<commit_before>{
    "global_tmp_dir": "$SNIC_TMP",
    "bowtie2_rules": {
        "load_env": "module load bioinfo-tools bowtie2/2.2.6 samtools/1.1",
        "platform": "Illumina",
        "mapping_params": {
            "default": ""
        }
    },
    "samtools_rules": {
        "load_env": "module load bioinfo-tools samtools/1.3 BEDTools/2.21.0 picard/1.118",
        "picard_jars": "/sw/apps/bioinfo/picard/1.118/milou",
        "threads_for_sorting": "16"
    },
    "mapping_report_rules": {},
    "kallisto_rules": {
        "load_env": "module load bioinfo-tools kallisto/0.43.0",
        "inputtable_script":  "toolbox/scripts/kallisto_concoct/input_table.py"
    },
    "concoct_rules": {
        "load_env": "source activate  && module load bioinfo-tools MUMmer/3.23 # CONCOCT dev f4cb9fcb",
        "mapper": "bowtie2",
        "mapping_params": "default",
        "concoct_params": {
            "cutoff-1000-maxcluster-1000": "-c 1000 -l 1000"
        },
        "scripts_dir": "CONCOCT/scripts"
    },
    "prodigal_rules": {
        "load_env": "module load bioinfo-tools prodigal/2.6.3 && source activate basic_sandbox",
        "length_script": "BLUEPRINT_pipeline/toolbox/scripts/fasta_lengths.py",<commit_msg>Added an actual environment for concoct to run in<commit_after>{
    "global_tmp_dir": "$SNIC_TMP",
    "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": {},
    "kallisto_rules": {
        "load_env": "module load bioinfo-tools kallisto/0.43.0",
        "inputtable_script":  "toolbox/scripts/kallisto_concoct/input_table.py"
    },
    "concoct_rules": {
        "load_env": "source activate snakemake_python2_env && 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": "CONCOCT/scripts"
    },
    "prodigal_rules": {
        "load_env": "module load bioinfo-tools prodigal/2.6.3 && source activate basic_sandbox",
        "length_script": "BLUEPRINT_pipeline/toolbox/scripts/fasta_lengths.py",
{'fraction_non_alphanumeric': 0.1519588444796201, 'fraction_numerical': 0.04155124653739612, 'mean_word_length': 2.6905109489051093, 'pattern_counts': {'":': 48, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4540039', 'n_tokens_mistral': 955, 'n_tokens_neox': 904, 'n_words': 146}