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58134cb929
* Initialise chromap module * Revert "Initialise chromap module" This reverts commit 47c67ae231a6f221ef5b9b7b444b583b5406852b. * Remake chromap base files with new layout * Copy chromap * Copy index * Add compression * Update padding * Update container * Update chromap input test data * Add chromap chromap tests * Add padding * Update comment * update yaml file * Remove TODOs * Add fasta input to yaml * Update YAML * Remove comment, update container * Remove comments * Import Chromap index * Update test.yml * Fix read input * Update test.yml * Add bcftools/concat module. (#641) * draft for bcftools modules [ci skip] * initial test for bcftools concat * Update the params for testing * fix tests * Accomodate code review [ci skip] Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update the meta file and open PR for review * Update the keyword * Update the tags for module [ci skip[ * add threads Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add module for dragonflye (#633) * add module for dragonflye * fix tests for dragonflye * Update test.yml * Update meta.yml * Update main.nf * Update main.nf * Update modules/dragonflye/meta.yml Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * update typos. change quote from ' to ". (#652) * Add bcftools/norm module (#655) * Initial draft [ci skip] * trigger first test * update output file path * Tests passing * finishing touches for meta.yml and update checksum * tweak checksum * add threads to the module * skip version info for matching test md5sum [ci skip] * Add ref fasta and finalize the module Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * Expansionhunter (#666) Please enter the commit message for your changes. Lines starting * adds expansionhunter module Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * Update test.yml (#668) * Specify in guidelines one should split CPUs when module has n > 1 tool (#660) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Describe CPU splitting * Update README.md Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * More CPU examples Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * Add dsh-bio export-segments module (#631) Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * update: `BWA/ALN` (#653) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Remove reads from output channel following module guidelines. Should do a .join() based on $meta, to reassociate. Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * Update seqwish reported version to match bioconda version. (#678) * Bbmap index (#683) BBMap index module * Initialise chromap module * Revert "Initialise chromap module" This reverts commit 47c67ae231a6f221ef5b9b7b444b583b5406852b. * Remove unnecessary files * Remove unnecessary files * Update modules/chromap/index/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/chromap/index/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/chromap/chromap/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/chromap/chromap/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/chromap/chromap/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/chromap/chromap/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/chromap/index/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Remove pytest_software.yml * Apply suggestions from code review Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: JIANHONG OU <jianhong@users.noreply.github.com> Co-authored-by: Anders Jemt <jemten@users.noreply.github.com> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> Co-authored-by: Michael L Heuer <heuermh@acm.org> Co-authored-by: Daniel Lundin <daniel.lundin@lnu.se> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> |
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.. | ||
abacas | ||
adapterremoval | ||
allelecounter | ||
arriba | ||
artic | ||
bamaligncleaner | ||
bandage/image | ||
bbmap | ||
bcftools | ||
bedtools | ||
bismark | ||
blast | ||
bowtie | ||
bowtie2 | ||
bwa | ||
bwamem2 | ||
bwameth | ||
cat/fastq | ||
chromap | ||
cnvkit | ||
cooler | ||
cutadapt | ||
damageprofiler | ||
deeptools | ||
delly/call | ||
dragonflye | ||
dshbio | ||
ensemblvep | ||
expansionhunter | ||
fastp | ||
fastqc | ||
fasttree | ||
fgbio | ||
flash | ||
gatk4 | ||
genmap | ||
gffread | ||
graphmap2 | ||
gubbins | ||
gunzip | ||
hifiasm | ||
hisat2 | ||
hmmer/hmmalign | ||
homer | ||
iqtree | ||
ivar | ||
kallisto/index | ||
kallistobustools | ||
kraken2/kraken2 | ||
last | ||
lofreq | ||
malt | ||
mash/sketch | ||
metaphlan3 | ||
methyldackel | ||
minia | ||
minimap2 | ||
mosdepth | ||
msisensor | ||
multiqc | ||
muscle | ||
nanolyse | ||
nanoplot | ||
nextclade | ||
optitype | ||
pairix | ||
pairtools | ||
pangolin | ||
picard | ||
plasmidid | ||
plink/vcf | ||
preseq/lcextrap | ||
prodigal | ||
prokka | ||
pycoqc | ||
qcat | ||
qualimap/bamqc | ||
quast | ||
rapidnj | ||
rasusa | ||
raxmlng | ||
rsem | ||
rseqc | ||
salmon | ||
samtools | ||
seacr/callpeak | ||
seqkit/split2 | ||
seqtk | ||
sequenzautils | ||
seqwish/induce | ||
shovill | ||
snpdists | ||
snpeff | ||
snpsites | ||
spades | ||
star | ||
strelka/germline | ||
stringtie | ||
subread/featurecounts | ||
tabix | ||
tiddit/sv | ||
trimgalore | ||
ucsc | ||
unicycler | ||
untar | ||
unzip | ||
variantbam | ||
vcftools | ||
yara |