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nf-core_modules/modules
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Júlia Mir Pedrol 9bda3dc7f0
Add new module: Pear (#1779) 
* create pear module

* add command and tests

* remove md5sum from known empty file

* add force -f to gzip and gunzip to avoid problems with symbolic links

* apply suggestions from review
2022-07-15 10:28:31 +02:00
..
abacas Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
abricate
adapterremoval
adapterremovalfixprefix Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
agrvate
allelecounter
ampir Apply suggestions from code review 2022-06-10 14:46:58 +02:00
amplify/predict Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
amps
amrfinderplus
antismash antismashlite: Support GBK input (#1840) 2022-07-01 09:29:53 +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 Add manual version definition for artic modules (#1867) 2022-07-12 11:33:51 +01:00
ascat Added output files to ASCAT (#1820) 2022-06-28 14:45:57 +02:00
assemblyscan Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ataqv Ataqv mkarv (#1857) 2022-07-07 22:40:31 +02:00
atlas Add atlas/call (#1809) 2022-07-01 15:06:07 +02:00
bakta update bakta to latest version (v1.4.0) (#1428) 2022-03-24 10:49:17 -06:00
bamaligncleaner Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bamcmp Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
bamtools Remove a blank line (#1793) 2022-06-17 10:58:24 +01:00
bamutil/trimbam Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bandage/image
bbmap Improve descriptions for modules with missing 2022-07-06 12:03:08 +02:00
bcftools Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
bcl2fastq Module/bcl2fastq (#1883) 2022-07-14 13:18:21 +02:00
bclconvert bclconvert: Update Dockerfile (#1819) 2022-06-28 11:11:16 +01:00
bedtools added bedtools split 2022-05-17 14:24:32 +02:00
biobambam replace regex with fixed extensions 2022-05-17 09:54:06 +02:00
biscuit
bismark
blast
bowtie Improve descriptions for modules with missing 2022-07-06 12:03:08 +02:00
bowtie2 Improve descriptions for modules with missing 2022-07-06 12:03:08 +02:00
bracken/bracken
busco Update meta.yml 2022-05-06 11:56:43 +00:00
bwa
bwamem2
bwameth
cat
cellranger Bugfix for CellRanger Dockerfile (#1812) 2022-06-27 11:07:33 +02:00
centrifuge
checkm/lineagewf
chromap
clonalframeml Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
cmseq/polymut Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
cnvkit added fasta_fai as input + changed if statements 2022-06-02 12:57:50 +02:00
cnvpytor removed extra ) in the version strings (#1850) 2022-07-05 15:24:08 +02:00
controlfreec
cooler
csvtk
custom Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
cutadapt
damageprofiler Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
dastool
dedup Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
deeparg
deeptools changed container + add cram2bam conversion 2022-06-02 10:38:05 +02:00
deepvariant Revert recent changes made to some of the modules (#1463) 2022-03-30 20:21:06 +02:00
delly/call
diamond Update DIAMOND module to output log file (#1879) 2022-07-14 16:18:28 +02:00
dragmap
dragonflye Update dragonflye to latest version (#1442) 2022-03-24 14:56:32 -04:00
dshbio
ectyper Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
elprep Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
emmtyper
ensemblvep update ensemblvep to 106.1 and cache to 106 (#1876) 2022-07-13 13:43:03 +02:00
entrezdirect/esummary Add ENTREZDIRECT/ESUMMARY (#1833) 2022-07-13 11:26:58 -06:00
expansionhunter Improve descriptions for modules with missing 2022-07-06 12:03:08 +02:00
faqcs Prettier (#1405) 2022-03-18 14:27:50 +01:00
fargene Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
fastani Improve descriptions for modules with missing 2022-07-06 12:03:08 +02:00
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 add stub to modules used in raredisease pipeline (#1206) 2022-03-28 17:48:39 +02:00
fastqscan
fasttree Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ffq Add ffq module (#1842) 2022-07-01 08:59:13 +02:00
fgbio Updated container versions for fgbio (#1878) 2022-07-14 13:51:34 +02:00
filtlong Update filtlong module to output log file (#1873) 2022-07-12 17:05:31 +02:00
flash
flye Add new module: Flye (#1164) 2022-06-30 22:45:55 +02:00
freebayes
gamma/gamma Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
gatk Apply suggestions from code review 2022-06-09 08:33:37 +02:00
gatk4 Variant recalibration (#1885) 2022-07-15 09:21:34 +02:00
gecco/run Add gecco/run module (#1790) 2022-06-22 13:43:45 +02:00
