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nf-core_modules/modules
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Matthieu Muffato de7b50fdd0
Updated dumpsoftwareversions.py to match the pipeline template (#2045) 
* Updated dumpsoftwareversions.py to match the pipeline template

* Fixed the test

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-09-26 18:45:07 +01:00
..
abacas Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
abricate
adapterremoval Refactor adapterremoval (#1491) 2022-04-04 21:40:35 +02:00
adapterremovalfixprefix Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
agrvate Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
allelecounter fix incorrect yaml formatting. (#1264) 2022-04-14 13:35:01 +02:00
ampir Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
amplify/predict
amps Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
amrfinderplus Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
antismash Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
ariba
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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ataqv
atlas
bakta Fix bakta: variable in main.nf (#2050) 2022-09-13 13:03:21 +02:00
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
bamutil/trimbam
bandage/image Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bases2fastq Add bases2fastq (#2054) 2022-09-15 13:50:33 +00:00
bbmap
bcftools Fix bcftools/stats module (#1953) 2022-09-21 16:10:38 +02:00
bcl2fastq Module/bcl2fastq (#1883) 2022-07-14 13:18:21 +02:00
bclconvert Bump bcl-convert version (#2077) 2022-09-16 14:34:52 +02:00
bedtools Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
biobambam
biscuit
bismark
blast Add blast/tblastn module (#2092) 2022-09-26 17:43:41 +02:00
bowtie
bowtie2
bracken
busco Update busco to v5.4.3 and tar small files (#1970) 2022-08-30 10:25:01 +02:00
bwa
bwamem2
bwameth Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
cat
cellranger Bugfix for CellRanger Dockerfile (#1812) 2022-06-27 11:07:33 +02:00
centrifuge
checkm/lineagewf Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
chromap
clonalframeml Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
cmseq/polymut
cnvkit
cnvpytor
controlfreec
cooler
csvtk
custom Updated dumpsoftwareversions.py to match the pipeline template (#2045) 2022-09-26 18:45:07 +01:00
cutadapt Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
damageprofiler Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
dastool
dedup Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
deeparg
deepbgc
deeptools
deepvariant Revert recent changes made to some of the modules (#1463) 2022-03-30 20:21:06 +02:00
delly/call
diamond
dragmap
dragonflye Update dragonflye to latest version (#1442) 2022-03-24 14:56:32 -04:00
dshbio Update dsh-bio to 2.1 (#2100) 2022-09-26 10:41:33 +01:00
ectyper Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
eido
elprep
emmtyper Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ensemblvep update ensemblvep to 106.1 and cache to 106 (#1876) 2022-07-13 13:43:03 +02:00
entrezdirect
epang Make epang output meta with the jplace channel (#2073) 2022-09-16 10:22:50 +02:00
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
fastawindows New module: fasta_windows (#1956) 2022-09-09 08:41:38 +01:00
fastk
fastp
fastqc add stub to modules used in raredisease pipeline (#1206) 2022-03-28 17:48:39 +02:00
fastqscan Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
fasttree Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ffq
fgbio
filtlong Update filtlong module to output log file (#1873) 2022-07-12 17:05:31 +02:00
flash Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
flye Add new module: Flye (#1164) 2022-06-30 22:45:55 +02:00
fq/lint
freebayes
gamma/gamma
gappa Adding gappa/examineheattree (#2084) 2022-09-22 15:51:25 +02:00
gatk
gatk4
gecco/run Update module: Gecco fix to no file generated if no hits found (#1930) 2022-07-27 15:19:43 +02:00
genescopefk Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
genmap fix typo in tag of genmap_mappability (#1527) 2022-09-26 16:21:45 +01:00
genmod
genomescope2
genotyphi/parse add module for mykrobe predict and genotyphi parse (#1818) 2022-09-26 15:18:04 +01:00
genrich Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
gffread Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
glimpse/chunk
glnexus add stub to modules used in raredisease pipeline (#1206) 2022-03-28 17:48:39 +02:00
goat/taxonsearch 2012 bug related to species input in goattaxonsearch module (#2099) 2022-09-23 10:58:40 -06:00
graphmap2
gstama
gtdbtk/classifywf
gubbins Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
gunc
gunzip
gvcftools/extractvariants
hamronization
haplocheck fix: stub output name 2022-06-08 10:10:24 -03:00
haplogrep2/classify Add haplogrep2 (#2030) 2022-09-14 14:58:02 +02:00
happy
hicap
hifiasm Add when: block (#1261) 2022-02-04 09:53:32 +01:00
hisat2
hmmcopy
hmmer
hmtnote Update main.nf 2022-05-16 15:20:15 +00:00
homer
hpsuissero Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
ichorcna
idr Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
imputeme/vcftoprs
instrain/profile Instrain profile (#1822) 2022-06-30 18:44:41 +02:00
iqtree Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ismapper Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
isoseq3
ivar
