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James A. Fellows Yates 03de60e6fa
Add CHECKM/QA (#2137) 
* Bump checkM version and add support for pre-defined database

* Add markfile output to checkm/lineagewf and add checkm/qa

* Remove unnecessary BAM from tests

* Fix channels to ensure single meta

* Blah

* Use secondary name evwyhere

* Remove second incovcatiojn

* Don't run module directrly for join

* And for the other test

* Correct module name

* Fix name again

* Try and fix out_format 9 not being picked up

* Contains to matches to allow regex

* Fix tests (finally)

* Fix verisoning

* [automated] Fix linting with Prettier

* Update modules/checkm/qa/main.nf

Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>

Co-authored-by: nf-core-bot <core@nf-co.re>
Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
2022-09-30 15:50:47 +02:00
..
abacas Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
abricate Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
adapterremoval Refactor adapterremoval (#1491) 2022-04-04 21:40:35 +02:00
adapterremovalfixprefix Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
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 Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
amplify/predict Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
amps Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
amrfinderplus Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
angsd/docounts Add: ANGSD_DOCOUNTS (#2044) 2022-09-27 13:21:44 +02:00
antismash Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
ariba add module for ariba (#1731) 2022-06-15 10:18:31 -06:00
arriba Update Arriba to 2.3.0 (#1827) 2022-06-29 14:39:13 +02:00
artic Add manual version definition for artic modules (#1867) 2022-07-12 11:33:51 +01:00
ascat Added output files to ASCAT (#1820) 2022-06-28 14:45:57 +02:00
assemblyscan Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ataqv Ataqv mkarv (#1857) 2022-07-07 22:40:31 +02:00
atlas New Module: atlas/recal (#1915) 2022-07-22 15:36:53 +02:00
bakta Fix bakta: variable in main.nf (#2050) 2022-09-13 13:03:21 +02:00
bamaligncleaner Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bamcmp Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
bamtools Adding module bamtools stats (#2104) 2022-09-27 06:24:43 +01:00
bamutil/trimbam Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
bandage/image Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bases2fastq Add bases2fastq (#2054) 2022-09-15 13:50:33 +00:00
bbmap New module - BBMap clumpify (#1978) 2022-09-05 08:23:08 +02:00
bcftools Fix bcftools/stats module (#1953) 2022-09-21 16:10:38 +02:00
bcl2fastq Module/bcl2fastq (#1883) 2022-07-14 13:18:21 +02:00
bclconvert Bump bcl-convert version (#2077) 2022-09-16 14:34:52 +02:00
bedtools Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
biobambam bamsormadup: add extra test case, fix single file input (#1905) 2022-07-19 13:52:37 +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 Add blast/tblastn module (#2092) 2022-09-26 17:43:41 +02:00
bowtie Improve descriptions for modules with missing 2022-07-06 12:03:08 +02:00
bowtie2 Improve descriptions for modules with missing 2022-07-06 12:03:08 +02:00
bracken Add bracken/combinebrackenoutputs (#2022) 2022-09-07 09:18:21 +02:00
busco Update busco input type (#2135) 2022-09-29 21:35:51 +01:00
bwa Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
bwamem2 Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
bwameth Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
cat bugfix: when there is a single input file, stageAs("?/*) returns the path directly, not in a list (#2114) 2022-09-28 13:28:52 +01:00
cellranger Fixes incorrectly quoted tags (#2113) 2022-09-27 20:37:56 +01:00
centrifuge Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
checkm Add CHECKM/QA (#2137) 2022-09-30 15:50:47 +02:00
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 Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
cnvkit added fasta_fai as input + changed if statements 2022-06-02 12:57:50 +02:00
cnvpytor removed extra ) in the version strings (#1850) 2022-07-05 15:24:08 +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 Fix broken Quast module and bump MultiQC version in dumpsoftwareversions (#2108) 2022-09-27 09:35:52 +01:00
cutadapt Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
damageprofiler Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
dastool Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
dedup Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
deeparg Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
deepbgc Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