genescopefk Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
genmap
genomescope2 Update outputs and test data set 2022-05-11 10:42:17 +00:00
genrich
gffread Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
glnexus add stub to modules used in raredisease pipeline (#1206) 2022-03-28 17:48:39 +02:00
graphmap2
gstama Adjust requested ressources for gstama/merge, isoseq3/refine, lima, ultra/align (#1858) 2022-07-07 11:10:18 +01:00
gtdbtk/classifywf Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
gubbins Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
gunc
gunzip Add stub run to gunzip module (#1849) 2022-07-04 17:33:55 +02:00
hamronization new module hamronization/rgi (#1844) 2022-07-01 12:03:08 +02:00
haplocheck fix: stub output name 2022-06-08 10:10:24 -03:00
happy Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
hicap Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
hifiasm Add when: block (#1261) 2022-02-04 09:53:32 +01:00
hisat2 Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
hmmcopy Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
hmmer
hmtnote Update main.nf 2022-05-16 15:20:15 +00:00
homer Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
hpsuissero Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
ichorcna Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
idr
imputeme/vcftoprs
instrain/profile Instrain profile (#1822) 2022-06-30 18:44:41 +02:00
iqtree
ismapper Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
isoseq3 Adjust requested ressources for gstama/merge, isoseq3/refine, lima, ultra/align (#1858) 2022-07-07 11:10:18 +01:00
ivar
jupyternotebook Add when: block (#1261) 2022-02-04 09:53:32 +01:00
kaiju Add KAIJU2KRONA module (#1800) 2022-06-23 16:38:50 +00:00
kallisto/index
kallistobustools Improved kbtools/count (#1884) 2022-07-14 14:27:56 +02:00
kat/hist Add module kat hist 2022-05-06 07:54:10 +00:00
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 Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
krona Fix Krona ktimporttaxonomy to allow multiple input files and simplifies database input (#1841) 2022-07-01 15:18:29 +02:00
last
leehom Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
legsta Prettier (#1405) 2022-03-18 14:27:50 +01:00
lima Adjust requested ressources for gstama/merge, isoseq3/refine, lima, ultra/align (#1858) 2022-07-07 11:10:18 +01:00
lissero Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
manta Update modules/manta/convertinversion/main.nf 2022-06-13 09:26:29 +02:00
mapdamage2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
mash Patch mash screen 2022-05-25 12:29:14 +00:00
mashtree Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
maxbin2 Fix for Maxbin2 emitting input files (#1376) 2022-03-08 15:56:23 +01:00
maxquant/lfq ran prettier 2022-05-16 14:30:40 +02:00
mcroni Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
md5sum fix software definitions 2022-05-06 11:07:05 +02:00
medaka Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
megahit
megan Add MEGAN/DAA2INFO (#1848) 2022-07-05 09:36:22 +02:00
meningotype Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
merqury Add Merqury (#1647) 2022-07-14 10:38:50 +02:00
merquryfk Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
meryl Merge branch 'master' into meryl_unionsum 2022-05-09 16:16:08 +02:00
metabat2
metaphlan3 Add additional handling of fq.gz file name suffix 2022-05-02 14:16:12 +02:00
methyldackel
minia Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
miniasm
minimap2 Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
mlst Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
mobsuite/recon
mosdepth Update main.nf 2022-05-25 19:42:15 +01:00
motus Update MOTUS/PROFILE module to output log file (#1871) 2022-07-13 11:26:27 +02:00
msisensor
msisensorpro
mtnucratio
multiqc Fix MultiQC conda (#1856) 2022-07-06 10:16:34 +02:00
multivcfanalyzer Add MultiVCFAnalyzer (#1845) 2022-07-05 09:47:10 +02:00
mummer Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
muscle Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
nanolyse Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
nanoplot Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
ncbigenomedownload Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
nextclade Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
ngmaster Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ngscheckmate/ncm NGSCheckMate doesn't generate a pdf for only one sample, made optional output (#1839) 2022-06-30 17:43:34 +01:00
nucmer Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
