nextflow-pipeline 105 nextflow 39 bioinformatics 17 bioinformatics-pipeline 9 workflow 8 pipeline 8 variant-calling 7 rna-seq 6 bacteria 5 genomics 5 nanopore 4 nanopore-analysis-pipeline 4 qc 4 metagenomics 4 annotation 4 nextflow-pipelines 4 illumina 4 dsl2 4 assembly 4 genome-assembly 3 microbial-genomics 3 nextflow-workflow 3 antimicrobial-resistance 3 docker 3 ngs-pipeline 3 denovo-assembly 3 metatranscriptomics 3 genome-annotation 3 nf-core 3 quality-control 3 bacterial-genome-analysis 3 bacterial-genomes 3 oxford-nanopore 2 python 2 research 2 nanopore-sequencing 2 singularity 2 wgs 2 nextflow-process 2 rna-seq-analysis 2 nextflow-dsl2 2 proteomics 2 rna-seq-pipeline 2 genome 2 rnaseq-analysis 2 somatic-variants 2 bioinformatics-tool 2 rna-structure 2 tuberculosis 2 workflows 2 sars-cov-2 2 mycobacterium-tuberculosis 2 ont 2 posseleff-paper 2 template 2 demultiplexing 2 clonal-evolution 1 scrnaseq 1 hybrid-assembly 1 downstream-analysis 1 next-generation-sequencing 1 rnaseq 1 bcl2fastq 1 fastq-files 1 sra-toolkit 1 interop 1 metrics 1 grapevine 1 low-frequency-variants 1 panel 1 wes 1 proteowizard 1 shotgun-metagenomics 1 dag 1 directed-acyclic-graph 1 groovy 1 groovy-language 1 nextflow-tutorial 1 nextflow-lang 1 nextflow-language 1 nextflow-training 1 sequence-alignment 1 quast 1 gene-prediction 1 fastp 1 consensus-sequences 1 scalability-across-computational-environments 1 spades 1 bash-script 1 bioconductor 1 dynamic-command-construction-for-preprocessing 1 metanetx 1 deseq2 1 snp 1 pangenome 1 dge-analysis 1 comparative-genomics 1 miniconda 1 a-detailed-demonstration-of-naming-consistency 1 miniconda-environments 1