Kevin 81ed0e0ff2 added meta.yml for umitools (#860) ... * added meta.yml for umitools * Update modules/umitools/dedup/meta.yml type: list --> type: file Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/umitools/dedup/meta.yml aww thanks @drpateh :D Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/umitools/dedup/meta.yml module can only handle one BAM at a time, ergo BAM files --> BAM file Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update meta.yml added `pattern` for input `bam` and `bai` * removed trailing whitespace to appease linter * added license to new meta.yml files * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>		2021-10-23 17:30:10 +01:00
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abacas	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
adapterremoval	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
agrvate	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
allelecounter	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
amps	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
arriba	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
artic	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
bamaligncleaner	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
bamtools/split	New module: bamtools/split (#798)	2021-10-12 14:43:08 +02:00
bandage/image	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
bbmap	Fix bug with SortMeRna not working on a single db file (#788)	2021-10-04 12:37:21 +01:00
bcftools	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
bedtools	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
bismark	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
blast	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
bowtie	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
bowtie2	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
bwa	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
bwamem2	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
bwameth	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
cat	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
chromap	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
cnvkit	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
cooler	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
csvtk/concat	patch output extension in csvtk/concat (#797)	2021-10-05 22:15:08 +01:00
custom/dumpsoftwareversions	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
cutadapt	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
damageprofiler	fix: reduce number of required input files for damage profiler (#612)	2021-10-20 10:02:30 +02:00
deeptools	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
delly/call	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
diamond	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
dragonflye	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
dshbio	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
ensemblvep	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
expansionhunter	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
fastani	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
fastp	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
fastqc	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
fasttree	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
fgbio	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
flash	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
freebayes	New module: freebayes (#818)	2021-10-20 15:19:31 +02:00
gatk4	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
genmap	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
genrich	New module: genrich (#877)	2021-10-22 12:22:02 +02:00
gffread	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
glnexus	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
graphmap2	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
gtdbtk/classifywf	Add gtdbtk/classifywf module (#765)	2021-10-05 21:23:01 +01:00
gubbins	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
gunzip	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
hicap	add hicap module (#772)	2021-10-05 21:42:09 +01:00
hifiasm	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
hisat2	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
hmmer/hmmalign	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
homer	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
iqtree	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
ismapper	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
isoseq3	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
ivar	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
kallisto/index	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
kallistobustools	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
kleborate	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
kraken2/kraken2	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
last	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
lib	Bulk update modules to use versions.yml (#739)	2021-09-27 09:41:24 +01:00
lima	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
lofreq	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
macs2/callpeak	Remove def software lines and emit versions channel as plural (#780)	2021-10-01 14:04:56 +01:00
malt	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
maltextract	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
mash/sketch	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
mashtree	add mashtree module (#767)	2021-10-05 21:27:30 +01:00
megahit	Add MEGAHIT (#810)	2021-10-12 16:06:06 +01:00
metaphlan3	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
methyldackel	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
minia	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
minimap2	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
mlst	added classic mlst module (#742)	2021-10-05 20:49:46 +01:00
mosdepth	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
msisensor	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
multiqc	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
muscle	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
nanolyse	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
nanoplot	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
nextclade	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
optitype	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
pairix	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
pairtools	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
pangolin	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
pbbam/pbmerge	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
pbccs	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
phantompeakqualtools	Remove def software lines and emit versions channel as plural (#780)	2021-10-01 14:04:56 +01:00
picard	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
pirate	add pirate module (#777)	2021-10-05 22:28:25 +01:00
plasmidid	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
plink/vcf	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
preseq/lcextrap	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
prodigal	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
prokka	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
pycoqc	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
pydamage	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
qcat	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
qualimap	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
quast	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
rapidnj	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
rasusa	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
raxmlng	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
roary	add roary module (#776)	2021-10-05 22:08:47 +01:00
rsem	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
rseqc	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
salmon	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
samtools	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
seacr/callpeak	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
seqkit/split2	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
seqtk	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
sequenzautils	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
seqwish/induce	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
shovill	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
snpdists	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
snpeff	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
snpsites	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
sortmerna	Fix sortmerna docker container pointer (#791)	2021-10-05 12:05:37 +02:00
spades	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
spatyper	add spatyper module (#784)	2021-10-05 22:21:35 +01:00
sratools	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
staphopiasccmec	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
star	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
strelka	Add strelka/somatic module (#866)	2021-10-18 22:34:23 +01:00
stringtie	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
subread/featurecounts	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
tabix	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
tiddit	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
trimgalore	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
ucsc	New module: ucsc/liftover (#868)	2021-10-21 18:04:15 +02:00
umitools	added meta.yml for umitools (#860)	2021-10-23 17:30:10 +01:00
unicycler	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
untar	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
unzip	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
variantbam	Backfill software licenses meta (#876)	2021-10-22 15:39:54 -07:00
vcftools	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
yara	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00