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---
##############################################################################
### Annotation
##############################################################################
other_RNAs_sequence: "../annotation/txome_rRNAs_joao.fa"
other_RNAs_index: "../prepare_annotation/results/other_RNAs_sequence.idx"
transcripts_sequence: "../prepare_annotation/results/longest_pc_transcript_per_gene.fa"
transcripts_index: "../prepare_annotation/results/longest_pc_transcript_per_gene.idx"
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transcript_id_gene_id_CDS: "../prepare_annotation/results/transcript_id_gene_id_CDS.tsv"
##############################################################################
### Output and log directory
##############################################################################
output_dir: "results"
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local_log: "logs/local_log"
cluster_log: "logs/cluster_log"
##############################################################################
### sample info
##############################################################################
input_dir: "samples"
input_reads_pattern: ".fastq.gz"
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sample: ["example", "example2", "SRR1536304", "SRR1536305"]
example: {adapter: GATCGGAAGAGCACA, minimum_quality: 20, quality_type: 33}
example2: {adapter: CTGTAGGCACCATCA, minimum_quality: 20, quality_type: 64}
SRR1536304: {adapter: CTGTAGGCACCATCA, minimum_quality: 20, quality_type: 33}
SRR1536305: {adapter: CTGTAGGCACCATCA, minimum_quality: 20, quality_type: 33}