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alyssa-ab c1eb9cce44
Trimmomatic (#1757) 
* Trimmomatic main only first draft

* Add test files

* SE PE Adjustment

* Remove extra reads input

* chore: Remove TODOs

* Apply suggestions from code review

Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>

* fix(trimmomatic): Handle SE output correctly

Since there's never going to be unpaired reads for SE reads we can get
away with it for SE

* fix(trimmomatic): Use correct elvis operator to handle logic

* fix(trimmomatic): Add hack to work with SE and PE reads

* Update test.yml

* use the PE and SE trimming correctly

* Made user set adaptors

* Add documentation

* test(trimmomatic): Add files to pytest_modules

* test(trimmomatic): Update name of failing test

Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-06-17 13:18:15 +00:00
..
abacas Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
abricate Prettier (#1405) 2022-03-18 14:27:50 +01:00
adapterremoval Refactor adapterremoval (#1491) 2022-04-04 21:40:35 +02:00
adapterremovalfixprefix Add AdapterRemovalFixPrefix (#1424) 2022-03-21 11:26:12 +01:00
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 Apply suggestions from code review 2022-06-10 14:46:58 +02:00
amplify/predict add module AMPlify (#1498) 2022-04-20 11:53:26 +02:00
amps Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
amrfinderplus Prettier (#1405) 2022-03-18 14:27:50 +01:00
antismash Apply suggestions from code review 2022-05-12 15:28:19 +02:00
ariba add module for ariba (#1731) 2022-06-15 10:18:31 -06:00
arriba update arriba module 2022-05-09 14:55:59 +02:00
artic Patch fix artic/minion and ivar/variants modules (#1326) 2022-02-18 17:36:09 +00:00
ascat Prettier (#1405) 2022-03-18 14:27:50 +01:00
assemblyscan Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ataqv/ataqv Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
atlas/splitmerge Create atlas/splitmerge Module (#1756) 2022-06-13 15:09:32 +02:00
bakta update bakta to latest version (v1.4.0) (#1428) 2022-03-24 10:49:17 -06:00
bamaligncleaner Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bamcmp Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bamtools Remove a blank line (#1793) 2022-06-17 10:58:24 +01:00
bamutil/trimbam Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bandage/image Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bbmap Samtools version update (#1507) 2022-04-11 14:26:28 +02:00
bcftools fix test 2022-06-08 14:48:16 +02:00
bclconvert update bclconvert module, as used in nf-core/demultiplex (#1569) 2022-06-16 15:03:13 +02:00
bedtools added bedtools split 2022-05-17 14:24:32 +02:00
biobambam replace regex with fixed extensions 2022-05-17 09:54:06 +02:00
biscuit Prettier (#1405) 2022-03-18 14:27:50 +01:00
bismark Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
blast Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bowtie Samtools version update (#1507) 2022-04-11 14:26:28 +02:00
bowtie2 add sort option to bowtie2 2022-05-13 15:26:41 +02:00
bracken/bracken Add bracken (#1423) 2022-03-22 16:40:21 +01:00
busco Update meta.yml 2022-05-06 11:56:43 +00:00
bwa feat: remove read_group which should be set up with task.ext.args (#1521) 2022-04-13 14:30:34 +02:00
bwamem2 feat: remove read_group which should be set up with task.ext.args (#1521) 2022-04-13 14:30:34 +02:00
bwameth Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
cat Replace vanilla Linux Biocontainer with Ubuntu (#1557) 2022-04-22 14:50:07 +01:00
cellranger Update main.nf 2022-06-10 11:05:59 +02:00
centrifuge Add centrifuge_kreport module (#1514) 2022-04-13 15:33:51 +02:00
checkm/lineagewf Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
chromap Samtools version update (#1507) 2022-04-11 14:26:28 +02:00
clonalframeml Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
cmseq/polymut Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
cnvkit added fasta_fai as input + changed if statements 2022-06-02 12:57:50 +02:00
cnvpytor remove prefix def in callcnvs 2022-05-06 10:56:58 +02:00
controlfreec Fix Controlfreec: Add stub runs to test single sample input & make conda work with R scripts (#1504) 2022-04-08 11:43:40 +02:00
cooler Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
csvtk Prettier (#1405) 2022-03-18 14:27:50 +01:00
custom refactor: rename module 2022-05-11 17:33:45 +02:00
cutadapt Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
