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nf-core_modules/modules
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Davi Marcon 59ca7444cf
Adding plink/vcf module (#656) 
* adding plink module using nf-core tool [ci skip]

* Restructures the project for plink/vcf (#1)

* Add version string for plink
* Create a plink/vcf module

* small tweaks on main.nf and started to test [ci skip]

* small changes on test args, local test with docker passed!

* Update plink/vcf module listing

* Update tag

* fix tags as per linting guidelines

* revert to the original state of tags

* adding --threads to `main.nf` and `meta.yml` information

Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com>
2021-09-14 08:51:40 +02:00
..
abacas Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
adapterremoval Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
allelecounter nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
arriba Added module arriba (#611) 2021-07-22 15:19:42 +01:00
artic Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
bandage/image Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
bbmap Bbmap index (#683) 2021-09-03 09:28:28 +02:00
bcftools Add bcftools/view module (#669) 2021-09-12 19:51:40 +02:00
bedtools Add bedtools/makewindows module (#658) 2021-09-07 14:36:06 -04:00
bismark Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
blast nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
bowtie Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
bowtie2 nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
bwa update: BWA/ALN (#653) 2021-08-17 15:55:54 +02:00
bwamem2 Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
bwameth Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
cat/fastq Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
cnvkit nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
cooler update typos. change quote from ' to ". (#652) 2021-08-16 11:57:22 +02:00
cutadapt nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
damageprofiler Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
deeptools nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
delly/call Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
dragonflye add module for dragonflye (#633) 2021-08-16 11:51:30 +02:00
dshbio Add dsh-bio export-segments module (#631) 2021-08-17 15:53:41 +02:00
ensemblvep Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
expansionhunter Expansionhunter (#666) 2021-08-16 17:47:42 +02:00
fastp enhance module fastp: add save_merged (#598) (#614) 2021-07-23 10:44:00 +01:00
fastqc Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
fasttree Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
fgbio Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
flash Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
gatk4 Mutect2 (#682) 2021-09-13 16:16:23 +01:00
genmap Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
gffread Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
graphmap2 Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
gubbins nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
gunzip Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
hifiasm Add hifiasm module (#596) 2021-07-20 21:50:22 +01:00
hisat2 nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
hmmer/hmmalign Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
homer Homer Modules (#75) 2021-09-08 15:40:34 +00:00
iqtree nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
ivar Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
kallisto/index Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
kallistobustools nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
kraken2/kraken2 Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
last nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
lib Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
lofreq fix: lofreq/callparallel missing arg (#562) (#586) 2021-07-19 09:19:27 +01:00
macs2/callpeak Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
malt module: MALT/RUN (#646) 2021-08-04 11:06:08 +02:00
mash/sketch Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
metaphlan3 nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
methyldackel nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
minia Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
minimap2 nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
mosdepth nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
msisensor Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
multiqc nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
muscle Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
nanolyse Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
nanoplot nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
nextclade Update Nextclade to output all files by default (#638) 2021-07-28 19:49:50 +01:00
optitype Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
pairix Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
pairtools Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
pangolin Bump Pangolin to 3.1.7 (#593) 2021-07-20 12:25:36 +01:00
phantompeakqualtools Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
picard nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
plasmidid Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
plink/vcf Adding plink/vcf module (#656) 2021-09-14 08:51:40 +02:00
preseq/lcextrap Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
prodigal nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
prokka Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
pycoqc Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
qcat Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
qualimap Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
quast Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
rapidnj Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
rasusa Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
raxmlng nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
rsem Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
rseqc Require r-base>=3.5 for RSeqC Conda envs (#654) 2021-08-05 18:59:56 +01:00
salmon nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
samtools nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
seacr/callpeak Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
seqkit/split2 nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
seqtk Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
sequenzautils Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
seqwish/induce Update seqwish reported version to match bioconda version. (#678) 2021-08-26 15:33:38 -05:00
shovill nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
snpeff Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
snpsites Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
sortmerna Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
spades nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
star Added PL tag in read group information for downstream analysis (#649) 2021-08-04 11:16:51 +02:00
strelka/germline Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
stringtie Add option -p to set the # of cpus on stringtie (#601) 2021-07-21 15:38:40 +02:00
subread/featurecounts Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
tabix nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
tiddit/sv Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
trimgalore nf-core modules bump-versions for all modules (#630) 2021-07-28 09:10:44 +01:00
ucsc Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
umitools Add --paired flag to umitools dedup and bump to 1.1.2 (#583) 2021-07-16 14:21:08 +01:00
unicycler Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
untar Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
unzip module: unzip (#642) 2021-08-02 09:40:57 +02:00
variantbam Add variantbam (#618) 2021-07-26 19:07:29 +01:00
vcftools Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00
yara Rename software/ directory to modules/ to re-organise module structure (#567) 2021-07-07 10:10:18 +01:00