├── .gitignore ├── LICENSE ├── README.md ├── bio └── ngs │ └── rules │ ├── annotation │ ├── dbcan.rules │ ├── ec.rules │ ├── eggnog.rules │ ├── eggnog_mapper.rules │ ├── hmmer.rules │ ├── pfam.rules │ ├── prodigal.rules │ └── prokka.rules │ ├── assembly │ ├── megahit.rules │ ├── merge.rules │ ├── ray.rules │ └── report.rules │ ├── binning │ ├── binning_annotation.rules │ ├── binning_eval.rules │ ├── concoct.rules │ └── metabat.rules │ ├── blast │ └── rpsblast.rules │ ├── duplicate_removal │ └── fastuniq.rules │ ├── mapping │ ├── bowtie2.rules │ ├── report.rules │ └── samtools.rules │ ├── quality_control │ ├── fastqc.rules │ └── internal_standards.rules │ ├── quantification │ ├── bowtie2.rules │ ├── bowtie2_average_coverage.rules │ ├── gattaca.rules │ ├── kallisto.rules │ └── khmer.rules │ ├── taxonomic_annotation │ ├── diamond.rules │ ├── lca_script.rules │ ├── megan.rules │ └── metaxa.rules │ └── trimming │ ├── cutadapt.rules │ └── trimmomatic.rules ├── common └── rules │ ├── compression.rules │ └── track_dir.rules ├── scheduling ├── Snakefile_qsub.py └── Snakefile_sbatch.py └── workflows ├── large_coassembly ├── Snakefile ├── config.json └── config_sbatch.json └── seperate_assemblies ├── Snakefile ├── config.json └── config_sbatch.json /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/README.md -------------------------------------------------------------------------------- /bio/ngs/rules/annotation/dbcan.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/annotation/dbcan.rules -------------------------------------------------------------------------------- /bio/ngs/rules/annotation/ec.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/annotation/ec.rules -------------------------------------------------------------------------------- /bio/ngs/rules/annotation/eggnog.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/annotation/eggnog.rules -------------------------------------------------------------------------------- /bio/ngs/rules/annotation/eggnog_mapper.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/annotation/eggnog_mapper.rules -------------------------------------------------------------------------------- /bio/ngs/rules/annotation/hmmer.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/annotation/hmmer.rules -------------------------------------------------------------------------------- /bio/ngs/rules/annotation/pfam.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/annotation/pfam.rules -------------------------------------------------------------------------------- /bio/ngs/rules/annotation/prodigal.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/annotation/prodigal.rules -------------------------------------------------------------------------------- /bio/ngs/rules/annotation/prokka.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/annotation/prokka.rules -------------------------------------------------------------------------------- /bio/ngs/rules/assembly/megahit.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/assembly/megahit.rules -------------------------------------------------------------------------------- /bio/ngs/rules/assembly/merge.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/assembly/merge.rules -------------------------------------------------------------------------------- /bio/ngs/rules/assembly/ray.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/assembly/ray.rules -------------------------------------------------------------------------------- /bio/ngs/rules/assembly/report.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/assembly/report.rules -------------------------------------------------------------------------------- /bio/ngs/rules/binning/binning_annotation.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/binning/binning_annotation.rules -------------------------------------------------------------------------------- /bio/ngs/rules/binning/binning_eval.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/binning/binning_eval.rules -------------------------------------------------------------------------------- /bio/ngs/rules/binning/concoct.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/binning/concoct.rules -------------------------------------------------------------------------------- /bio/ngs/rules/binning/metabat.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/binning/metabat.rules -------------------------------------------------------------------------------- /bio/ngs/rules/blast/rpsblast.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/blast/rpsblast.rules -------------------------------------------------------------------------------- /bio/ngs/rules/duplicate_removal/fastuniq.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/duplicate_removal/fastuniq.rules -------------------------------------------------------------------------------- /bio/ngs/rules/mapping/bowtie2.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/mapping/bowtie2.rules -------------------------------------------------------------------------------- /bio/ngs/rules/mapping/report.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/mapping/report.rules -------------------------------------------------------------------------------- /bio/ngs/rules/mapping/samtools.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/mapping/samtools.rules -------------------------------------------------------------------------------- /bio/ngs/rules/quality_control/fastqc.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/quality_control/fastqc.rules -------------------------------------------------------------------------------- /bio/ngs/rules/quality_control/internal_standards.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/quality_control/internal_standards.rules -------------------------------------------------------------------------------- /bio/ngs/rules/quantification/bowtie2.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/quantification/bowtie2.rules -------------------------------------------------------------------------------- /bio/ngs/rules/quantification/bowtie2_average_coverage.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/quantification/bowtie2_average_coverage.rules -------------------------------------------------------------------------------- /bio/ngs/rules/quantification/gattaca.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/quantification/gattaca.rules -------------------------------------------------------------------------------- /bio/ngs/rules/quantification/kallisto.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/quantification/kallisto.rules -------------------------------------------------------------------------------- /bio/ngs/rules/quantification/khmer.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/quantification/khmer.rules -------------------------------------------------------------------------------- /bio/ngs/rules/taxonomic_annotation/diamond.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/taxonomic_annotation/diamond.rules -------------------------------------------------------------------------------- /bio/ngs/rules/taxonomic_annotation/lca_script.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/taxonomic_annotation/lca_script.rules -------------------------------------------------------------------------------- /bio/ngs/rules/taxonomic_annotation/megan.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/taxonomic_annotation/megan.rules -------------------------------------------------------------------------------- /bio/ngs/rules/taxonomic_annotation/metaxa.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/taxonomic_annotation/metaxa.rules -------------------------------------------------------------------------------- /bio/ngs/rules/trimming/cutadapt.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/trimming/cutadapt.rules -------------------------------------------------------------------------------- /bio/ngs/rules/trimming/trimmomatic.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/bio/ngs/rules/trimming/trimmomatic.rules -------------------------------------------------------------------------------- /common/rules/compression.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/common/rules/compression.rules -------------------------------------------------------------------------------- /common/rules/track_dir.rules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/common/rules/track_dir.rules -------------------------------------------------------------------------------- /scheduling/Snakefile_qsub.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/scheduling/Snakefile_qsub.py -------------------------------------------------------------------------------- /scheduling/Snakefile_sbatch.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/scheduling/Snakefile_sbatch.py -------------------------------------------------------------------------------- /workflows/large_coassembly/Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/workflows/large_coassembly/Snakefile -------------------------------------------------------------------------------- /workflows/large_coassembly/config.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/workflows/large_coassembly/config.json -------------------------------------------------------------------------------- /workflows/large_coassembly/config_sbatch.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/workflows/large_coassembly/config_sbatch.json -------------------------------------------------------------------------------- /workflows/seperate_assemblies/Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/workflows/seperate_assemblies/Snakefile -------------------------------------------------------------------------------- /workflows/seperate_assemblies/config.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/workflows/seperate_assemblies/config.json -------------------------------------------------------------------------------- /workflows/seperate_assemblies/config_sbatch.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EnvGen/snakemake-workflows/HEAD/workflows/seperate_assemblies/config_sbatch.json --------------------------------------------------------------------------------