### Run NEO from Existing Outputs (CSV and Bash)

Source: https://context7.com/nf-core/oncoanalyser/llms.txt

Resume analysis from intermediate outputs, specifically for running the NEO process. This example uses a CSV file to define input BAM files and their associated metadata, followed by a Bash command to execute the NEO process.

```csv
# samplesheet.neo_inputs.csv - Run NEO from existing outputs
group_id,subject_id,sample_id,sample_type,sequence_type,filetype,filepath
PATIENT1,PATIENT1,PATIENT1-N,normal,dna,bam,/path/to/PATIENT1-N.dna.wgs.bam
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,bam,/path/to/PATIENT1-T.dna.wgs.bam
PATIENT1,PATIENT1,PATIENT1-T-RNA,tumor,rna,bam,/path/to/PATIENT1-T.rna.wgs.bam
PATIENT1,PATIENT1,PATIENT1-T-RNA,tumor,rna,isofox_dir,/path/to/PATIENT1.isofox_dir/
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,purple_dir,/path/to/PATIENT1.purple_dir/
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,linx_anno_dir,/path/to/PATIENT1.linx_anno_dir/
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,lilac_dir,/path/to/PATIENT1.lilac_dir/

```

```bash
# Run only NEO from existing outputs
nextflow run nf-core/oncoanalyser \
  -revision 2.3.0 \
  -profile docker \
  --mode wgts \
  --processes_manual neo \
  --genome GRCh38_hmf \
  --input samplesheet.neo_inputs.csv \
  --outdir output/

```

--------------------------------

### Configure Singularity container settings

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

Example of a Nextflow configuration block for enabling and tuning Singularity containers. This includes setting cache directories, auto-mounting, and pull timeouts.

```groovy
singularity {
    enabled = true
    cacheDir = '/path/to/cache_dir/'
    autoMounts = true
    runOptions = "-B </path/to/desired/mounted/volume/>"
    pullTimeout = '2h'
}
```

--------------------------------

### Run nf-core/oncoanalyser Pipeline

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

Example command to run the nf-core/oncoanalyser pipeline. It specifies the Nextflow revision, configuration profile, analysis mode, genome build, input samplesheet, and output directory. The '-config' argument is optional but recommended for specifying reference data.

```bash
nextflow run nf-core/oncoanalyser \
  -revision 2.3.0 \
  -config reference_data.config \
  -profile docker \
  --mode wgts \
  --genome GRCh38_hmf \
  --input samplesheet.csv \
  --outdir output/ \

```

--------------------------------

### Run Variant Calling Processes with Nextflow

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage/faq_and_troubleshooting.md

This command demonstrates how to run the nf-core/oncoanalyser pipeline, specifically selecting only the variant calling processes. It assumes DNA sequencing data starting from FASTQ files and uses Docker for execution.

```bash
nextflow run nf-core/oncoanalyser \
  -revision 2.3.0 \
  -profile docker \
  --mode wgts \
  --processes_manual alignment,redux,amber,cobalt,sage,pave,esvee,purple \
  --genome GRCh38_hmf \
  --input samplesheet.csv \
  --outdir output/
```

--------------------------------

### Start Analysis from REDUX BAM Input (CSV)

Source: https://context7.com/nf-core/oncoanalyser/llms.txt

Initiate analysis using existing REDUX-processed BAM files. This CSV format specifies the input files, including BAM, BAI, and associated REDUX TSV files, for both local and cloud storage.

```csv
# samplesheet.redux_bam.csv - REDUX BAM input
group_id,subject_id,sample_id,sample_type,sequence_type,filetype,filepath
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,bam_redux,/path/to/PATIENT1-T.dna.redux.bam
PATIENT1,PATIENT1,PATIENT1-N,normal,dna,bam_redux,/path/to/PATIENT1-N.dna.redux.bam

# For cloud storage, explicitly provide all REDUX files
group_id,subject_id,sample_id,sample_type,sequence_type,filetype,filepath
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,bam_redux,gs://bucket/PATIENT1-T.dna.redux.bam
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,bai,gs://bucket/PATIENT1-T.dna.redux.bam.bai
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,redux_jitter_tsv,gs://bucket/PATIENT1-T.dna.jitter_params.tsv
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,redux_ms_tsv,gs://bucket/PATIENT1-T.dna.ms_table.tsv.gz

