dntap_config.yaml

################################################################################
#
# This is the configuration file to provided to the DNTAP program.
#
# It contains paths, inputs and parameters necessary to complete 
# the pipeline steps.
#
# You must fill the "software", "directories" and "samples" part.
# It is strongly recommanded to use absolute path to indicate software and
# input file location. 
# You can use the command "pwd" in the software install location to obtain
# the absolute path to it. 
# 
# Parameters can be changed or leave as it is.
# For more detailed informations on parameters, we strongly encourage you to 
# refer to the original software README and tutorial.
#
# Fastqc: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
# Trimmomatic: http://www.usadellab.org/cms/?page=trimmomatic
# Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
# Transrate: http://hibberdlab.com/transrate/
# Transdecoder: https://transdecoder.github.io/
# Interproscan: https://github.com/ebi-pf-team/interproscan/wiki/HowToRun
#
# date: 07/2017
#
################################################################################


software:
    # You must provide absolute path to the executable file
    # e.g. fastqc: /path/to/fastqc/install/directory/fastqc
    
    fastqc: path/to/src/FastQC/fastqc
    trimmomatic: path/to/src/Trimmomatic-0.36/trimmomatic-0.36.jar
    trinity: /path/to/src/trinityrnaseq-Trinity-v2.4.0/Trinity
    transrate: /path/to/src/transrate-1.0.3-linux-x86_64/transrate
    transdecoder_longorfs: /path/to/src/TransDecoder-3.0.1/TransDecoder.LongOrfs
    transdecoder_predict: /path/to/src/TransDecoder-3.0.1/TransDecoder.Predict
    interproscan: /path/to/src/interproscan-5.24-63.0/interproscan.sh

directories:
    # The output directory will be created is not existing and will contains
    # all output results from the pipeline.

    outdir: /path/to/outdir/

data_type:
    # You must specify either 'pe' or 'se' depending on the use of paired-end 
    # files of single-end file respectively.

    type: pe

samples:
    # You must provide absolute path to read sample RNA-seq file (.fastq / .fq).

    forward: /path/to/sample/reads.left.fq
    reverse: /path/to/sample/reads.right.fq
    single: none

threads:
    # You can set maximum threads to be use be each step.

    fastqc: 20
    trimmomatic: 6
    trinity: 20
    transrate: 20
    transdecoder: 20
    interproscan: 20

trimmomatic_params:
    MINLEN:32 SLIDINGWINDOW:10:20 LEADING:5 TRAILING:5
    
trinity_params:
    max_memory: 20G
    
transdecoder_params:
    min_protein_len: 100
    
interproscan_params:
    out_format: tsv
    db: TIGRFAM, SFLD, ProDom, Hamap, SMART, CDD, ProSiteProfiles, ProSitePatterns, SUPERFAMILY, PRINTS, PANTHER, Gene3D, PIRSF, Pfam, Coils