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nf-core_modules/tests/modules
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Lasse Folkersen d6244b42f5
ASCAT (#1332) 
* First commit

* putting correct links for singularity and docker containers (just had to search for bioconda+ascat to find them, and then put them in like the rest of the nf-core tools had it

* adding first try of relevant commands (not working yet, just took their basic pipeline example

* test commit

* remove test

* starting up work with module after 3.0.0 upgrade

* add ascat.prepareHTS statemet

* add location of docker for new mulled alleleCounter+ASCAT container

* first full run with ASCAT on HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam

* add notes on dropbox download

* use a newer pytest_modules.yml

* add outpit

* trying to align with current Sarek output

* adding in FH comments

* busy clearing up arguments and testing. Still WIP

* first working run, in nextflow, with sarek-like output. Still needs more work on input arguments

* cleaning up before writing up findings

* testing with putting in arguments in args

* draft for solution 3 style for arguments

* one more test added

* adding FH map

* finished testing maps for args

* wrap-up cram/crai test successfully

* updates to address ability to put in ref.fasta argument for cram running

* adding remaining import-HTS commands in as args, and removing the chr21/chr22 only testing to test-nextflow.config

* first test with auto-downloading the s3-data (when not given as an argument)

* removing download-logic for supporting files, documenting in meta.yml, fixing ref_fasta bug

