Config And Output

Required Inputs

• --tumor-bam: tumor BAM path
• --normal-bam: normal BAM path
• --patient-id
• --tumor-sample-id
• --normal-sample-id
• --outdir
• one reference mode:
  • --fasta, or
  • --genome

Core Optional Controls

• --profile: Nextflow profile list (for example singularity,sanger)
• --pipeline-version: release pin for reproducibility
• --params-file: structured pipeline params
• --resume: rerun interrupted work
• --with-report: Nextflow report path
• --with-dag: Nextflow DAG path

Execution Backend Controls

• --executor: local, none, lsf, slurm, pbs, or sge

Direct CLI execution is supported in all modes. When --run is used, the helper runs backend-native launch commands:

• local / none: bash <script>
• lsf: bsub < <script>
• slurm: sbatch <script>
• pbs / sge: qsub <script>

Scheduler Controls (when executor is scheduler-backed)

• --project
• --queue
• --cpus
• --memory-gb
• --walltime
• --job-name
• --logdir
• --stdout-file
• --stderr-file

Helper Outputs

The helper writes:

• samplesheet CSV (default <outdir>/samplesheet.csv)
• launch script (default <outdir>/run_pacsomatic.<executor>.sh)

It also prints:

• backend-specific run command (for example bash, bsub, sbatch, or qsub)
• launcher output when --run is used
• detected job ID when parseable from scheduler output

Samplesheet Schema

Expected columns:

• patient
• sample
• status
• bam
• pbi

Notes:

• bam should be the full path to the sample BAM.
• pbi is optional.

Status values:

• tumor: 1
• normal: 0

Run Modes

• generate only (default): write artifacts, no scheduler submission
• --dry-run: validate inputs/dependencies and write artifacts
• --run: execute or submit generated launch script using selected --executor

Official Output Anchors

nf-core/pacsomatic organizes results under grouped directories, including:

• alignment
• germline_snv
• somatic_snv
• somatic_sv
• somatic_cnv
• methylation
• tumor_clonality
• signature_analysis
• pipeline_info
• multiqc