optitype Add BAM indexes as input for optitype module. (#1388) 2022-03-15 17:02:40 +01:00
pairix
pairtools
panaroo/run
pangolin Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
paraclu Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
pbbam/pbmerge
pbccs
pear Add new module: Pear (#1779) 2022-07-15 10:28:31 +02:00
peddy Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
phantompeakqualtools Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
phyloflash Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
picard Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
pirate add module for panaroo, fix pirate tests (#1444) 2022-03-24 20:11:04 -06:00
plasmidfinder Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
plasmidid Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
plink
plink2
pmdtools/filter Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
porechop Update PORECHOP module to output log file (#1870) 2022-07-12 16:07:31 +02:00
preseq
prinseqplusplus Add PRINSEQPLUSPLUS (#1481) 2022-04-03 16:06:22 +02:00
prodigal fix yml formatting (#1263) 2022-02-07 18:16:43 +01:00
prokka Prokka: Fix typo in variable name (#1846) 2022-07-04 15:04:59 +02:00
pycoqc Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
pydamage
qcat Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
qualimap
quast Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
racon Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
rapidnj Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
rasusa Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
raven Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
raxmlng Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
rgi/main Update RGI: add database version reporting to module (#1824) 2022-06-29 16:30:51 -06:00
rhocall/annotate fix versions.yaml 2022-06-07 14:43:35 +02:00
rmarkdownnotebook
roary
rsem
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 more generic name because of multiple extension (#1880) 2022-07-14 11:42:00 +02:00
scoary Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
seacr/callpeak Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
seqkit
seqsero2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
seqtk
sequenzautils
seqwish/induce Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
sexdeterrmine Apply suggestions from code review 2022-06-10 11:03:01 +02:00
shasum fix software definitions 2022-05-06 11:07:05 +02:00
shigatyper Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
shovill Add when: block (#1261) 2022-02-04 09:53:32 +01:00
sistr Prettier (#1405) 2022-03-18 14:27:50 +01:00
slimfastq Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
snapaligner snapaligner: improve index detection (#1836) 2022-06-30 12:19:46 +02:00
snippy/run Update main.nf 2022-06-03 13:05:43 -06:00
snpdists
snpeff update snpeff to 5.1 and cache up to 105 (#1877) 2022-07-13 15:16:21 +02:00
snpsift/split
snpsites Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
sortmerna
sourmash/sketch
spades Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
spatyper
sratools refactor: move files to custom section 2022-05-11 17:33:45 +02:00
srst2/srst2 added tests 2022-05-02 11:30:19 -04:00
ssuissero Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
stadeniolib/scramble
staphopiasccmec
star Bump container version for STAR to 2.7.10a 2022-05-27 11:35:04 +01:00
stranger
strelka
stringtie
subread/featurecounts
svdb update svdb version 2022-05-06 00:18:16 +02:00
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 Add Trimgalore output for unpaired reads (#1568) 2022-04-26 19:15:24 +01:00
trimmomatic Trimmomatic (#1757) 2022-06-17 13:18:15 +00:00
ucsc Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
ultra Adjust requested ressources for gstama/merge, isoseq3/refine, lima, ultra/align (#1858) 2022-07-07 11:10:18 +01:00
umitools Set randomseed for UMI tools if not otherwise set (#1837) 2022-06-30 16:30:38 +01:00
unicycler
untar fix untar output dir 2022-06-02 11:09:55 +02:00
unzip Untar unzip meta (#1408) 2022-03-21 14:49:28 +01:00
vardictjava Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
variantbam Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
vcf2db Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
vcf2maf Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
vcfanno small changes to vcfanno (#1804) 2022-06-24 08:58:26 +02:00
vcflib/vcfuniq Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
vcftools Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
vsearch/usearchglobal Merge branch 'vsearch_usearch_global' of https://github.com/jtangrot/nf-core_modules into vsearch_usearch_global 2022-05-30 13:05:00 +02:00
yara