deeptools changed container + add cram2bam conversion 2022-06-02 10:38:05 +02:00
deepvariant Deepvariant - Update main.nf (#2110) 2022-09-27 15:34:10 +02:00
delly/call updated the version of delly (#2105) 2022-09-27 08:57:36 +02:00
diamond Update DIAMOND module to output log file (#1879) 2022-07-14 16:18:28 +02:00
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 2.1 (#2100) 2022-09-26 10:41:33 +01:00
ectyper Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
eido Fixes incorrectly quoted tags (#2113) 2022-09-27 20:37:56 +01:00
elprep Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
emmtyper Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
endorspy New Module: endorspy (#1916) 2022-09-28 11:28:11 +02:00
ensemblvep add stub and the option to compress output for vep (#2111) 2022-09-28 14:34:41 +02:00
entrezdirect Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
epang Make epang output meta with the jplace channel (#2073) 2022-09-16 10:22:50 +02:00
expansionhunter Improve descriptions for modules with missing 2022-07-06 12:03:08 +02:00
faqcs Prettier (#1405) 2022-03-18 14:27:50 +01:00
fargene Add HAMRONIZATION/FARGENE and updates all HARMONIZATION tools to 1.1.1 (#2107) 2022-09-27 15:32:18 +02:00
fastani Improve descriptions for modules with missing 2022-07-06 12:03:08 +02:00
fastawindows New module: fasta_windows (#1956) 2022-09-09 08:41:38 +01:00
fastk Add FastK/Merge (#1828) 2022-06-29 18:04:36 +02:00
fastp Fix duplicated input in single-end fastp command (#2034) 2022-09-09 11:08:52 +02:00
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
ffq Add ffq module (#1842) 2022-07-01 08:59:13 +02:00
fgbio Fgbio/fastqtobam (#1980) 2022-09-05 11:57:55 +02:00
filtlong Update filtlong module to output log file (#1873) 2022-07-12 17:05:31 +02:00
flash Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
flye Add new module: Flye (#1164) 2022-06-30 22:45:55 +02:00
fq/lint Added fq/lint module (#1968) 2022-08-24 10:20:39 +02:00
freebayes Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
gamma/gamma Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
gappa Adding gappa/examineheattree (#2084) 2022-09-22 15:51:25 +02:00
gatk Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
gatk4 Adding stubs to PicardLiftovervcf, GATK4_mergevcfs and filterMutectCalls (#1621) 2022-09-28 09:50:11 +02:00
gecco/run Update module: Gecco fix to no file generated if no hits found (#1930) 2022-07-27 15:19:43 +02:00
genescopefk Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
genmap Fixes incorrectly quoted tags (#2113) 2022-09-27 20:37:56 +01:00
genmod update options (#1959) 2022-08-22 16:26:05 +02:00
genomescope2 Update outputs and test data set 2022-05-11 10:42:17 +00:00
genotyphi/parse add module for mykrobe predict and genotyphi parse (#1818) 2022-09-26 15:18:04 +01:00
genrich Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
gfaffix Adding new module gfaffix (#1149) 2022-09-28 10:23:18 +02:00
gffread Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
glimpse/chunk Creation of Glimpse Chunk (#1985) 2022-09-01 10:01:49 +02:00
glnexus add stub to modules used in raredisease pipeline (#1206) 2022-03-28 17:48:39 +02:00
goat/taxonsearch 2012 bug related to species input in goattaxonsearch module (#2099) 2022-09-23 10:58:40 -06:00
graphmap2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
gstama Adjust requested ressources for gstama/merge, isoseq3/refine, lima, ultra/align (#1858) 2022-07-07 11:10:18 +01:00
gtdbtk/classifywf Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
gubbins Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
gunc Fixes incorrectly quoted tags (#2113) 2022-09-27 20:37:56 +01:00
gunzip Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
gvcftools/extractvariants added gvcftools/extractvariants (#1924) 2022-07-25 13:30:35 +02:00
hamronization Add HAMRONIZATION/FARGENE and updates all HARMONIZATION tools to 1.1.1 (#2107) 2022-09-27 15:32:18 +02:00
haplocheck fix: stub output name 2022-06-08 10:10:24 -03:00
haplogrep2/classify Add haplogrep2 (#2030) 2022-09-14 14:58:02 +02:00
happy Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
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 Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
hmmcopy Fixes incorrectly quoted tags (#2113) 2022-09-27 20:37:56 +01:00
hmmer Fixes incorrectly quoted tags (#2113) 2022-09-27 20:37:56 +01:00
hmtnote Update main.nf 2022-05-16 15:20:15 +00:00
homer Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
hpsuissero Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
ichorcna Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
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
