├── .dockerignore ├── .gitignore ├── Dockerfile ├── LICENSE ├── README.md ├── bin ├── bracken2dt.R └── bracken2summary.R ├── environment.yml ├── main.nf ├── nextflow.config └── testdata ├── minigut_sample1_R1.fastq.gz ├── minigut_sample1_R2.fastq.gz ├── minigut_sample2_R1.fastq.gz ├── minigut_sample2_R2.fastq.gz └── zymo-test.fastq /.dockerignore: -------------------------------------------------------------------------------- 1 | .git 2 | .nextflow* 3 | work 4 | results* 5 | testdata* -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .nextflow* 2 | .DS_Store 3 | *.report 4 | results* 5 | work 6 | .Rhistory 7 | -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/angelovangel/nxf-kraken2/HEAD/Dockerfile -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/angelovangel/nxf-kraken2/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/angelovangel/nxf-kraken2/HEAD/README.md -------------------------------------------------------------------------------- /bin/bracken2dt.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/angelovangel/nxf-kraken2/HEAD/bin/bracken2dt.R -------------------------------------------------------------------------------- /bin/bracken2summary.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/angelovangel/nxf-kraken2/HEAD/bin/bracken2summary.R -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/angelovangel/nxf-kraken2/HEAD/environment.yml -------------------------------------------------------------------------------- /main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/angelovangel/nxf-kraken2/HEAD/main.nf -------------------------------------------------------------------------------- /nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/angelovangel/nxf-kraken2/HEAD/nextflow.config -------------------------------------------------------------------------------- /testdata/minigut_sample1_R1.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/angelovangel/nxf-kraken2/HEAD/testdata/minigut_sample1_R1.fastq.gz -------------------------------------------------------------------------------- /testdata/minigut_sample1_R2.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/angelovangel/nxf-kraken2/HEAD/testdata/minigut_sample1_R2.fastq.gz -------------------------------------------------------------------------------- /testdata/minigut_sample2_R1.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/angelovangel/nxf-kraken2/HEAD/testdata/minigut_sample2_R1.fastq.gz -------------------------------------------------------------------------------- /testdata/minigut_sample2_R2.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/angelovangel/nxf-kraken2/HEAD/testdata/minigut_sample2_R2.fastq.gz -------------------------------------------------------------------------------- /testdata/zymo-test.fastq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/angelovangel/nxf-kraken2/HEAD/testdata/zymo-test.fastq --------------------------------------------------------------------------------