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sprokopec edited this page Feb 27, 2026 · 1 revision

Pipeline Configuration

The pipeline-suite runs using parameters provided in YAML format. There are two types of required configuration files:

Tool configs:

  • these specify common parameters, including:
    • project name
    • sequencing type (wgs, exome, rna or targeted), sequencing centre and platform
    • is_ctdna (true or false)
    • hpc_group to indicate group to use for job submission (ie, slurm -A group argument)
    • ref_type (ie, hg19 or hg38)
    • path to desired output directory (will be created if this is the initial run)
    • paths to tool-specific reference files/directories
    • desired versions of tools
  • and, for each tool, memory and run time parameters for each step

Data configs:

The fastq_config.yaml should include the following information for each fastq file:

  • patient ID (ie, TGL01_0001)
  • sample ID (ie, TGL01_0001_Ov_P)
  • sample type (tumour or normal)
  • library ID (ie, TGL01_0001_Ov_P_PE_420_EX)
  • lane ID (ie, 210220_A00469_0160_BAVYWVDTXY_LOO1)

Similarly, the bam_config.yaml should include the following information for each BAM file:

  • patient ID (ie, TGL01_0001)
  • sample ID (ie, TGL01_0001_Ov_P)
  • sample type (tumour or normal)

Example fastq format:

---
TGL01_0001:
    TGL01_0001_Ov_P:
        type: tumour
        libraries:
            TGL01_0001_Ov_P_PE_420_EX:
                runlanes:
                    210220_A00469_0160_BAVYWVDTXY_L001:
                        fastq:
                            R1: /cluster/projects/pughlab/data/PROJECTNAME/EXOME/TGL01_0001_Ov_P_PE_420_EX_210220_A00469_0160_BAVYWVDTXY_1_CTGATCGT-GCGCATAT_R1.fastq.gz
                            R2: /cluster/projects/pughlab/data/PROJECTNAME/EXOME/TGL01_0001_Ov_P_PE_420_EX_210220_A00469_0160_BAVYWVDTXY_1_CTGATCGT-GCGCATAT_R2.fastq.gz
    TGL01_0001_Ov_R:
        type: normal
        libraries:
            TGL01_0001_Ov_R_PE_420_EX:
                runlanes:
                    210220_A00469_0160_BAVYWVDTXY_L001:
                        fastq:
                            R1: /cluster/projects/pughlab/data/PROJECTNAME/EXOME/TGL01_0001_Ov_R_PE_420_EX_210220_A00469_0160_BAVYWVDTXY_1_CTGATCGT-GCGCATAT_R1.fastq.gz
                            R2: /cluster/projects/pughlab/data/PROJECTNAME/EXOME/TGL01_0001_Ov_R_PE_420_EX_210220_A00469_0160_BAVYWVDTXY_1_CTGATCGT-GCGCATAT_R2.fastq.gz
TGL01_0002:
    TGL01_0002_Ov_P:
        type: tumour
        libraries:
            TGL01_0002_Ov_P_PE_465_EX:
                runlanes:
                    210220_A00469_0160_BAVYWVDTXY_1_CTGATCGT-GCGCATAT:
                        fastq:
                            R1: /cluster/projects/pughlab/data/PROJECTNAME/EXOME/TGL01_0002_Ov_P_PE_465_EX_210220_A00469_0160_BAVYWVDTXY_1_CTGATCGT-GCGCATAT_R1.fastq.gz
                            R2: /cluster/projects/pughlab/data/PROJECTNAME/EXOME/TGL01_0002_Ov_P_PE_465_EX_210220_A00469_0160_BAVYWVDTXY_1_CTGATCGT-GCGCATAT_R2.fastq.gz
    TGL01_0002_Ov_M:
        type: tumour
        libraries:
            TGL01_0002_Ov_P_PE_845_EX:
                runlanes:
                    210220_A00469_0160_BAVYWVDTXY_1_CTGATCGT-GCGCATAT:
                        fastq:
                            R1: /cluster/projects/pughlab/data/PROJECTNAME/EXOME/TGL01_0002_Ov_M_PE_845_EX_210220_A00469_0160_BAVYWVDTXY_1_CTGATCGT-GCGCATAT_R1.fastq.gz
                            R2: /cluster/projects/pughlab/data/PROJECTNAME/EXOME/TGL01_0002_Ov_M_PE_845_EX_210220_A00469_0160_BAVYWVDTXY_1_CTGATCGT-GCGCATAT_R2.fastq.gz
                    210220_A00469_0160_BAVYWVDTXY_2_CTGATCGT-GCGCATAT:
                        fastq:
                            R1: /cluster/projects/pughlab/data/PROJECTNAME/EXOME/TGL01_0002_Ov_M_PE_845_EX_210220_A00469_0160_BAVYWVDTXY_2_CTGATCGT-GCGCATAT_R1.fastq.gz
                            R2: /cluster/projects/pughlab/data/PROJECTNAME/EXOME/TGL01_0002_Ov_M_PE_845_EX_210220_A00469_0160_BAVYWVDTXY_2_CTGATCGT-GCGCATAT_R2.fastq.gz
    TGL01_0002_Ov_R:
        type: normal
        libraries:
            TGL01_0002_Ov_R_PE_333_EX:
                runlanes:
                    210220_A00469_0160_BAVYWVDTXY_1_CTGATCGT-GCGCATAT:
                        fastq:
                            R1: /cluster/projects/pughlab/data/PROJECTNAME/EXOME/TGL01_0002_Ov_R_PE_333_EX_210220_A00469_0160_BAVYWVDTXY_1_CTGATCGT-GCGCATAT_R1.fastq.gz
                            R2: /cluster/projects/pughlab/data/PROJECTNAME/EXOME/TGL01_0002_Ov_R_PE_333_EX_210220_A00469_0160_BAVYWVDTXY_1_CTGATCGT-GCGCATAT_R2.fastq.gz

Example BAM format:

---
TGL01_0001:
    tumour:
        TGL01_0001_Ov_P: /cluster/projects/pughlab/data/PROJECTNAME/EXOME/TGL01_0001_Ov_P_PE_420_EX_aligned_recalibrated.bam
    normal:
        TGL01_0001_Ov_R: /cluster/projects/pughlab/data/PROJECTNAME/EXOME/TGL01_0001_Ov_R_PE_420_EX_aligned_recalibrated.bam
TGL01_0002:
    tumour:
        TGL01_0002_Ov_P: /cluster/projects/pughlab/data/PROJECTNAME/EXOME/TGL01_0002_Ov_P_PE_465_EX_aligned_recalibrated.bam
        TGL01_0002_Ov_M: /cluster/projects/pughlab/data/PROJECTNAME/EXOME/TGL01_0002_Ov_M_PE_845_EX_aligned_recalibrated.bam
    normal:
        TGL01_0002_Ov_R: /cluster/projects/pughlab/data/PROJECTNAME/EXOME/TGL01_0002_Ov_R_PE_333_EX_aligned_recalibrated.bam

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