```

--------------------------------

### Sample Setup: Tumor-Only DNA (CSV)

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

This CSV sample sheet configures a tumor-only DNA analysis setup for Oncoanalyser. It includes the necessary fields for group, subject, sample IDs, types, sequence type, file type (BAM), and the corresponding file path.

```csv
group_id,subject_id,sample_id,sample_type,sequence_type,filetype,filepath
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,bam,/path/to/PATIENT1-T.dna.bam
```

--------------------------------

### Samplesheet for Starting from Existing Inputs (CSV)

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

This CSV formatted samplesheet is designed to initiate an oncoanalyser analysis from intermediate files generated by tools like PURPLE, LILAC, and ISOFOX. It specifies the necessary input files (BAMs and directory paths) for neoepitope calling, allowing the pipeline to resume or start from a later stage.

```csv
group_id,subject_id,sample_id,sample_type,sequence_type,filetype,filepath
PATIENT1,PATIENT1,PATIENT1-N,normal,dna,bam,/path/to/PATIENT1-N.dna.wgs.bam
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,bam,/path/to/PATIENT1-T.dna.wgs.bam
PATIENT1,PATIENT1,PATIENT1-T-RNA,tumor,rna,bam,/path/to/PATIENT1-T.rna.wgs.bam
PATIENT1,PATIENT1,PATIENT1-T-RNA,tumor,rna,isofox_dir,/path/to/PATIENT1.isofox_dir/
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,purple_dir,/path/to/PATIENT1.purple_dir/
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,linx_anno_dir,/path/to/PATIENT1.linx_anno_dir/
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,lilac_dir,/path/to/PATIENT1.lilac_dir/
```

--------------------------------

### Sample Setup: Paired Tumor-Normal DNA with Tumor-Only RNA (CSV)

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

This CSV sample sheet configures a complex sample setup for Oncoanalyser, including paired tumor and normal DNA samples alongside a tumor-only RNA sample. All necessary fields for each sample type are included.

```csv
group_id,subject_id,sample_id,sample_type,sequence_type,filetype,filepath
PATIENT1,PATIENT1,PATIENT1-N,normal,dna,bam,/path/to/PATIENT1-N.dna.bam
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,bam,/path/to/PATIENT1-T.dna.bam
PATIENT1,PATIENT1,PATIENT1-T-RNA,tumor,rna,bam,/path/to/PATIENT1-T.rna.bam
```

--------------------------------

### Run Neoepitope Calling from Existing Inputs (Bash)

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

This Nextflow command executes the oncoanalyser pipeline, specifically targeting the 'neo' process for neoepitope calling. It utilizes a pre-defined samplesheet (samplesheet.neo_inputs.csv) containing paths to intermediate analysis results, enabling the pipeline to start from this point.

```bash
nextflow run nf-core/oncoanalyser \
  -revision 2.3.0 \
  -profile docker \
  --mode wgts \
  --processes_manual neo \
  --genome GRCh38_hmf \
  --input samplesheet.neo_inputs.csv \
  --outdir output/
```

--------------------------------

### Estimate Purity for Longitudinal Samples (CSV and Bash)

Source: https://context7.com/nf-core/oncoanalyser/llms.txt

Estimate tumor fraction in longitudinal samples, such as ctDNA for MRD detection. This example uses a CSV file to define longitudinal and normal samples, along with existing Amber and Purple directories, and a Bash command to run the purity estimation.

```csv
# samplesheet.purity_estimate.csv
group_id,subject_id,sample_id,sample_type,sequence_type,filetype,info,filepath
PATIENT1,PATIENT1,PATIENT1-L,tumor,dna,bam,longitudinal_sample,/path/to/PATIENT1-T.dna.longitudinal.bam
PATIENT1,PATIENT1,PATIENT1-N,normal,dna,bam_redux,,/path/to/PATIENT1-N.dna.redux.bam
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,amber_dir,,/path/to/PATIENT1-T/amber/
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,purple_dir,,/path/to/PATIENT1-T/purple/

```

```bash
# Run purity estimation
nextflow run nf-core/oncoanalyser \
  -revision 2.3.0 \
  -profile docker \
  --mode purity_estimate \
  --purity_estimate_mode targeted \
  --genome GRCh38_hmf \
  --input samplesheet.purity_estimate.csv \
  --outdir output/

