
# CDNA ONT: https://app.terra.bio/#workspaces/methods-dev-lab/LR_Fusion_Benchmarking/job_history/303dd595-f129-41ba-a28d-b0b0a0071e53

        {"mergefusionWorkflow.min_novel_junction_support":"${}","mergefusionWorkflow.pbmmi":"gs://fc-d438f734-542a-445f-96e1-e07b4a7cddbc/references/ref_genome.mmi","mergefusionWorkflow.mem":"${}","mergefusionWorkflow.fasta":"gs://fc-d438f734-542a-445f-96e1-e07b4a7cddbc/references/GRCh38.primary_assembly.genome.fa","mergefusionWorkflow.boot_disk_size":"${50}","mergefusionWorkflow.pbmm2_platform":"pacbio","mergefusionWorkflow.run_pbfusion":"${true}","mergefusionWorkflow.gtf":"gs://fc-d438f734-542a-445f-96e1-e07b4a7cddbc/references/gencode.v22.chr_patch_hapl_scaff.annotation.gtf","mergefusionWorkflow.readType":"SplicedLongReads","mergefusionWorkflow.min_sumJS":"${}","mergefusionWorkflow.disk_space_multiplier":"${}","mergefusionWorkflow.genome_lib_tar_mm2_only":"gs://mdl-ctat-genome-libs/__genome_libs_StarFv1.10/GRCh38_gencode_v22_CTAT_lib_Mar012021.for_mm2fusion.tar","mergefusionWorkflow.ubam":"${}","mergefusionWorkflow.run_jaffal":"${true}","mergefusionWorkflow.sample_id":"${this.sample_id}","mergefusionWorkflow.FusionSeekerTask.readthresh":"${}","mergefusionWorkflow.pbfusionTask.strand_option":"${}","mergefusionWorkflow.min_J":"${}","mergefusionWorkflow.pbfusionTask.threshold":"${}","mergefusionWorkflow.cpu":"${12}","mergefusionWorkflow.illumina_right_fq":"${}","mergefusionWorkflow.genome_lib_tar_with_STAR_idx":"gs://mdl-ctat-genome-libs/__genome_libs_StarFv1.10/GRCh38_gencode_v22_CTAT_lib_Mar012021.for_mm2fusion.withSTARidx.tar","mergefusionWorkflow.run_fusionseeker":"${true}","mergefusionWorkflow.monitoring_script":"${}","mergefusionWorkflow.platform":"ont","mergefusionWorkflow.pbfusion_gtf_bin":"gs://fc-d438f734-542a-445f-96e1-e07b4a7cddbc/references/broad-gencode-v22.v0.4.0.gtf.bin","mergefusionWorkflow.preemptible":"${2}","mergefusionWorkflow.illumina_left_fq":"${}","mergefusionWorkflow.min_per_id":"${}","mergefusionWorkflow.fastq":"${this.input_fastq}","mergefusionWorkflow.run_longgf":"${true}","mergefusionWorkflow.run_ctat":"${true}","mergefusionWorkflow.disk_space":"${100}"}


# direct RNA: https://app.terra.bio/#workspaces/methods-dev-lab/LR_Fusion_Benchmarking/job_history/a72c78f0-96dd-4c06-a0e8-fa837f6dcfc3

{"mergefusionWorkflow.min_novel_junction_support":"${}","mergefusionWorkflow.pbmmi":"gs://fc-d438f734-542a-445f-96e1-e07b4a7cddbc/references/ref_genome.mmi","mergefusionWorkflow.mem":"${}","mergefusionWorkflow.fasta":"gs://fc-d438f734-542a-445f-96e1-e07b4a7cddbc/references/GRCh38.primary_assembly.genome.fa","mergefusionWorkflow.boot_disk_size":"${50}","mergefusionWorkflow.pbmm2_platform":"pacbio","mergefusionWorkflow.run_pbfusion":"${true}","mergefusionWorkflow.gtf":"gs://fc-d438f734-542a-445f-96e1-e07b4a7cddbc/references/gencode.v22.chr_patch_hapl_scaff.annotation.gtf","mergefusionWorkflow.readType":"ONTDirectRNA","mergefusionWorkflow.min_sumJS":"${}","mergefusionWorkflow.disk_space_multiplier":"${}","mergefusionWorkflow.genome_lib_tar_mm2_only":"gs://mdl-ctat-genome-libs/__genome_libs_StarFv1.10/GRCh38_gencode_v22_CTAT_lib_Mar012021.for_mm2fusion.tar","mergefusionWorkflow.ubam":"${}","mergefusionWorkflow.run_jaffal":"${true}","mergefusionWorkflow.sample_id":"${this.sample_id}","mergefusionWorkflow.FusionSeekerTask.readthresh":"${}","mergefusionWorkflow.pbfusionTask.strand_option":"${}","mergefusionWorkflow.min_J":"${}","mergefusionWorkflow.pbfusionTask.threshold":"${}","mergefusionWorkflow.cpu":"${12}","mergefusionWorkflow.illumina_right_fq":"${}","mergefusionWorkflow.genome_lib_tar_with_STAR_idx":"gs://mdl-ctat-genome-libs/__genome_libs_StarFv1.10/GRCh38_gencode_v22_CTAT_lib_Mar012021.for_mm2fusion.withSTARidx.tar","mergefusionWorkflow.run_fusionseeker":"${true}","mergefusionWorkflow.monitoring_script":"${}","mergefusionWorkflow.platform":"ont","mergefusionWorkflow.pbfusion_gtf_bin":"gs://fc-d438f734-542a-445f-96e1-e07b4a7cddbc/references/broad-gencode-v22.v0.4.0.gtf.bin","mergefusionWorkflow.preemptible":"${2}","mergefusionWorkflow.illumina_left_fq":"${}","mergefusionWorkflow.min_per_id":"${}","mergefusionWorkflow.fastq":"${this.input_fastq}","mergefusionWorkflow.run_longgf":"${true}","mergefusionWorkflow.run_ctat":"${true}","mergefusionWorkflow.disk_space":"${100}"}
    