damageprofiler Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
dastool DASTool output channels update (#1489) 2022-04-04 13:31:36 +02:00
dedup Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
deeparg Deeparg singularity container fix 2 (#1406) 2022-03-18 16:21:55 +01:00
deeptools changed container + add cram2bam conversion 2022-06-02 10:38:05 +02:00
deepvariant Revert recent changes made to some of the modules (#1463) 2022-03-30 20:21:06 +02:00
delly/call Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
diamond Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
dragmap feat: remove read_group which should be set up with task.ext.args (#1521) 2022-04-13 14:30:34 +02:00
dragonflye Update dragonflye to latest version (#1442) 2022-03-24 14:56:32 -04:00
dshbio Update dsh-bio to version 2.0.8. (#1483) 2022-04-09 11:13:47 -05:00
ectyper Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
elprep Update modules/elprep/merge/main.nf 2022-04-29 15:07:09 +02:00
emmtyper Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ensemblvep Same version on conda and in the dockerfile (#1791) 2022-06-16 16:25:54 +02:00
expansionhunter add stub to modules used in raredisease pipeline (#1206) 2022-03-28 17:48:39 +02:00
faqcs Prettier (#1405) 2022-03-18 14:27:50 +01:00
fargene Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
fastani Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
fastk Add FastK/Histex (#1776) 2022-06-14 16:30:37 +02:00
fastp fix fastp to allow exporting of only *.merged.fastq.gz (#1325) 2022-02-18 15:38:05 +01:00
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
fgbio Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
filtlong Actually add the changes 2022-05-31 15:49:57 +02:00
flash Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
freebayes Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
gamma/gamma updating paths in test.yml 2022-05-24 16:27:00 -04:00
gatk Apply suggestions from code review 2022-06-09 08:33:37 +02:00
gatk4 GATK/Getpileupsummaries: If no intervals use variants instead (#1787) 2022-06-16 15:00:01 +02:00
genescopefk Add GeneScopeFK (#1781) 2022-06-14 20:49:06 +02:00
genmap Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
genomescope2 Update outputs and test data set 2022-05-11 10:42:17 +00:00
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
glnexus add stub to modules used in raredisease pipeline (#1206) 2022-03-28 17:48:39 +02:00
graphmap2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
gstama New Module: gstama/polyacleanup (#1468) 2022-03-31 09:11:51 -04:00
gtdbtk/classifywf Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
gubbins Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
gunc Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
gunzip Replace vanilla Linux Biocontainer with Ubuntu (#1557) 2022-04-22 14:50:07 +01:00
hamronization Prettier (#1405) 2022-03-18 14:27:50 +01:00
haplocheck fix: stub output name 2022-06-08 10:10:24 -03:00
happy Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
hicap Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
hifiasm Add when: block (#1261) 2022-02-04 09:53:32 +01:00
hisat2 Samtools version update (#1507) 2022-04-11 14:26:28 +02:00
hmmcopy Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
hmmer Prettier (#1405) 2022-03-18 14:27:50 +01:00
hmtnote Update main.nf 2022-05-16 15:20:15 +00:00
homer Fix homer/maketagdirectory output collision (#1456) 2022-03-27 03:17:42 +00:00
hpsuissero Prettier (#1405) 2022-03-18 14:27:50 +01:00
ichorcna Prettier (#1405) 2022-03-18 14:27:50 +01:00
idr Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
imputeme/vcftoprs Add when: block (#1261) 2022-02-04 09:53:32 +01:00
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 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 Add when: block (#1261) 2022-02-04 09:53:32 +01:00
kaiju Kaiju2table module (#1545) 2022-04-22 11:26:30 +02:00
kallisto/index Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
kallistobustools Add when: block (#1261) 2022-02-04 09:53:32 +01:00
kat/hist Add module kat hist 2022-05-06 07:54:10 +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 to kraken2: breaking change - output channels renamed (#1525) 2022-04-21 14:33:59 +02:00
krakentools/kreport2krona New module: krakentools/kreport2krona (#1746) 2022-06-13 20:14:44 +02:00
krona Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
last Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
leehom Fix: Leehom meta output channel descriptions (#1356) 2022-02-27 14:35:47 +01:00
legsta Prettier (#1405) 2022-03-18 14:27:50 +01:00
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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
macs2/callpeak Prettier (#1405) 2022-03-18 14:27:50 +01:00
mafft Prettier (#1405) 2022-03-18 14:27:50 +01:00
malt Add missing $prefix definition for MALT_RUN (#1373) 2022-03-03 17:58:04 +01:00
maltextract Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
manta Update modules/manta/convertinversion/main.nf 2022-06-13 09:26:29 +02:00
mapdamage2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
mash Patch mash screen 2022-05-25 12:29:14 +00:00
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 ran prettier 2022-05-16 14:30:40 +02:00
mcroni add module for mcroni (#1750) 2022-06-13 15:04:01 +02:00
md5sum fix software definitions 2022-05-06 11:07:05 +02:00
medaka Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
megahit Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
megan/rma2info Add MEGAN/RMA2INFO (#1513) 2022-04-12 08:35:36 +02:00
meningotype Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
merquryfk Add MerquryFK PloidyPlot (#1780) 2022-06-14 20:50:58 +02:00
meryl Merge branch 'master' into meryl_unionsum 2022-05-09 16:16:08 +02:00
metabat2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
metaphlan3 Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
methyldackel Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
minia Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
miniasm Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
minimap2 Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
mlst Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
mobsuite/recon Prettier (#1405) 2022-03-18 14:27:50 +01:00
mosdepth Update main.nf 2022-05-25 19:42:15 +01:00
motus fix the typo in motus_profile. 2022-05-12 09:20:32 -04:00
msisensor Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
msisensorpro Prettier (#1405) 2022-03-18 14:27:50 +01:00
mtnucratio Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
multiqc Update modules/multiqc/main.nf 2022-06-08 14:41:10 +02:00
mummer Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
muscle Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
nanolyse Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
nanoplot Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ncbigenomedownload Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
nextclade Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ngmaster Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ngscheckmate/ncm Prettier (#1405) 2022-03-18 14:27:50 +01:00
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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
panaroo/run add module for panaroo, fix pirate tests (#1444) 2022-03-24 20:11:04 -06:00
pangolin Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
paraclu Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
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
peddy Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
phantompeakqualtools Allow to pass arguments to the phantompeakqualtools script itself (#1562) 2022-04-25 19:07:43 +02:00
phyloflash Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
picard bump picard versions 2022-05-30 10:15:40 +02:00
pirate add module for panaroo, fix pirate tests (#1444) 2022-03-24 20:11:04 -06:00
plasmidfinder add module for plasmidfinder (#1773) 2022-06-15 10:25:51 -06:00
plasmidid Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
plink Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
plink2 Prettier (#1405) 2022-03-18 14:27:50 +01:00
pmdtools/filter Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
porechop Add when: block (#1261) 2022-02-04 09:53:32 +01:00
preseq Split preseq lcextrap and ccurve (#1440) 2022-03-25 17:11:40 +00:00
prinseqplusplus Add PRINSEQPLUSPLUS (#1481) 2022-04-03 16:06:22 +02:00
prodigal fix yml formatting (#1263) 2022-02-07 18:16:43 +01:00
prokka Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
pycoqc Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
pydamage Update PyDamage module (#1467) 2022-03-31 09:18:18 -04:00
qcat Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
qualimap Samtools version update (#1507) 2022-04-11 14:26:28 +02:00
