data.template.ini

[GLOBAL]
; add all genomes, use semi-colons to separate multiple cfr. zma;ath
genomes=zma

; enter email to receive status updates from the cluster
; setting the email to None will disable this
email=None

; orthofinder settings (runs on all species)
orthofinder_output=./output/orthofinder

[zma]
cds_fasta=
protein_fasta=
genome_fasta=
gff_file=

gff_feature=CDS
gff_id=Parent

fastq_dir=./data/zma/fastq

tophat_cutoff=65
htseq_cutoff=40

indexing_output=./output/bowtie-build/zma
trimmomatic_output=./output/trimmed_fastq/zma
tophat_output=./output/tophat/zma
samtools_output=./output/samtools/zma
htseq_output=./output/htseq/zma

exp_matrix_output=./output/zma/exp_matrix.txt
exp_matrix_tpm_output=./output/zma/exp_matrix.tpm.txt
exp_matrix_rpkm_output=./output/zma/exp_matrix.rpkm.txt
interpro_output=./output/interpro/zma

pcc_output=./output/zma/pcc.std.txt
pcc_mcl_output=./output/zma/pcc.mcl.txt
mcl_cluster_output=./output/zma/mcl.clusters.txt