* adding mulled singularity container

* removing tests

* fix left padding lint issue

* lint failure in meta.yml

* more linting errors

* add when argument

* adding stub functionality

* add stub run

* correct md5sum for versions.yml

* more testing with -runstub

* stub code in pure bash - not mixed with R

* reformat version.yml

* get rid of absolute paths in test.yml

* correct wrong md5sum

* adding allelecount conda link

* rename normal_bam to input_bam etc

* let the pipeline dev worry about matching the right loci and allele files

* dont hardcode default genomebuild

* adding download instruction comment

* add doi

* fix conda addition bug

* add args documentation

* test new indent

* new test with meta.yml indentation

* retry with new meta.yml

* retry with new meta.yml - now with empty lines around

* retry with new meta.yml - remove trailing whitepsace

* trying to fix found quote character that cannot start any token error

* try with one empty line above triple-quote and no empty line below

* trying with pipe character

* checking if its the ending triple quote

* one more try with meta.yml

* test update bioconda versioning for linting failure

* test update bioconda versioning for linting failure 2

* testing allelecounter version error on conda

Co-authored-by: @lassefolkersen 
Co-authored-by: @FriederikeHanssen
2022-03-15 11:18:43 +01:00
..
abacas Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
abricate add module for abricate (#1280) 2022-02-18 18:00:21 -07:00
adapterremoval Adapterremoval glob fix (#1391) 2022-03-14 07:32:21 +01:00
agrvate Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
allelecounter Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
amps Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
amrfinderplus add amrfinderplus module (#1284) 2022-02-19 23:02:23 +00:00
arriba Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
artic Patch fix artic/minion and ivar/variants modules (#1326) 2022-02-18 17:36:09 +00:00
ascat ASCAT (#1332) 2022-03-15 11:18:43 +01:00
assemblyscan Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ataqv/ataqv Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bakta Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bamaligncleaner Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bamcmp bamcmp (#1244) 2022-02-02 16:38:41 +00:00
bamtools New module: bamtools/convert (#1219) 2022-01-28 09:58:25 +00:00
bamutil/trimbam Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bandage/image Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bbmap Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bcftools bcftools/annotate follow up corrections (#1359) 2022-02-28 10:16:29 -05:00
bedtools Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
biobambam/bammarkduplicates2 First version of the biobambam/bammarkduplicates2 module (#1247) 2022-02-14 16:30:48 +00:00
biscuit Add core Biscuit tools (#1354) 2022-03-14 09:34:22 -04:00
bismark Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
blast Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bowtie Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
bowtie2 Bump software versions for viralrecon modules (#1198) 2022-01-07 17:52:39 +00:00
bwa Update samtools version (#1361) 2022-02-28 23:13:11 +01:00
bwamem2 Add new boolean sort_bam as input to be able to chose between sort and view in bwamem and bwamem2mem (#1125) 2021-12-08 14:31:27 +00:00
bwameth Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
cat Editing the CAT/CAT module to handle single files (#1196) 2022-01-06 16:41:36 +00:00
cellranger Add bcl2fastq2 to cellranger dockerfile (#1115) 2022-01-25 19:58:22 +01:00
checkm/lineagewf Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
chromap Bump chromap version 0.2.0 (#1374) 2022-03-10 09:23:45 +01:00
clonalframeml Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
cmseq/polymut Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
cnvkit/batch Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
cnvpytor Cnvpytor (#1297) 2022-03-15 10:20:46 +01:00
controlfreec add controlfreec (#1333) 2022-02-28 19:08:58 +01:00
cooler Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
csvtk Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
custom Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
cutadapt Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
damageprofiler Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
dastool Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
dedup Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
deeparg Add deeparg (#1234) 2022-01-26 15:19:16 +01:00
deeptools Add deeptools bamcoverage (#1316) 2022-02-18 09:35:41 +01:00
deepvariant Update version & add intervals usage (#1214) 2022-01-17 16:40:31 +01:00
delly/call Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
diamond Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
dragmap Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
dragonflye Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
dshbio Update dsh-bio to version 2.0.7, add support for compressed GFA 1.0 format (#1207) 2022-01-17 09:24:40 +00:00
ectyper Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
emmtyper Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ensemblvep greatly simplify syntax (#1121) 2021-12-07 11:18:12 +01:00
expansionhunter Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
faqcs Faqcs patch to add tests for --debug output (#1368) 2022-03-02 08:53:05 -05:00
fargene takes gunzip out of fargene main.nf (#1090) 2021-11-29 14:32:23 +01:00
fastani Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fastp Bump software versions for viralrecon modules (#1198) 2022-01-07 17:52:39 +00:00
fastqc Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fastqscan Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fasttree Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fgbio Added UMI sub-workflow (#1098) 2021-12-09 11:16:40 +01:00
filtlong Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
flash Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
freebayes Update intervals (#1278) 2022-02-10 10:34:22 +01:00
gatk4 Gatk4 selectvariants (#1346) 2022-02-24 09:51:48 +01:00
genmap Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
genrich Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gffread Replace remaining task.ext.suffix with task.ext.prefix (#1117) 2021-12-07 15:00:43 +01:00
glnexus Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
graphmap2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gstama Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
gtdbtk/classifywf Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gubbins Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gunc Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
gunzip Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
hamronization Add hamronization/summarize (#1366) 2022-03-03 08:02:04 +01:00
hicap Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
hifiasm Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
hisat2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
hmmcopy hmmcopy/mapCounter (#1175) 2021-12-17 15:39:50 +00:00
hmmer feat: add hmmsearch module and tests (#1273) 2022-02-23 15:32:33 +01:00
homer Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
hpsuissero add module for hpsuisero (#1331) 2022-02-27 17:58:35 -07:00
ichorcna New module: ichorCNA (#1182) 2022-02-11 16:56:13 +01:00
idr Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
imputeme/vcftoprs Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
iqtree Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ismapper Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
isoseq3 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ivar Patch fix artic/minion and ivar/variants modules (#1326) 2022-02-18 17:36:09 +00:00
jupyternotebook Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
kallisto/index Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
kallistobustools Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