```

--------------------------------

### Sample Setup: Tumor-Only RNA (CSV)

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

This CSV sample sheet sets up a tumor-only RNA analysis in Oncoanalyser. It specifies the sample details including group, subject, sample ID, types, sequence type (RNA), file type (BAM), and the file path.

```csv
group_id,subject_id,sample_id,sample_type,sequence_type,filetype,filepath
PATIENT1,PATIENT1,PATIENT1-T-RNA,tumor,rna,bam,/path/to/PATIENT1-T.rna.bam
```

--------------------------------

### Run Targeted Sequencing Mode for Panel Data (TSO500)

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

This command runs the nf-core/oncoanalyser pipeline in 'targeted' mode, specifically configured for panel sequencing data. The example demonstrates the setup for TSO500 panels, including specifying the panel type, genome, input samplesheet, and output directory.

```bash
nextflow run nf-core/oncoanalyser \
  -revision 2.3.0 \
  -config reference_data.config \
  -profile docker \
  --mode targeted \
  --panel tso500 \
  --genome GRCh38_hmf \
  --input samplesheet.csv \
  --outdir output/
```

--------------------------------

### Configure oncoanalyser parameters via config file

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage/faq_and_troubleshooting.md

Demonstrates how to move command-line arguments into a Groovy-based configuration file. This allows for cleaner execution commands by referencing the config file with the -config flag.

```shell
nextflow run nf-core/oncoanalyser \
  -revision 2.3.0 \
  -profile docker \
  -config refdata.config \
  --mode wgts \
  --genome GRCh38_hmf \
  --input samplesheet.csv \
  --outdir output/
```

```groovy
params {
    mode   = "wgts"
    genome = "GRCh38_hmf"
    input  = "samplesheet.csv"
    outdir = "outdir/"
}
```

```shell
nextflow run nf-core/oncoanalyser \
  -revision 2.3.0 \
  -config refdata.config \
  -config params.config \
  -profile docker
```

--------------------------------

### Sample Setup: Paired Tumor and Normal DNA (CSV)

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

This CSV sample sheet defines a paired tumor and normal DNA sample setup for Oncoanalyser. It specifies the group, subject, sample IDs, types, sequence types, file types (BAM), and file paths.

```csv
group_id,subject_id,sample_id,sample_type,sequence_type,filetype,filepath
PATIENT1,PATIENT1,PATIENT1-N,normal,dna,bam,/path/to/PATIENT1-N.dna.bam
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,bam,/path/to/PATIENT1-T.dna.bam
```

--------------------------------

### Display Pipeline Configuration Summary (Groovy)

Source: https://github.com/nf-core/oncoanalyser/blob/master/assets/email_template.txt

This snippet iterates through a 'summary' map and formats its key-value pairs into a list of strings, each prefixed with ' - '. This is used to display the pipeline's configuration parameters. It assumes 'summary' is a map containing configuration details.

```Groovy
<% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %>
```

--------------------------------

### Prepare Reference Indexes for Custom Genome (Bash)

Source: https://context7.com/nf-core/oncoanalyser/llms.txt

This command prepares reference indexes for a custom genome using the nf-core/oncoanalyser pipeline. It specifies the custom genome configuration, profile, reference data types (e.g., WGS, BWA-MEM2 index, GRIDSS index), genome details, and forces genome regeneration.

```bash
# Create indexes for custom genome
nextflow run nf-core/oncoanalyser \
  -revision 2.3.0 \
  -config genome.custom.config \
  -profile docker \
  --mode prepare_reference \
  --ref_data_types wgs,bwamem2_index,gridss_index \
  --genome CustomGenome \
  --genome_version 38 \
  --genome_type no_alt \
  --force_genome \
  --outdir output/
```

--------------------------------

### Run Nextflow Pipeline with YAML Parameters File (Bash)

Source: https://context7.com/nf-core/oncoanalyser/llms.txt

This command executes the nf-core/oncoanalyser pipeline using parameters defined in a YAML file and the Docker profile. This approach promotes reproducibility by externalizing and managing pipeline configurations.

```bash
# Run with parameters file
nextflow run nf-core/oncoanalyser \
  -revision 2.3.0 \
  -profile docker \
  -params-file params.yaml
```