instrain/profile Instrain profile (#1822) 2022-06-30 18:44:41 +02:00
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 Adjust requested ressources for gstama/merge, isoseq3/refine, lima, ultra/align (#1858) 2022-07-07 11:10:18 +01:00
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 Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
kallisto/index add stub for kallisto/index (#1944) 2022-08-09 09:23:55 +02:00
kallistobustools Improved kbtools/count (#1884) 2022-07-14 14:27:56 +02:00
kat/hist Add module kat hist 2022-05-06 07:54:10 +00:00
khmer Add khmer unique-kmers.py module (#1838) 2022-06-30 16:23:30 +01:00
kleborate Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
kraken2/kraken2 Improves kraken2 output glob (#1987) 2022-08-31 15:42:44 +02:00
krakentools Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
krona Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
last Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
leehom Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
legsta Prettier (#1405) 2022-03-18 14:27:50 +01:00
lima Adjust requested ressources for gstama/merge, isoseq3/refine, lima, ultra/align (#1858) 2022-07-07 11:10:18 +01:00
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 Update MALT to older version due to major bug in most recent version (#1796) 2022-06-20 08:20:22 +02:00
maltextract Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
manta Reduce resource requests (#2021) 2022-09-07 10:33:05 +02:00
mapdamage2 Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
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 Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
md5sum Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +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 Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
meningotype Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
merqury Add Merqury (#1647) 2022-07-14 10:38:50 +02:00
merquryfk Update Merqury version and sha (#2132) 2022-09-29 15:23:58 +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 Update METAPHLAN3_METAPHLAN3 to correct module name (#2056) 2022-09-15 09:09:55 +02:00
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 Added the meta map to minimap2/index (#1934) 2022-09-08 09:27:14 +01:00
mlst Add args to mlst (#1962) 2022-09-26 15:48:35 +01:00
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 Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
msisensor Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
msisensor2 Fixes incorrectly quoted tags (#2113) 2022-09-27 20:37:56 +01:00
msisensorpro Prettier (#1405) 2022-03-18 14:27:50 +01:00
mtnucratio Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
multiqc Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
multivcfanalyzer Fixes incorrectly quoted tags (#2113) 2022-09-27 20:37:56 +01:00
mummer Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
muscle Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
mykrobe/predict add module for mykrobe predict and genotyphi parse (#1818) 2022-09-26 15:18:04 +01:00
nanolyse Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
nanoplot Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
ncbigenomedownload Use a newer container version because the previous one is broken (#1933) 2022-08-22 11:18:09 +01:00
nextclade Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
nextgenmap New Module: NextGenMap (#1938) 2022-09-27 20:44:47 +01:00
ngmaster Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
ngscheckmate/ncm NGSCheckMate doesn't generate a pdf for only one sample, made optional output (#1839) 2022-06-30 17:43:34 +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 Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
paraclu Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
pasty add module for pasty (#2003) 2022-09-07 09:29:28 -06:00
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
pbptyper add module for pbptyper (#2005) 2022-09-07 15:29:03 -06:00
pear Add new module: Pear (#1779) 2022-07-15 10:28:31 +02:00
peddy Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
phantompeakqualtools Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
phyloflash Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
picard Adding stubs to PicardLiftovervcf, GATK4_mergevcfs and filterMutectCalls (#1621) 2022-09-28 09:50:11 +02:00
pints/caller fix(pints): Remove update check (#1989) 2022-09-08 05:03:48 +02:00
pirate add module for panaroo, fix pirate tests (#1444) 2022-03-24 20:11:04 -06:00
plasmidfinder Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
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 Update PORECHOP module to output log file (#1870) 2022-07-12 16:07:31 +02:00
