mirror of
https://github.com/MillironX/nf-core_modules.git
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63b3975292
* new gubbins module * new gubbins module * new gubbins module * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * Update tests/config/test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * new gubbins module * new gubbins module * new snpsites module * new snpsites module * new snpsites module * new snpsites module * adding fasttree module * correct trailing whitespace * using sarscov2 as a test dir * use sars-cov-2 alignment * remove old test alignment * new snpsites module * new snpsites module * new snpsites module * updated test file names * new snpsites module * remove snpsites from gubbins branch * remove redundant test_fas alignment * update md5 sums Co-authored-by: avantonder <avt@sanger.ac.uk> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: avantonder <ajv37@cam.ac.uk> |
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| .. | ||
| adapterremoval | ||
| allelecounter | ||
| bandage/image | ||
| bcftools | ||
| bedtools | ||
| bismark | ||
| blast | ||
| bowtie | ||
| bowtie2 | ||
| bwa | ||
| bwamem2 | ||
| bwameth | ||
| cat/fastq | ||
| cnvkit | ||
| cutadapt | ||
| dsh | ||
| fastp | ||
| fastqc | ||
| fasttree | ||
| fgbio | ||
| flash | ||
| gatk4 | ||
| gffread | ||
| gubbins | ||
| gunzip | ||
| hisat2 | ||
| homer/annotatepeaks | ||
| ivar | ||
| kallisto/index | ||
| kraken2/run | ||
| methyldackel | ||
| minia | ||
| minimap2/align | ||
| mosdepth | ||
| msisensor | ||
| multiqc | ||
| optitype | ||
| pangolin | ||
| picard | ||
| plasmidid | ||
| preseq/lcextrap | ||
| prodigal | ||
| prokka | ||
| qualimap/bamqc | ||
| quast | ||
| salmon | ||
| samtools | ||
| seacr/callpeak | ||
| seqkit/split2 | ||
| sequenzautils | ||
| seqwish/induce | ||
| shovill | ||
| spades | ||
| star | ||
| strelka/germline | ||
| stringtie | ||
| subread/featurecounts | ||
| tabix | ||
| tiddit/sv | ||
| trimgalore | ||
| ucsc | ||
| unicycler | ||
| untar | ||
| vcftools | ||
| yara | ||