config.json

{
    "bowtie2_rules": {
        "load_env": "module load bioinfo-tools bowtie2/2.2.6 samtools/1.1",
        "platform": "Illumina",
        "mapping_params": {
            "default": ""
        }
    },
    "samtools_rules": {
        "load_env": "module load bioinfo-tools samtools/1.3 BEDTools/2.21.0 picard/1.118",
        "picard_jars": "/sw/apps/bioinfo/picard/1.118/milou",
        "threads_for_sorting": "16"
    },
    "mapping_report_rules": {},
    "concoct_rules": {
        "load_env": "source activate  && module load bioinfo-tools MUMmer/3.23 # CONCOCT dev f4cb9fcb",
        "mapper": "bowtie2",
        "mapping_params": "default",
        "concoct_params": {
            "cutoff-1000-maxcluster-1000": "-c 1000 -l 1000"
        },
        "scripts_dir": "~/repos/CONCOCT/scripts"
    },
    "prodigal_rules": {
        "load_env": "module load bioinfo-tools prodigal/2.60",
        "prodigal_params": {
            "default-meta": "-p meta"
        }
    },
    "rpsblast_rules": {
        "load_env": "module load bioinfo-tools blast/2.2.29+ gnuparallel/20140222",
        "rpsblast_params": {
            "default-concoct": "-outfmt '6 qseqid sseqid evalue pident score qstart qend sstart send length slen' -max_target_seqs 1 -evalue 0.00001",
            "only-evalue": "-outfmt '6 qseqid sseqid evalue pident score qstart qend sstart send length slen' -evalue 0.00001"
        },
        "databases": {
            "cog": "/sw/data/uppnex/cdd/little_endian/Cog",
            "pfam": "/sw/data/uppnex/cdd/little_endian/Pfam",
            "tigr": "/sw/data/uppnex/cdd/little_endian/Tigr"
        },
        "parallel_params": "-N 16 --env PATH",
        "query_aas": {}
    },
    "hmmer_rules": {
        "load_env": "module load bioinfo-tools hmmer/3.1b1-gcc",
        "hmmer_params": {
            "default-concoct": "-E 0.0001 --cpu 16"
        },
        "databases": {
            "all_pog": ""
        }
    },
    "fastqc_rules": {
        "load_env": "module load bioinfo-tools FastQC/0.11.2"
    },
    "cutadapt_rules": {
        "load_env": "module load bioinfo-tools cutadapt/1.8.0",
        "trim_params": {
            "quality_and_indices": {
                "1": {
                    "trim_end": "-q 15,15",
                    "trim_start": "-u 0"
                    },
                "2": {
                    "trim_end": "-q 15,15",
                    "trim_start": "-u 0"
                    },
                "variable_template": "-n 3 --minimum-length 31 -a {R1_first}{R1_index}{R1_end} -G '^CGTGTGCTCTTCCGATCT' -A {R2_rev_end}{R2_rev_index}{R2_rev_first}",
                "common_variables": {
                    "R1_first": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
                    "R1_end": "ATCTCGTATGCCGTCTTCTGCTTG",
                    "R2_rev_end": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT",
                    "R2_rev_first": "GTGTAGATCTCGGTGGTCGCCGTATCATT"
                }
            }
        }
    },
    "fastuniq_rules": {
    },
    "megahit_rules": {
        "load_env": "source activate concoct",
        "assembly_params": {"default": ""},
        "coassembly_params": {"default": "-m 0.99 --continue"},
        "filter_length_script": "toolbox/scripts/filter_fasta_on_length.py",
        "split_in_parts_script": "toolbox/scripts/split_fasta.py",
        "coassembly_pre_annotation_length_threshold": "500",
        "coassembly_pre_annotation_sequences_per_part": "100000"
    },
    "assembly_dir": ["assembly/"],
    "toolbox_dir": "toolbox",
    "prokka_extended_rules": {
        "dbs": ["cog", "pfam", "tigr"],
        "prokka_name": "prokka_mod",
        "load_env": "source activate concoct && module load bioinfo-tools BioPerl blast/2.2.28+ hmmer prodigal gnuparallel",
        "cddid_all": "/proj/b2010008/nobackup/database/cddid_all.tbl",
        "get_prokka_annotation_script": "toolbox/scripts/extended_prokka/get.prokka.annotation.py",
        "collate_annotations_script": "toolbox/scripts/extended_prokka/collate.annotations.py",
        "gff_to_bed_script": "toolbox/scripts/extended_prokka/prokkagff2bed.sh",
        "prokka_ops": "--metagenome",
        "EXTEND": {
            "gff": "toolbox/scripts/extended_prokka/extend_gff.py"
        },
        "contigs": {},
        "threads": "4",
        "locustags": {},
        "include_evalue_for_tables": "true",
        "rpsblast_parameter_set": {
            "pfam": "only-evalue",
            "cog": "default-concoct",
            "tigr": "default-concoct"
        },
        "multiple_annotations_per_gene": {
            "pfam": "true",
            "cog": "false",
            "tigr", "false"
        }
    },
    "kallisto_rules": {
        "load_env": "",
        "references": {},
        "samples": {},
        "units": {}
    },
    "bowtie2_quant_rules": {
        "load_env": "source activate basic_sandbox && module load bioinfo-tools BEDTools/2.25.0",
        "references": {},
        "samples": {},
        "units": {},
        "reference_for_ref_set": {},
        "mapping_params": {
            "default": ""
        },
        "mapper": "bowtie2",
        "scripts_dir": "~/repos/CONCOCT/scripts",
        "rpkm_table_script": "toolbox/scripts/rpkm_table.py",
        "coverage_for_genes_script": "toolbox/scripts/extended_prokka/get_gene_coverage.py",
        "split_ref_sets": {},
        "rpkm_annotations_table_script": "toolbox/scripts/rpkm_annotations_table.py"
    }
}