quast Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
racon Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
rapidnj Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
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 Prettier (#1405) 2022-03-18 14:27:50 +01:00
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 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
rsem Bump STAR version to 2.7.10a for RSEM modules (#1573) 2022-04-27 19:21:26 +01:00
rseqc Change label for rseqc/tin to process_high (#1327) 2022-02-21 13:26:51 +00:00
rtgtools new module rtgtools/pedfilter (#1777) 2022-06-14 16:02:18 +02:00
salmon Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
samblaster Samtools version update (#1507) 2022-04-11 14:26:28 +02:00
samtools samtools/*stats*: use prefix for outputs (#1788) 2022-06-16 13:42:01 +02:00
scoary Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
seacr/callpeak Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
seqkit feat: add module for seqkit stats (#1466) 2022-03-30 23:01:17 +02:00
seqsero2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
seqtk Prettier (#1405) 2022-03-18 14:27:50 +01:00
sequenzautils Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
seqwish/induce Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
sexdeterrmine Apply suggestions from code review 2022-06-10 11:03:01 +02:00
shasum fix software definitions 2022-05-06 11:07:05 +02:00
shigatyper Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
shovill Add when: block (#1261) 2022-02-04 09:53:32 +01:00
sistr Prettier (#1405) 2022-03-18 14:27:50 +01:00
slimfastq Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
snapaligner merge snapaligner modes into one 2022-05-06 14:10:44 +02:00
snippy/run Update main.nf 2022-06-03 13:05:43 -06:00
snpdists Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
snpeff Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
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
sortmerna Add when: block (#1261) 2022-02-04 09:53:32 +01:00
sourmash/sketch Prettier (#1405) 2022-03-18 14:27:50 +01:00
spades Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
spatyper Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
sratools refactor: require NCBI user settings always 2022-05-11 13:02:52 +02:00
srst2/srst2 Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
ssuissero Prettier (#1405) 2022-03-18 14:27:50 +01:00
stadeniolib/scramble new tool: staden_io_lib (#1499) 2022-04-08 09:54:15 -04:00
staphopiasccmec Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
star Bump container version for STAR to 2.7.10a 2022-05-27 11:35:04 +01:00
stranger add stubs for stranger (#1543) 2022-04-22 10:10:43 +02:00
strelka Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
stringtie Rename process from STRINGTIE to STRINGTIE_STRINGTIE (#1546) 2022-04-22 15:13:06 +01:00
subread/featurecounts Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
svdb update svdb version 2022-05-06 00:18:16 +02:00
tabix fix bgziptabix extension (#1784) 2022-06-15 10:33:10 +02:00
tbprofiler/profile Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
tiddit TIDDIT - add --skip_assembly when no bwa specified (#1769) 2022-06-13 17:02:59 +02:00
transdecoder Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
trimgalore Add Trimgalore output for unpaired reads (#1568) 2022-04-26 19:15:24 +01:00
trimmomatic Trimmomatic (#1757) 2022-06-17 13:18:15 +00:00
ucsc add stub to modules used in raredisease pipeline (#1206) 2022-03-28 17:48:39 +02:00
ultra/pipeline Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
umitools Update umitools/dedup module to make --output-stats optional 2022-05-23 22:31:09 +01:00
unicycler Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
untar fix untar output dir 2022-06-02 11:09:55 +02:00
unzip Untar unzip meta (#1408) 2022-03-21 14:49:28 +01:00
vardictjava Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
variantbam Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
vcfanno add stub to modules used in raredisease pipeline (#1206) 2022-03-28 17:48:39 +02:00
vcflib/vcfuniq Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
vcftools Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
vsearch/usearchglobal Merge branch 'vsearch_usearch_global' of https://github.com/jtangrot/nf-core_modules into vsearch_usearch_global 2022-05-30 13:05:00 +02:00
yara Samtools version update (#1507) 2022-04-11 14:26:28 +02:00