khmer/normalizebymedian Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
kleborate Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
kraken2/kraken2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
krona Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
last Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
leehom Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
legsta add module for legsta (#1319) 2022-02-18 17:42:18 -07:00
lima Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
lissero Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
lofreq Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
macrel/contigs Add new module macrel/contigs (#1109) 2021-12-09 13:17:50 +01:00
macs2/callpeak Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mafft Add MAFFT module (#1351) 2022-02-28 00:40:24 -07:00
malt Add missing $prefix definition for MALT_RUN (#1373) 2022-03-03 17:58:04 +01:00
maltextract Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
manta update manta to enable jointcalling (#1218) 2022-02-10 10:37:31 +01:00
mapdamage2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mash add module for mash dist (#1193) 2022-01-04 17:29:49 +01:00
mashtree Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
maxbin2 Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
medaka Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
megahit Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
meningotype Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
metabat2 Update metabat2 output channels and compression (#1111) 2021-12-09 15:00:32 +01:00
metaphlan3 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
methyldackel Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
minia Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
miniasm Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
minimap2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
mlst Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mobsuite/recon add mobsuite_recon module (#1270) 2022-02-18 17:52:38 -07:00
mosdepth Update mosdepth (#1256) 2022-02-09 12:45:55 +00:00
msisensor Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
msisensorpro Add msisensorpro (#1267) 2022-02-09 21:05:49 +01:00
mtnucratio Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
multiqc Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mummer Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
muscle Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
nanolyse Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
nanoplot Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ncbigenomedownload Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
nextclade Bump Nextclade version to 1.10.1 (#1236) 2022-01-27 12:53:14 +00:00
ngmaster Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ngscheckmate/ncm New module: NGSCheckMate (#1290) 2022-03-11 09:02:10 +00:00
nucmer Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
optitype Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
pairix Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pairtools Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
pangolin Bump Pangolin version to 3.1.20 (#1296) 2022-02-15 10:46:20 +00:00
paraclu Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pbbam/pbmerge Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
pbccs Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
peddy Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
phyloflash Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
picard Add picard/sortvcf (#1370) 2022-03-03 11:40:16 -05:00
pirate Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
plasmidid Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
plink Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
plink2 implement plink2/score module (#1259) 2022-03-07 13:02:40 -05:00
pmdtools/filter Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
porechop Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
preseq/lcextrap Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
prodigal Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
prokka Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pycoqc Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
pydamage Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
qcat Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
qualimap add qualimap with cram files + remove val from qualimap/bam, instead use empty list as everywhere else (#1320) 2022-02-18 09:43:53 +01:00
quast Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
racon Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
rapidnj Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
rasusa Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
raven Raven assembler (#1087) 2022-02-01 11:47:01 +01:00
raxmlng Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
rgi/main add module for rgi (#1321) 2022-02-18 17:23:44 -07:00
rmarkdownnotebook Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
roary Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
rsem Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
rseqc Provide BAI when running rseqc/tin (#1177) 2021-12-17 10:00:09 +00:00
salmon Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
samblaster Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
samtools update samtools version to 1.15 (#1358) 2022-02-28 12:42:29 +01:00
scoary Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
seacr/callpeak Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
seqkit added module seqkit replace (#1382) 2022-03-09 10:36:05 -07:00
seqsero2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
seqtk Decrease indent in seqtk/seq versions.yml output (#1384) 2022-03-09 11:56:35 -05:00
sequenzautils Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
seqwish/induce Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
shovill Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
sistr add module for sistr (#1323) 2022-02-18 17:33:48 -07:00
snpdists Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
snpeff greatly simplify syntax (#1121) 2021-12-07 11:18:12 +01:00
snpsift/split Added new module snpsift/split (#1031) 2021-12-17 09:08:14 +01:00
snpsites Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
sourmash/sketch feat: add sourmash sketch (#1287) 2022-02-15 12:30:28 +01:00
spades Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
spatyper Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
sratools Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ssuissero add module for ssuisero (#1329) 2022-02-27 20:04:03 -07:00
staphopiasccmec Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
star Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
stranger Add stranger (#1360) 2022-03-01 14:29:46 +01:00
strelka Update intervals (#1278) 2022-02-10 10:34:22 +01:00
stringtie Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
subread/featurecounts Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
svdb update svdb merge (#1274) 2022-02-24 09:49:30 +01:00
tabix Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
tbprofiler/profile Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
tiddit Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
transdecoder Transdecoder predict (#1251) 2022-02-02 09:46:07 +01:00
trimgalore Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
ucsc ucsc/wigtobigwig: add meta map (#1199) 2022-01-11 21:31:37 +00:00
ultra/pipeline Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
unicycler Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
untar Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
unzip Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
variantbam Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
vcfanno refactored vcfanno (#1266) 2022-02-21 11:49:21 +01:00
vcflib/vcfuniq Add new vcflib/vcfuniq module (#1208) 2022-01-14 18:18:11 +00:00
vcftools Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
yara Add samtools index to yara_mapper module (#1353) 2022-03-04 10:08:02 -05:00