--------------------------------

### Execute oncoanalyser with custom configuration

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

Command to run the oncoanalyser pipeline using a specific configuration file. This demonstrates how to override default settings with user-provided reference data paths.

```bash
nextflow run nf-core/oncoanalyser \
  -revision 2.3.0 \
  -config reference_data.config  \
  <...>
```

--------------------------------

### Execute oncoanalyser in panel_resource_creation mode

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

Command to run the pipeline for generating custom panel reference data. It requires a samplesheet and specific manually created reference files as input arguments.

```bash
nextflow run nf-core/oncoanalyser \
  -revision 2.3.0 \
  -config reference_data.config \
  -profile docker \
  --mode panel_resource_creation \
  --genome GRCh38_hmf \
  --input samplesheet.panel_resource_creation.csv \
  --driver_gene_panel DriverGenePanel.38.tsv \
  --target_regions_bed target_regions_definition.38.bed.gz \
  --isofox_gene_ids rna_gene_ids.csv \
  --outdir output/
```

--------------------------------

### Configure BAM and BAI input in samplesheet

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

Demonstrates how to specify BAM files and optional explicit BAI index paths. The pipeline expects index files to be co-located by default.

```csv
group_id,subject_id,sample_id,sample_type,sequence_type,filetype,filepath
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,bam,/path/to/PATIENT1-T.dna.bam
```

```csv
group_id,subject_id,sample_id,sample_type,sequence_type,filetype,filepath
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,bam,/path/to/PATIENT1-T.dna.bam
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,bai,/other/dir/PATIENT1-T.dna.bam.bai
```

--------------------------------

### Purity Estimate Samplesheet Example

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

This CSV file defines the input samples for the purity estimation mode. It includes paths to the longitudinal tumor BAM, primary tumor AMBER and PURPLE directories, and optionally the REDUX BAM of the normal sample from the primary run.

```csv
group_id,subject_id,sample_id,sample_type,sequence_type,filetype,info,filepath
PATEINT1,PATIENT1,PATIENT1-L,tumor,dna,bam,longitudinal_sample,/path/to/PATIENT1-T.dna.longitudinal.bam
PATIENT1,PATIENT1,PATIENT1-N,normal,dna,bam_redux,,/path/to/PATIENT1-N.dna.redux.bam
PATEINT1,PATIENT1,PATIENT1-T,tumor,dna,amber_dir,,/path/to/PATIENT1-T/amber/
PATEINT1,PATIENT1,PATIENT1-T,tumor,dna,purple_dir,,/path/to/PATIENT1-T/purple/
```

--------------------------------

### Prepare STAR Index for Custom RNA Genome (Bash)

Source: https://context7.com/nf-core/oncoanalyser/llms.txt

This command prepares a STAR index for a custom RNA genome reference using the nf-core/oncoanalyser pipeline. It requires the custom genome configuration, profile, STAR index type, genome details, and the path to the GTF annotation file.

```bash
# For STAR index (RNA), also provide GTF
nextflow run nf-core/oncoanalyser \
  -revision 2.3.0 \
  -config genome.custom.config \
  -profile docker \
  --mode prepare_reference \
  --ref_data_types star_index \
  --genome CustomGenome \
  --genome_version 38 \
  --ref_data_genome_gtf /path/to/gencode.v38.annotation.gtf \
  --force_genome \
  --outdir output/
```

--------------------------------

### Sample Setup: Paired Tumor-Normal DNA with Donor Sample (CSV)

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

This CSV sample sheet demonstrates how to include a donor sample in an Oncoanalyser analysis, alongside paired tumor and normal DNA samples. This is useful for germline variant subtraction, with 'donor' specified in the sample_type.

```csv
group_id,subject_id,sample_id,sample_type,sequence_type,filetype,filepath
PATIENT1,PATIENT1,PATIENT1-N,normal,dna,bam,/path/to/PATIENT1-N.dna.bam
PATIENT1,PATIENT1,PATIENT1-D,donor,dna,bam,/path/to/PATIENT1-D.dna.bam
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,bam,/path/to/PATIENT1-T.dna.bam
```

