inputs

{
	"{{ project_name }}.read1": "{{ read1 }}",
	"{{ project_name }}.read2": "{{ read2 }}",
	"{{ project_name }}.sample_id": "{{ sample_id }}",
	"{{ project_name }}.fastp_docker": "{{ fastp_docker }}",
	"{{ project_name }}.fastp_cluster": "{{ fastp_cluster }}",
	"{{ project_name }}.trim_front1": "{{ trim_front1 }}",
	"{{ project_name }}.trim_tail1": "{{ trim_tail1 }}",
	"{{ project_name }}.max_len1": "{{ max_len1 }}",
	"{{ project_name }}.trim_front2": "{{ trim_front2 }}",
	"{{ project_name }}.trim_tail2": "{{ trim_tail2 }}",
	"{{ project_name }}.max_len2": "{{ max_len2 }}",
	"{{ project_name }}.adapter_sequence": "{{ adapter_sequence }}",
	"{{ project_name }}.adapter_sequence_r2": "{{ adapter_sequence_r2 }}",
	"{{ project_name }}.disable_adapter_trimming": "{{ disable_adapter_trimming }}",
	"{{ project_name }}.length_required1": "{{ length_required1 }}",
	"{{ project_name }}.UMI": "{{ UMI }}",
	"{{ project_name }}.umi_loc": "{{ umi_loc }}",
	"{{ project_name }}.umi_len": "{{ umi_len }}",
	"{{ project_name }}.length_required": "{{ length_required }}",
	"{{ project_name }}.qualified_quality_phred": "{{ qualified_quality_phred }}",
	"{{ project_name }}.disable_quality_filtering": "{{ disable_quality_filtering }}",
	"{{ project_name }}.hisat2_docker": "{{ hisat2_docker }}",
	"{{ project_name }}.hisat2_cluster": "{{ hisat2_cluster }}",
	"{{ project_name }}.idx_prefix": "{{ idx_prefix }}",
	"{{ project_name }}.idx": "{{ idx }}",
	"{{ project_name }}.fasta": "{{ fasta }}",
	"{{ project_name }}.pen_cansplice": "{{ pen_cansplice }}",
	"{{ project_name }}.pen_noncansplice": "{{ pen_noncansplice }}",
	"{{ project_name }}.pen_intronlen": "{{ pen_intronlen }}",
	"{{ project_name }}.min_intronlen": "{{ min_intronlen }}",
	"{{ project_name }}.max_intronlen": "{{ max_intronlen }}",
	"{{ project_name }}.maxins": "{{ maxins }}",
	"{{ project_name }}.minins": "{{ minins }}",
	"{{ project_name }}.samtools_docker": "{{ samtools_docker }}",
	"{{ project_name }}.samtools_cluster": "{{ samtools_cluster }}",
	"{{ project_name }}.insert_size": "{{ insert_size }}",
	"{{ project_name }}.gtf": "{{ gtf }}",
	"{{ project_name }}.stringtie_docker": "{{ stringtie_docker }}",
	"{{ project_name }}.stringtie_cluster": "{{ stringtie_cluster }}",
	"{{ project_name }}.minimum_length_allowed_for_the_predicted_transcripts": "{{ minimum_length_allowed_for_the_predicted_transcripts }}",
	"{{ project_name }}.minimum_isoform_abundance": "{{ minimum_isoform_abundance }}",
	"{{ project_name }}.Junctions_no_spliced_reads": "{{ Junctions_no_spliced_reads }}",
	"{{ project_name }}.maximum_fraction_of_muliplelocationmapped_reads": "{{ maximum_fraction_of_muliplelocationmapped_reads }}",
	"{{ project_name }}.fastqc_cluster_config": "{{ fastqc_cluster_config }}",
	"{{ project_name }}.fastqc_docker": "{{ fastqc_docker }}",
	"{{ project_name }}.fastqc_disk_size": "{{ fastqc_disk_size }}",
	"{{ project_name }}.qualimapBAMqc_docker": "{{ qualimapBAMqc_docker }}",
	"{{ project_name }}.qualimapBAMqc_cluster_config": "{{ qualimapBAMqc_cluster_config }}",
	"{{ project_name }}.qualimapBAMqc_disk_size": "{{ qualimapBAMqc_disk_size }}",
	"{{ project_name }}.qualimapRNAseq_docker": "{{ qualimapRNAseq_docker }}",
	"{{ project_name }}.qualimapRNAseq_cluster_config": "{{ qualimapRNAseq_cluster_config }}",
	"{{ project_name }}.qualimapRNAseq_disk_size": "{{ qualimapRNAseq_disk_size }}",
	"{{ project_name }}.fastqscreen_docker": "{{ fastqscreen_docker }}",
	"{{ project_name }}.fastqscreen_cluster_config": "{{ fastqscreen_cluster_config }}",
	"{{ project_name }}.screen_ref_dir": "{{ screen_ref_dir }}",
	"{{ project_name }}.fastq_screen_conf": "{{ fastq_screen_conf }}",
	"{{ project_name }}.fastqscreen_disk_size": "{{ fastqscreen_disk_size }}",
	"{{ project_name }}.ref_dir": "{{ ref_dir }}",
	"{{ project_name }}.multiqc_cluster_config": "{{ multiqc_cluster_config }}",
	"{{ project_name }}.multiqc_docker": "{{ multiqc_docker }}",
	"{{ project_name }}.multiqc_disk_size": "{{ multiqc_disk_size }}",
	"{{ project_name }}.ballgown_docker": "{{ ballgown_docker }}",
	"{{ project_name }}.ballgown_cluster": "{{ ballgown_cluster }}",
	"{{ project_name }}.disk_size": "{{ disk_size if disk_size != '' else 200}}"
}