millironx/nf-core_modules
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nf-core_modules/modules
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James A. Fellows Yates e971f538a9
Module new version reporting fixes (#753) 
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Fix IQ tree

* Fix picard markdup and merge sam

* Fix plink/vcf version

* Fix plink version output

* Fix prokka version command

* Fix pydamage

* Try fixing markduplicates

* Fix snpEff

* Fix vcftools version

* Fix pydamage and filtersamreads test run

* Fix MarkDuplicates tests

* Add missing unsorted checks

* Remove MD5 sym due to stochasicity in BAM file
2021-09-28 10:51:19 +01:00
..
abacas Fix version commands (#749) 2021-09-27 22:10:37 +01:00
adapterremoval Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
agrvate Fix version commands (#749) 2021-09-27 22:10:37 +01:00
allelecounter Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
arriba Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
artic Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
bamaligncleaner Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
bandage/image Fix version commands (#749) 2021-09-27 22:10:37 +01:00
bbmap Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
bcftools Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
bedtools Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
bismark Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
blast Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +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 version commands (#749) 2021-09-27 22:10:37 +01:00
bwamem2 Fix version commands (#749) 2021-09-27 22:10:37 +01:00
bwameth Fix version commands (#749) 2021-09-27 22:10:37 +01:00
cat Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
chromap Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
cnvkit Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
cooler Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
cutadapt Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
damageprofiler Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
deeptools Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
delly/call Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
diamond Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
dragonflye Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
dshbio Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
ensemblvep Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
expansionhunter Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
fastani Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
fastp Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
fastqc Update fastqc to produce multi-version versions.yml (#665) 2021-09-24 10:01:54 +01:00
fasttree Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
fgbio Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
flash Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
gatk4 Fix version commands (#749) 2021-09-27 22:10:37 +01:00
genmap Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
gffread Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
glnexus Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
graphmap2 Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
gubbins Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
gunzip Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
hifiasm Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
hisat2 Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
hmmer/hmmalign Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
homer Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
iqtree Module new version reporting fixes (#753) 2021-09-28 10:51:19 +01:00
ivar Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
kallisto/index Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
kallistobustools Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
kleborate Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
kraken2/kraken2 Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
last Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
lib Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
lima New module: LIMA (#719) 2021-09-27 16:14:35 +01:00
lofreq Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
macs2/callpeak Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
malt Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
maltextract Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
mash/sketch Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
metaphlan3 Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
methyldackel Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
minia Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
minimap2 Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
mosdepth Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
msisensor Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
multiqc Update fastqc to produce multi-version versions.yml (#665) 2021-09-24 10:01:54 +01:00
muscle Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
nanolyse Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
nanoplot Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
nextclade Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
optitype Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
pairix Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
pairtools Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
pangolin Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
pbccs Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
phantompeakqualtools Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
picard Module new version reporting fixes (#753) 2021-09-28 10:51:19 +01:00
plasmidid Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
plink/vcf Module new version reporting fixes (#753) 2021-09-28 10:51:19 +01:00
preseq/lcextrap Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
prodigal Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
prokka Module new version reporting fixes (#753) 2021-09-28 10:51:19 +01:00
pycoqc Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
pydamage Module new version reporting fixes (#753) 2021-09-28 10:51:19 +01:00
qcat Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
qualimap Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
quast Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
rapidnj Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
rasusa Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
raxmlng Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
rsem Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
rseqc Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
salmon Fix version commands (#749) 2021-09-27 22:10:37 +01:00
samtools Fix version commands (#749) 2021-09-27 22:10:37 +01:00
seacr/callpeak Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
seqkit/split2 Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
seqtk Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
sequenzautils Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
seqwish/induce Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
shovill Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
snpdists Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
snpeff Module new version reporting fixes (#753) 2021-09-28 10:51:19 +01:00
snpsites Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
sortmerna Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
spades Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
staphopiasccmec Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
star Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
strelka/germline Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
stringtie Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
subread/featurecounts Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
tabix Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
tiddit/sv Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
trimgalore Fix version commands (#749) 2021-09-27 22:10:37 +01:00
ucsc Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
umitools Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
unicycler Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
untar Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
unzip Fix more version commands (#750) 2021-09-28 06:56:27 +01:00
variantbam Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00
vcftools Module new version reporting fixes (#753) 2021-09-28 10:51:19 +01:00
yara Bulk update modules to use versions.yml (#739) 2021-09-27 09:41:24 +01:00