--------------------------------

### Configure Custom Panel and UMI Processing

Source: https://context7.com/nf-core/oncoanalyser/llms.txt

Defines custom panel data paths and UMI extraction parameters for the pipeline. These configurations allow for flexible integration of specific panel resources and UMI-aware deduplication settings.

```groovy
params {
    ref_data_panel_data_path = "/directory/containing/my_custom_panel_resources/"

    panel_data_paths {
        my_custom_panel {
            '38' {
                driver_gene_panel           = 'DriverGenePanel.38.tsv'
                pon_artefacts               = 'pave.somatic_artefacts.38.tsv'
                target_region_bed           = 'target_regions_definition.38.bed.gz'
                target_region_normalisation = 'cobalt.region_normalisation.38.tsv'
                target_region_ratios        = 'target_regions_ratios.38.tsv'
                target_region_msi_indels    = 'target_regions_msi_indels.38.tsv'
                isofox_counts               = 'read_151_exp_counts.38.csv'
                isofox_gc_ratios            = 'read_100_exp_gc_ratios.38.csv'
                isofox_gene_ids             = 'rna_gene_ids.csv'
                isofox_tpm_norm             = 'isofox.gene_normalisation.38.csv'
            }
        }
    }
}

params {
    fastp_umi_enabled = true
    fastp_umi_location = "per_read"
    fastp_umi_length = 7
    fastp_umi_skip = 0
    redux_umi_enabled = true
    redux_umi_duplex_delim = "_"
}
```

--------------------------------

### Run Nextflow Pipeline with SLURM and Singularity (Bash)

Source: https://context7.com/nf-core/oncoanalyser/llms.txt

This command executes the nf-core/oncoanalyser pipeline using the SLURM executor and Singularity for containerization. It specifies the pipeline revision, configuration file, profile, and essential parameters like mode, genome, input samplesheet, and output directory.

```bash
# Run with SLURM executor
nextflow run nf-core/oncoanalyser \
  -revision 2.3.0 \
  -config slurm.config \
  -profile singularity \
  --mode wgts \
  --genome GRCh38_hmf \
  --input samplesheet.csv \
  --outdir output/
```

--------------------------------

### Configure SLURM Executor and Singularity Settings (Groovy)

Source: https://context7.com/nf-core/oncoanalyser/llms.txt

This configuration sets up the SLURM executor for HPC environments and defines Singularity container settings, including enabling Singularity, specifying a cache directory, and configuring auto-mounts and run options. It is intended for use with Nextflow.

```groovy
// slurm.config - SLURM HPC executor
process {
    executor = "slurm"
}

executor {
    queueSize         = 100
    queueStatInterval = '10 sec'
    pollInterval      = '10 sec'
    submitRateLimit   = '10 sec'
}

// singularity.config - Singularity container settings
singularity {
    enabled    = true
    cacheDir   = '/path/to/cache_dir/'
    autoMounts = true
    runOptions = "-B /path/to/mounted/volume/"
    pullTimeout = '2h'
}
```

--------------------------------

### Configure custom panel reference paths

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

A Groovy configuration file snippet to define the directory and file paths for custom panel resources. This configuration is used by the pipeline to locate the generated and manual reference files.

```groovy
params {
    ref_data_panel_data_path = "/directory/containing/my_custom_panel_resources/"

    panel_data_paths {
        my_custom_panel {
            '38' {
                driver_gene_panel           = 'DriverGenePanel.38.tsv'
                pon_artefacts               = 'pave.somatic_artefacts.38.tsv'
                target_region_bed           = 'target_regions_definition.38.bed.gz'
                target_region_normalisation = 'cobalt.region_normalisation.38.tsv'
                target_region_ratios        = 'target_regions_ratios.38.tsv'
            }
        }
    }
}
```

--------------------------------

### Create Custom Panel Resources for nf-core/oncoanalyser

Source: https://context7.com/nf-core/oncoanalyser/llms.txt

Generates reference data for non-TSO500 targeted panels. It requires a samplesheet, driver gene panel, and target region definitions to produce the necessary resource files.

```bash
nextflow run nf-core/oncoanalyser \
  -revision 2.3.0 \
  -profile docker \
  --mode panel_resource_creation \
  --genome GRCh38_hmf \
  --input samplesheet.panel_resource_creation.csv \
  --driver_gene_panel DriverGenePanel.38.tsv \
  --target_regions_bed target_regions_definition.38.bed.gz \
  --isofox_gene_ids rna_gene_ids.csv \
  --outdir output/
```

