{
  "align_out_prefix": "bespin-rna-seq-0001_",
  "alignment_file": {
    "class": "File",
    "path": "/home/ubuntu/GCBA_RO/generated_data/alignment_data/Control1_Aligned.sortedByCoord.out.bam"
  },
  "gff_file": {
    "class": "File",
    "path": "/home/ubuntu/GCBA_RO/raw_data/genome_files/dmel-all-r5.53.gff"
  },
  "reads": [
    {
      "class": "File",
      "path": "/home/ubuntu/GCBA_RO/raw_data/fastq_files/Control1_R1.fastq"
    },
    {
      "class": "File",
      "path": "/home/ubuntu/GCBA_RO/raw_data/fastq_files/Control1_R2.fastq"
    }
  ],
  "ref_gene_model": {
    "class": "File",
    "path" : "/home/ubuntu/GCBA_RO/raw_data/genome_files/dm3_flyBase.bed"
  },
  "star_genome": {
    "class": "Directory",
    "path": "/home/ubuntu/GCBA_RO/generated_data/GenomeIndex"
  },
  "threads": 20
}

{
  "align_out_prefix": "bespin-rna-seq-0001_",
  "gff_file": {
    "class": "File",
    "path": "/home/ubuntu/GCBA_RO/raw_data/genome_files/dmel-all-r5.53.gff"
  },
  "reads": [
    {
      "class": "File",
      "path": "/home/ubuntu/GCBA_RO/raw_data/fastq_files/Control1_R1.fastq"
    },
    {
      "class": "File",
      "path": "/home/ubuntu/GCBA_RO/raw_data/fastq_files/Control1_R2.fastq"
    }
  ],
  "ref_gene_model": {
    "class": "File",
    "path" : "/home/ubuntu/GCBA_RO/raw_data/genome_files/dm3_flyBase.bed"
  },
  "star_genome": {
    "class": "Directory",
    "path": "/home/ubuntu/GCBA_RO/generated_data/GenomeIndex"
  },
  "threads": 20
}

Remove alignment_file from sample json job
Remove alignment_file from sample json job

- Alignment is part of the workflow, this input is not used
