Add MerquryFK KatGC (#1798)	2022-06-23 20:57:15 +02:00
meryl	Merge branch 'master' into meryl_unionsum	2022-05-09 16:16:08 +02:00
metabat2
metaphlan3
methyldackel
minia
miniasm
minimap2	Update minimap2/align module (#1537)	2022-04-26 16:32:20 +02:00
mlst
mobsuite/recon
mosdepth	Update main.nf	2022-05-25 19:38:12 +01:00
motus	Update tests/modules/motus/profile/test.yml	2022-05-12 20:55:54 +01:00
msisensor
msisensorpro
mtnucratio
multiqc	formatting	2022-06-08 14:42:58 +02:00
mummer
muscle
nanolyse
nanoplot
ncbigenomedownload
nextclade
ngmaster
ngscheckmate/ncm
nucmer
optitype
pairix
pairtools
panaroo/run
pangolin
paraclu
pbbam/pbmerge
pbccs
peddy
phantompeakqualtools	Add task.ext.args to phantompeakqualtools and finish the module (#1474)	2022-03-31 22:59:21 +01:00
phyloflash
picard	fix tests (again)	2022-05-22 06:54:09 +02:00
pirate
plasmidfinder	add module for plasmidfinder (#1773)	2022-06-15 10:25:51 -06:00
plasmidid
plink
plink2
pmdtools/filter
porechop
preseq	Split preseq lcextrap and ccurve (#1440)	2022-03-25 17:11:40 +00:00
prinseqplusplus	Add PRINSEQPLUSPLUS (#1481)	2022-04-03 16:06:22 +02:00
prodigal
prokka
pycoqc
pydamage
qcat
qualimap
quast
racon
rapidnj
rasusa
raven
raxmlng
rgi/main	Update RGI: add database version reporting to module (#1824)	2022-06-29 16:30:51 -06:00
rhocall/annotate	update test	2022-06-08 16:36:02 +02:00
rmarkdownnotebook
roary	Update test.yml (#1419)	2022-03-19 15:06:21 +00:00
rsem	Bump STAR version to 2.7.10a for RSEM modules (#1573)	2022-04-27 19:21:26 +01:00
rseqc
rtgtools	new module rtgtools/pedfilter (#1777)	2022-06-14 16:02:18 +02:00
salmon
samblaster	Samtools version update (#1507)	2022-04-11 14:26:28 +02:00
samtools	samtools/*stats*: use prefix for outputs (#1788)	2022-06-16 13:42:01 +02:00
scoary
seacr/callpeak
seqkit	feat: add module for seqkit stats (#1466)	2022-03-30 23:01:17 +02:00
seqsero2
seqtk
sequenzautils
seqwish/induce
sexdeterrmine	Corrected test-datasets input	2022-05-23 17:08:40 +02:00
shasum	added sha256sum	2022-05-06 10:28:14 +02:00
shigatyper	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
shovill
sistr
slimfastq	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
snapaligner	snapaligner: improve index detection (#1836)	2022-06-30 12:19:46 +02:00
snippy/run	make prettier	2022-05-11 18:00:36 +00:00
snpdists
snpeff
snpsift/split
snpsites
sourmash/sketch
spades
spatyper
sratools	refactor: move files to custom section	2022-05-11 17:33:45 +02:00
srst2/srst2	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
ssuissero
stadeniolib/scramble	new tool: staden_io_lib (#1499)	2022-04-08 09:54:15 -04:00
staphopiasccmec
star	Fix tests	2022-05-27 12:14:10 +01:00
stranger	add stubs for stranger (#1543)	2022-04-22 10:10:43 +02:00
strelka
stringtie	Rename process from STRINGTIE to STRINGTIE_STRINGTIE (#1546)	2022-04-22 15:13:06 +01:00
subread/featurecounts
svdb
tabix	fix bgziptabix extension (#1784)	2022-06-15 10:33:10 +02:00
tbprofiler/profile
tiddit	TIDDIT - add --skip_assembly when no bwa specified (#1769)	2022-06-13 17:02:59 +02:00
transdecoder
trimgalore
trimmomatic	Trimmomatic (#1757)	2022-06-17 13:18:15 +00:00
ucsc
ultra/pipeline
umitools	Fix Conda tests	2022-05-23 22:39:12 +01:00
unicycler
untar	fix untar output dir	2022-06-02 11:09:55 +02:00
unzip
vardictjava	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
variantbam
vcf2db	new module vcf2db (#1795)	2022-06-17 15:54:02 +02:00
vcf2maf	vcf2maf module with built in VEP (#1768)	2022-06-20 18:27:12 +02:00
vcfanno	small changes to vcfanno (#1804)	2022-06-24 08:58:26 +02:00
vcflib/vcfuniq
vcftools
vsearch/usearchglobal	prettier	2022-05-30 13:35:12 +02:00
yara