--------------------------------

### Query process labels via command line

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage/compute_resources.md

A bash command to recursively search for process labels within the modules directory, useful for auditing resource allocation across the pipeline.

```bash
grep -r "label 'process_" modules/*/ | sort
```

--------------------------------

### Select or Exclude Processes for Analysis (Bash)

Source: https://context7.com/nf-core/oncoanalyser/llms.txt

Customize analysis workflows by selecting or excluding specific processes. This Bash script demonstrates how to run the pipeline with specific profiles, modes, and process configurations.

```bash
# Exclude specific processes (e.g., skip Virusbreakend and ORANGE report)
nextflow run nf-core/oncoanalyser \
  -revision 2.3.0 \
  -profile docker \
  --mode wgts \
  --processes_exclude virusinterpreter,orange \
  --genome GRCh38_hmf \
  --input samplesheet.csv \
  --outdir output/

# Manually select only specific processes
nextflow run nf-core/oncoanalyser \
  -revision 2.3.0 \
  -profile docker \
  --mode wgts \
  --processes_manual alignment,redux,sage,amber,cobalt,esvee,pave,purple \
  --genome GRCh38_hmf \
  --input samplesheet.csv \
  --outdir output/

# Available processes:
# alignment, amber, bamtools, chord, cider, cobalt, cuppa, esvee,
# isofox, lilac, linx, neo, orange, pave, peach, purple, redux,
# sage, sigs, teal, virusinterpreter, wisp

```

--------------------------------

### Prepare reference genome indices

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

Command to trigger the index generation process for a custom genome. This prepares the necessary indices for WGS analysis using the specified reference data types.

```bash
nextflow run nf-core/oncoanalyser \
  -revision 2.3.0 \
  -config genome.custom.config \
  -profile docker \
  --mode prepare_reference \
  --ref_data_types wgs,bwamem2_index,gridss_index \
  --genome CustomGenome \
  --genome_version <37|38> \
  --genome_type <alt|no_alt> \
  --force_genome \
  --outdir output/
```

--------------------------------

### Configure FASTQ input in samplesheet

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

Defines the CSV format for paired-end FASTQ files. Requires specifying filetype as 'fastq' and providing library/lane info and file paths separated by semicolons.

```csv
group_id,subject_id,sample_id,sample_type,sequence_type,filetype,info,filepath
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,fastq,library_id:S1;lane:001,/path/to/PATIENT1-T_S1_L001_R1_001.fastq.gz;/path/to/PATIENT1-T_S1_L001_R2_001.fastq.gz
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,fastq,library_id:S1;lane:002,/path/to/PATIENT1-T_S1_L002_R1_001.fastq.gz;/path/to/PATIENT1-T_S1_L002_R2_001.fastq.gz
```

--------------------------------

### Execute oncoanalyser pipeline

Source: https://github.com/nf-core/oncoanalyser/blob/master/README.md

Command to launch the nf-core/oncoanalyser pipeline using Nextflow. It requires specifying the execution profile, pipeline mode, reference genome, and input samplesheet path.

```bash
nextflow run nf-core/oncoanalyser \
  -profile <docker/singularity/.../institute> \
  -revision 2.3.0 \
  --mode <wgts/targeted> \
  --genome <GRCh37_hmf/GRCh38_hmf> \
  --input samplesheet.csv \
  --outdir output/
```

--------------------------------

### Reusing CLI Arguments with Parameter File

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

Demonstrates how to reuse command-line arguments for the nf-core/oncoanalyser pipeline by specifying them in a YAML parameter file. This simplifies running the pipeline with consistent settings across multiple executions.

```yaml
mode: 'wgts'
genome: 'GRCh38_hmf'
input: 'samplesheet.csv'
outdir: 'output/'
<...>

```

```bash
nextflow run nf-core/oncoanalyser -revision 2.3.0 -profile docker -params-file params.yaml

