[reference]

reference_prefix = chr21-GRCh38

[inputs]

#
# List the inputs to process. Each line can either be a pair
# of forward and reverse files, separated by a space:
#
#    input1 = forward.fastq.gz reverse.fastq.gz
#
# or a single SRR number. Example:
#
#    input2 = DRR046893
#
# or a single fastq file for single end reads.  Example:
#    input3 = SRR4343300.fastq.gz

input1 = ./Test_data/TEST_1.fastq.gz ./Test_data/TEST_2.fastq.gz
#input1 = ./Test_data/SRR4343300.fastq.gz
#input2 = SRR4343300
#input2 = DRR046893


[config]


# Memory available to the jobs. This should be roughly 2X the
# size of the reference genome, rounded up whole GB
memory = 4 GB

# Reads are single end
single = False

# Reads are paired end
paired = True

# process using TopHat2
tophat2 = False

# process using Hisat2
hisat2 = True

# process using STAR
star = False

# process using Cufflinks
cufflinks = False

# process using StringTie
stringtie = True