Sébastien Guizard 5a49d2c1bf New module: isoseq3/cluster (#801) ... * 📦 NEW: Add isoseq3/cluster module * 🐛FIX: Fix reports channel and add .pbi to it * 🐛FIX: Fix report channel definition * 👌IMPROVE: Move .pbi file into reports channel * 👌IMPROVE: remove --use_qvs option from command line * 👌 IMPROVE: Add in addParams removed options from command line * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 📦 NEW: Add galgal6 chr30 test data * 📦 NEW: Add bamtools module * 👌 IMPROVE: Ignore test data * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: add singletons parameter and improve outputs * 🐛 FIX: Update test with last module model * 👌 IMPROVE: Add test tag * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update test data config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Remove unused index * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Fill contains args * 📦 NEW: Add isoseq3/cluster module * 🐛FIX: Fix reports channel and add .pbi to it * 🐛FIX: Fix report channel definition * 👌IMPROVE: Move .pbi file into reports channel * 👌IMPROVE: remove --use_qvs option from command line * 👌 IMPROVE: Add in addParams removed options from command line * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: add singletons parameter and improve outputs * 🐛 FIX: Update test with last module model * 👌 IMPROVE: Add test tag * 👌 IMPROVE: Update test data config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Remove unused index * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Fill contains args * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 📦 NEW: Add galgal6 chr30 test data * 📦 NEW: Add bamtools module * 👌 IMPROVE: Ignore test data * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Update code to new versions capture + better output channels * 👌 IMPROVE: Update with new versions.yml file * 🐛 FIX: Update meta.yml + correct typos * 👌 IMPROVE: Clean output file names + correct typo * 🐛 FIX: Remove bamtools/split module from isoseq3/cluster		2021-10-07 10:06:02 +01:00
..
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
bandage/image	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
bbmap	Fix bug with SortMeRna not working on a single db file (#788)	2021-10-04 12:37:21 +01:00
bcftools	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
bedtools	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
bismark	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
blast	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
bowtie	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
bowtie2	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
bwa	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
bwamem2	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
bwameth	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
cat	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
chromap	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
cnvkit	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
cooler	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
csvtk/concat	patch output extension in csvtk/concat (#797)	2021-10-05 22:15:08 +01:00
custom/dumpsoftwareversions	Correct parsing versions with trailing zeros (#795)	2021-10-06 08:16:36 +02:00
cutadapt	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
damageprofiler	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
deeptools	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
delly/call	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
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	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
ensemblvep	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
expansionhunter	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
fastani	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
fastp	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
fastqc	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
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
gatk4	new module: gatk4/calculatecontamination (#778)	2021-10-05 22:52:00 +01:00
genmap	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
gffread	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
glnexus	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
graphmap2	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
gtdbtk/classifywf	Add gtdbtk/classifywf module (#765)	2021-10-05 21:23:01 +01:00
gubbins	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
gunzip	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
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	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
homer	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
iqtree	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
ismapper	add ismapper module (#773)	2021-10-05 21:55:41 +01:00
isoseq3	New module: isoseq3/cluster (#801)	2021-10-07 10:06:02 +01:00
ivar	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
kallisto/index	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
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	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
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	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
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
metaphlan3	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
methyldackel	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
minia	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
minimap2	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
mlst	added classic mlst module (#742)	2021-10-05 20:49:46 +01:00
mosdepth	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
msisensor	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
multiqc	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
muscle	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
nanolyse	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
nanoplot	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
nextclade	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
optitype	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
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	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
pbbam/pbmerge	New module: pbbam/pbmerge (#752)	2021-10-05 23:16:45 +01:00
pbccs	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
phantompeakqualtools	Remove def software lines and emit versions channel as plural (#780)	2021-10-01 14:04:56 +01:00
picard	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
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	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
qualimap	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
quast	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
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	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
rseqc	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
salmon	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
samtools	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
seacr/callpeak	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
seqkit/split2	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
seqtk	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
sequenzautils	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
seqwish/induce	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
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	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
snpsites	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
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
staphopiasccmec	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
star	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
strelka/germline	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
stringtie	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
subread/featurecounts	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
tabix	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
tiddit/sv	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
trimgalore	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
ucsc	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
umitools	Remove def software lines and emit versions channel as plural (#780)	2021-10-01 14:04:56 +01:00
unicycler	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
untar	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
unzip	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
variantbam	Update versions key in meta.yml for all modules (#787)	2021-10-03 08:20:26 +01:00
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