```

--------------------------------

### Configure CRAM and REDUX CRAM input in samplesheet

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

Shows the samplesheet configuration for standard CRAM and REDUX CRAM formats, including optional CRAI index file specification.

```csv
group_id,subject_id,sample_id,sample_type,sequence_type,filetype,filepath
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,cram,/path/to/PATIENT1-T.dna.cram
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,crai,/other/dir/PATIENT1-T.dna.cram.crai
```

```csv
group_id,subject_id,sample_id,sample_type,sequence_type,filetype,filepath
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,cram_redux,/path/to/PATIENT1-T.dna.redux.cram
PATIENT1,PATIENT1,PATIENT1-T,tumor,dna,crai,/other/dir/PATIENT1-T.dna.cram.crai
```

--------------------------------

### Configure granular process resources

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage/compute_resources.md

Shows how to override resource requirements for specific processes or groups of processes using the 'withName' directive and regular expressions in a Nextflow configuration.

```groovy
process {
    withName: 'FASTP'            { memory = 72.GB; cpus = 12; disk = 375.GB }
    withName: '.*ALIGN'          { memory = 72.GB; cpus = 12; disk = 750.GB }
    withName: 'AMBER'            { memory = 24.GB; cpus = 16; disk = 375.GB }
    withName: 'BAMTOOLS'         { memory = 24.GB; cpus = 16; disk = 375.GB }
    withName: 'CHORD'            { memory = 12.GB; cpus = 4 }
    withName: 'CIDER'            { memory = 24.GB; cpus = 16; disk = 375.GB }
    withName: 'COBALT'           { memory = 24.GB; cpus = 16; disk = 375.GB }
    withName: 'CUPPA'            { memory = 16.GB; cpus = 4 }
    withName: 'ESVEE'            { memory = 96.GB; cpus = 32; disk = 375.GB }
    withName: 'ISOFOX'           { memory = 24.GB; cpus = 16; disk = 375.GB }
    withName: 'LILAC'            { memory = 64.GB; cpus = 16; disk = 375.GB }
    withName: 'LINX_.*'          { memory = 16.GB; cpus = 8 }
    withName: 'ORANGE'           { memory = 16.GB; cpus = 4 }
    withName: 'PAVE.*'           { memory = 32.GB; cpus = 8 }
    withName: 'PEACH'            { memory = 4.GB ; cpus = 2 }
    withName: 'PURPLE'           { memory = 40.GB; cpus = 8 }
    withName: 'REDUX'            { memory = 72.GB; cpus = 16; disk = 750.GB }
    withName: 'SAGE.*'           { memory = 72.GB; cpus = 16; disk = 375.GB }
    withName: 'TEAL_PREP'        { memory = 72.GB; cpus = 16; disk = 375.GB }
    withName: 'TEAL_PIPELINE'    { memory = 32.GB; cpus = 8 ; disk = 375.GB }
    withName: 'VIRUSBREAKEND'    { memory = 64.GB; cpus = 16; disk = 375.GB }
    withName: 'VIRUSINTERPRETER' { memory = 8.GB ; cpus = 2 }
    withName: 'WISP'             { memory = 16.GB; cpus = 4 ; disk = 375.GB }
}
```

--------------------------------

### Define Pipeline Parameters in YAML Format (YAML)

Source: https://context7.com/nf-core/oncoanalyser/llms.txt

This YAML file defines key parameters for the nf-core/oncoanalyser pipeline, including the analysis mode, genome reference, input samplesheet, and output directory. It also includes optional parameters for excluding specific processes and specifying reference data paths.

```yaml
# params.yaml - Pipeline parameters
mode: 'wgts'
genome: 'GRCh38_hmf'
input: 'samplesheet.csv'
outdir: 'output/'

# Optional: exclude processes
processes_exclude: 'virusinterpreter,orange'

# Optional: reference data paths
ref_data_hmf_data_path: '/path/to/hmftools_data/'
ref_data_panel_data_path: '/path/to/panel_data/'
```

--------------------------------

### Run Specific Processes with --processes_manual (Bash)

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

This command demonstrates how to use the --processes_manual argument in Nextflow to execute only a subset of the oncoanalyser pipeline's processes. It specifies alignment, redux, sage, amber, cobalt, esvee, and pave for a whole-genome tumor-only (wgts) mode analysis, using Docker for containerization and GRCh38 as the reference genome.

```bash
nextflow run nf-core/oncoanalyser \
  -revision 2.3.0 \
  -profile docker \
  --mode wgts \
  --processes_manual alignment,redux,sage,amber,cobalt,esvee,sage,pave,purple \
  --genome GRCh38_hmf \
  --input samplesheet.csv \
  --outdir output/
```