preseq Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
prinseqplusplus Add PRINSEQPLUSPLUS (#1481) 2022-04-03 16:06:22 +02:00
prodigal Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
prokka [bug] pin bioperl version in Prokka module (#1307) 2022-09-28 01:34:23 +01:00
pycoqc Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
pydamage Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
qcat Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
qualimap Fix broken Quast module and bump MultiQC version in dumpsoftwareversions (#2108) 2022-09-27 09:35:52 +01:00
quast Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
racon Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
rapidnj Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
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 RGI/main export versions as explicit emission strings (#1909) 2022-07-20 10:33:53 +02:00
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 fasta module (#2128) 2022-09-29 08:10:44 +01:00
scoary Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
scramble New module: scramble (#2015) 2022-09-07 13:19:18 +02:00
seacr/callpeak Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
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 Fixes incorrectly quoted tags (#2113) 2022-09-27 20:37:56 +01:00
sequenzautils Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
seqwish/induce Bump seqwish/induce to v0.7.6 (#2083) 2022-09-26 17:01:21 +01:00
seroba/run add module for seroba (#1816) 2022-09-26 16:06:08 +01:00
sexdeterrmine Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +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 Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
snapaligner snapaligner: improve index detection (#1836) 2022-06-30 12:19:46 +02:00
snippy add snippy/core module (#1855) 2022-09-08 06:58:10 +02:00
snpdists Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
snpeff DRAFT: Extend output from snpeff (#1895) 2022-07-16 20:08:52 +02:00
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
somalier Somalier relate (#2001) 2022-09-19 13:22:24 +02:00
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 Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
spatyper Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
sratools refactor: move files to custom section 2022-05-11 17:33:45 +02:00
srst2/srst2 Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
ssuissero Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
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 Add stub star align genomegenerate (#1948) 2022-08-09 09:42:19 +02:00
stranger add stubs for stranger (#1543) 2022-04-22 10:10:43 +02:00
strelka Reduce resource requests (#2021) 2022-09-07 10:33:05 +02:00
stringtie Make stringtie/merge arguments configurable (#2049) 2022-09-26 14:26:53 +01:00
subread/featurecounts Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
svdb update stub for svdb/merge (#2066) 2022-09-15 14:20:09 +02:00
svtk/standardize new module: svtk/standardize (#2031) 2022-09-08 15:03:08 +02:00
tabix Explicitly name the output files to avoid the gzi index being flown through the output channel (#2136) 2022-09-30 13:31:48 +01:00
tailfindr Tailfindr (#1904) 2022-07-22 16:20:53 +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 Update cores specification in TrimGalore module (#2127) 2022-09-28 15:47:27 +02:00
trimmomatic Trimmomatic (#1757) 2022-06-17 13:18:15 +00:00
ucsc Set process label to process_single for modules with no task.cpus usage (#2076) 2022-09-19 11:54:47 +02:00
ultra Adjust requested ressources for gstama/merge, isoseq3/refine, lima, ultra/align (#1858) 2022-07-07 11:10:18 +01:00
umitools Set PYTHONHASHSEED for umitools dedup (#1932) 2022-08-31 14:05:12 +01:00
unicycler Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
untar Fix for nested directories in tar archive (#2062) 2022-09-15 11:32:36 +02:00
unzip Reduce resource requests (#2021) 2022-09-07 10:33:05 +02:00
vardictjava Added java options to vardict java (#1695) 2022-08-10 14:13:03 +02:00
variantbam Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
vcf2db Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
vcf2maf Update manual versioning (#1813) 2022-06-27 10:35:41 +02:00
vcfanno small changes to vcfanno (#1804) 2022-06-24 08:58:26 +02:00
vcflib/vcfuniq Bump tool versions for modules required in viralrecon (#1859) 2022-07-07 14:48:04 +01:00
vcftools Reduce resource requests (#2021) 2022-09-07 10:33:05 +02:00
vsearch New module: Vsearch sintax (#2094) 2022-09-26 14:45:01 +01:00
whamg New module: Whamg (#1994) 2022-09-02 13:33:48 +02:00
yara Samtools version update (#1507) 2022-04-11 14:26:28 +02:00