rnaseq-engineering/inputs

{
  "{{ project_name }}.read1": "{{ read1 }}",
  "{{ project_name }}.read2": "{{ read2 }}",
  "{{ project_name }}.sample_id": "{{ sample_id }}",
  "{{ project_name }}.screen_ref_dir": "{{ screen_ref_dir }}",
  "{{ project_name }}.fastq_screen_conf": "{{ fastq_screen_conf }}",
  "{{ project_name }}.idx": "{{ idx }}",
  "{{ project_name }}.gtf": "{{ gtf }}",
  "{{ project_name }}.disk_size": "{{ disk_size if disk_size else 200}}",
  "{{ project_name }}.idx_prefix": "{{ idx_prefix }}",
  "{{ project_name }}.fastqscreen_docker": "{{ fastqscreen_docker }}",
  "{{ project_name }}.fastqscreen_cluster": "{{ fastqscreen_cluster }}",
  "{{ project_name }}.fastqc_cluster": "{{ fastqc_cluster }}",
  "{{ project_name }}.fastqc_docker": "{{ fastqc_docker }}",
  "{{ project_name }}.fastp_docker": "{{ fastp_docker }}",
  "{{ project_name }}.fastp_cluster": "{{ fastp_cluster }}",
  "{{ project_name }}.adapter_sequence": "{{ adapter_sequence }}",
  "{{ project_name }}.adapter_sequence_r2": "{{ adapter_sequence_r2 }}",
  "{{ project_name }}.hisat2_docker": "{{ hisat2_docker }}",
  "{{ project_name }}.hisat2_cluster": "{{ hisat2_cluster }}",
  "{{ project_name }}.insert_size": "{{ insert_size }}",
  "{{ project_name }}.samtools_docker": "{{ samtools_docker }}",
  "{{ project_name }}.samtools_cluster": "{{ samtools_cluster }}",
  "{{ project_name }}.qualimap_docker": "{{ qualimap_docker }}",
  "{{ project_name }}.qualimap_cluster": "{{ qualimap_cluster }}",
  "{{ project_name }}.stringtie_docker": "{{ stringtie_docker }}",
  "{{ project_name }}.stringtie_cluster": "{{ stringtie_cluster }}",
  "{{ project_name }}.ballgown_docker": "{{ ballgown_docker }}",
  "{{ project_name }}.ballgown_cluster": "{{ ballgown_cluster }}",
  "{{ project_name }}.count_docker": "{{ count_docker }}",
  "{{ project_name }}.count_cluster": "{{ count_cluster }}",
  "{{ project_name }}.count_length": "{{ count_length }}",
  "{{ project_name }}.trim_adapter":  {{ trim_adapter | tojson }},
  "{{ project_name }}.pre_alignment_qc": {{ pre_alignment_qc | tojson }},
  "{{ project_name }}.qualimap_qc": {{ qualimap_qc | tojson }}
}