<commit_before>samples_pe:
    pe1:
        forward: data/fastq_raw/test1_1.fastq.gz
        reverse: data/fastq_raw/test1_2.fastq.gz
        adaptor: ./data/adapters/TruSeq3-PE-2.fa
        phred:   phred33
    pe2:
        forward: data/fastq_raw/test2_1.fastq.gz
        reverse: data/fastq_raw/test2_2.fastq.gz
        adaptor: ./src/adapters/TruSeq3-PE-2.fa
        phred:   phred33

samples_se:
    se3:
        single:   data/fastq_raw/test3.fastq.gz
        adaptor:  ./data/adapters/TruSeq3-PE-2.fa
        phred:    phred33


trimmomatic_params:
    "LEADING:20 TRAILING:20 AVGQUAL:30 MINLEN:32 TOPHRED33"


# Consider this if you change the values:
# http://khmer.readthedocs.org/en/v1.0/choosing-table-sizes.html
diginorm_params:
    ksize: "32" # Remember to set MINLEN in trimmomatic_params at least this value!
    cutoff: "20"
    n_tables: "4"   # n_tables * max_table_size must be < your RAM in bytes
    max_table_size: "1e9" # 4 tables * 1e9 (~1GB) ~ 4Gb - Raise it to 4e9 for nontesting purposes

trinity_params:
    memory: "2G"

kallisto_params:
    "--bootstrap-samples=100 --bias"<commit_msg>Reduced ram usage for travis<commit_after>samples_pe:
    pe1:
        forward: data/fastq_raw/test1_1.fastq.gz
        reverse: data/fastq_raw/test1_2.fastq.gz
        adaptor: ./data/adapters/TruSeq3-PE-2.fa
        phred:   phred33
    pe2:
        forward: data/fastq_raw/test2_1.fastq.gz
        reverse: data/fastq_raw/test2_2.fastq.gz
        adaptor: ./src/adapters/TruSeq3-PE-2.fa
        phred:   phred33

samples_se:
    se3:
        single:   data/fastq_raw/test3.fastq.gz
        adaptor:  ./data/adapters/TruSeq3-PE-2.fa
        phred:    phred33


trimmomatic_params:
    "LEADING:20 TRAILING:20 AVGQUAL:30 MINLEN:32 TOPHRED33"


# Consider this if you change the values:
# http://khmer.readthedocs.org/en/v1.0/choosing-table-sizes.html
diginorm_params:
    ksize: "32" # Remember to set MINLEN in trimmomatic_params at least this value!
    cutoff: "20"
    n_tables: "4"   # n_tables * max_table_size must be < your RAM in bytes
    max_table_size: "1e8" # 4 tables * 1e9 (~1GB) ~ 4Gb - Raise it to 4e9 for nontesting purposes

trinity_params:
    memory: "2G"

kallisto_params:
    "--bootstrap-samples=100 --bias"
{'fraction_non_alphanumeric': 0.10671409515340151, 'fraction_numerical': 0.04802134281903068, 'mean_word_length': 2.71900826446281, 'pattern_counts': {'":': 0, '<': 5, '<?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': '4844285', 'n_tokens_mistral': 947, 'n_tokens_neox': 888, 'n_words': 175}