jupyternotebook Add when: block (#1261) 2022-02-04 09:53:32 +01:00
kaiju
kallisto/index add stub for kallisto/index (#1944) 2022-08-09 09:23:55 +02:00
kallistobustools
kat/hist Add module kat hist 2022-05-06 07:54:10 +00:00
khmer
kleborate Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
kraken2/kraken2
krakentools Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
krona
last
leehom
legsta Prettier (#1405) 2022-03-18 14:27:50 +01:00
lima
lissero Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
lofreq
macrel/contigs
macs2/callpeak
mafft Prettier (#1405) 2022-03-18 14:27:50 +01:00
malt
maltextract Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
manta
mapdamage2
mash
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
mcroni
md5sum Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
medaka
megahit
megan
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
meryl
metabat2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
metaphlan3 Update METAPHLAN3_METAPHLAN3 to correct module name (#2056) 2022-09-15 09:09:55 +02:00
methyldackel
minia
miniasm Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
minimap2
mlst Add args to mlst (#1962) 2022-09-26 15:48:35 +01:00
mobsuite/recon Prettier (#1405) 2022-03-18 14:27:50 +01:00
mosdepth
motus
msisensor
msisensor2
msisensorpro
mtnucratio Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
multiqc Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
multivcfanalyzer Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
mummer Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
muscle Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
mykrobe/predict add module for mykrobe predict and genotyphi parse (#1818) 2022-09-26 15:18:04 +01:00
nanolyse Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
nanoplot
ncbigenomedownload
nextclade
ngmaster Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ngscheckmate/ncm
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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
pairtools
panaroo/run add module for panaroo, fix pirate tests (#1444) 2022-03-24 20:11:04 -06:00
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
pasty add module for pasty (#2003) 2022-09-07 09:29:28 -06:00
pbbam/pbmerge Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
pbccs Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
pbptyper
pear Add new module: Pear (#1779) 2022-07-15 10:28:31 +02:00
peddy
phantompeakqualtools Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
phyloflash
picard
pints/caller fix(pints): Remove update check (#1989) 2022-09-08 05:03:48 +02:00
pirate add module for panaroo, fix pirate tests (#1444) 2022-03-24 20:11:04 -06:00
plasmidfinder
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
prodigal Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
prokka
pycoqc
pydamage
qcat Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
qualimap add stub for qualimap/rnaseq (#1946) 2022-08-09 15:24:35 +02:00
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
rhocall/annotate fix versions.yaml 2022-06-07 14:43:35 +02:00
rmarkdownnotebook Add when: block (#1261) 2022-02-04 09:53:32 +01:00
roary
rsem
rseqc
rtgtools
salmon
samblaster Samtools version update (#1507) 2022-04-11 14:26:28 +02:00
samtools Multithreaded samtools commands (#2080) 2022-09-26 17:44:36 +01:00
scoary Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
scramble
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 Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
sequenzautils
seqwish/induce Bump seqwish/induce to v0.7.6 (#2083) 2022-09-26 17:01:21 +01:00
seroba/run add module for seroba (#1816) 2022-09-26 16:06:08 +01:00
sexdeterrmine
shasum fix software definitions 2022-05-06 11:07:05 +02:00
shigatyper Update modules/shigatyper/main.nf 2022-04-22 08:49:44 -06:00
shovill Add when: block (#1261) 2022-02-04 09:53:32 +01:00
sistr
slimfastq
snapaligner
snippy
snpdists Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
snpeff DRAFT: Extend output from snpeff (#1895) 2022-07-16 20:08:52 +02:00
snpsift/split Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
snpsites Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
somalier
sortmerna Add when: block (#1261) 2022-02-04 09:53:32 +01:00
sourmash/sketch
spades Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
spatyper Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
sratools
srst2/srst2 added tests 2022-05-02 11:30:19 -04:00
ssuissero
stadeniolib/scramble
staphopiasccmec Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
star
stranger add stubs for stranger (#1543) 2022-04-22 10:10:43 +02:00
strelka
stringtie Make stringtie/merge arguments configurable (#2049) 2022-09-26 14:26:53 +01:00
subread/featurecounts
svdb
svtk/standardize
tabix
tailfindr Tailfindr (#1904) 2022-07-22 16:20:53 +02:00
tbprofiler/profile
tiddit
transdecoder
trimgalore Add Trimgalore output for unpaired reads (#1568) 2022-04-26 19:15:24 +01:00
trimmomatic
ucsc
ultra
umitools
unicycler Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
untar Fix for nested directories in tar archive (#2062) 2022-09-15 11:32:36 +02:00
unzip Reduce resource requests (#2021) 2022-09-07 10:33:05 +02:00
vardictjava
variantbam
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
vcftools
vsearch New module: Vsearch sintax (#2094) 2022-09-26 14:45:01 +01:00
whamg New module: Whamg (#1994) 2022-09-02 13:33:48 +02:00
yara