--------------------------------

### Automatic Reference Data Staging with Nextflow

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

This Nextflow command automatically stages required reference data for WGS analysis, including GRCh38_hmf genome and WiGiTS resources. It uses the 'prepare_reference' mode and specifies the genome and output directory.

```bash
nextflow run nf-core/oncoanalyser \
  -revision 2.3.0 \
  -profile docker \
  --mode prepare_reference \
  --ref_data_types wgs \
  --genome GRCh38_hmf \
  --outdir output/
```

--------------------------------

### Configure Custom Genome Reference (Groovy)

Source: https://context7.com/nf-core/oncoanalyser/llms.txt

This Groovy configuration file defines parameters for a custom genome reference within the Nextflow pipeline. It specifies the path to the custom genome's FASTA file, allowing the pipeline to use non-standard references.

```groovy
// genome.custom.config - Custom genome configuration
params {
    genomes {
        CustomGenome {
            fasta = "/path/to/custom_genome.fa"
        }
    }
}
```

--------------------------------

### Configure Local Reference Data Paths (Groovy)

Source: https://context7.com/nf-core/oncoanalyser/llms.txt

Configure local paths for reference data to avoid repeated downloads. This Groovy script defines genome-specific FASTA, FAI, DICT, IMG, and index paths, as well as HMF tools and panel data paths.

```groovy
// refdata.local.config - Reference data configuration
params {
    genomes {
        GRCh38_hmf {
            fasta         = "/path/to/GRCh38_masked_exclusions_alts_hlas.fasta"
            fai           = "/path/to/GRCh38_masked_exclusions_alts_hlas.fasta.fai"
            dict          = "/path/to/GRCh38_masked_exclusions_alts_hlas.fasta.dict"
            img           = "/path/to/GRCh38_masked_exclusions_alts_hlas.fasta.img"
            bwamem2_index = "/path/to/bwa-mem2_index/"
            gridss_index  = "/path/to/gridss_index/"
            star_index    = "/path/to/star_index/"
        }
    }
    ref_data_hmf_data_path   = "/path/to/hmftools_data/"
    ref_data_panel_data_path = "/path/to/tso500_panel_data/"
}

// Usage: nextflow run nf-core/oncoanalyser -config refdata.local.config ...

```

--------------------------------

### Navigate Nextflow work directory structure

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage/faq_and_troubleshooting.md

Illustrates the directory hierarchy created by Nextflow processes. It highlights key log files like .command.err and .command.out which are essential for debugging pipeline crashes.

```shell
work/
├── e5
│   └── f6e2e8f18ef70add9349164d5fb37e
│       ├── .command.sh
│       ├── .command.run
│       ├── .command.log
│       ├── .command.err
│       ├── .command.out
│       ├── .command.trace
│       ├── .exitcode
│       └── versions.yml
```

--------------------------------

### Resume Failed Nextflow Run with Docker Profile (Bash)

Source: https://context7.com/nf-core/oncoanalyser/llms.txt

This command demonstrates how to resume a previously failed or interrupted Nextflow pipeline run using the Docker profile. It specifies the pipeline revision, profile, and core parameters, allowing the pipeline to pick up where it left off.

```bash
# Resume failed/interrupted run
nextflow run nf-core/oncoanalyser \
  -revision 2.3.0 \
  -profile docker \
  -resume \
  --mode wgts \
  --genome GRCh38_hmf \
  --input samplesheet.csv \
  --outdir output/
```

--------------------------------

### Run WGTS Mode for Whole Genome/Transcriptome Sequencing

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

This command executes the nf-core/oncoanalyser pipeline in 'wgts' mode, suitable for analyzing whole genome and whole transcriptome sequencing data. It requires specifying the genome build, input samplesheet, and output directory.

```bash
nextflow run nf-core/oncoanalyser \
  -revision 2.3.0 \
  -config reference_data.config \
  -profile docker \
  --mode wgts \
  --genome GRCh38_hmf \
  --input samplesheet.csv \
  --outdir output/
```

--------------------------------

### Nextflow Profile Options (Text)

Source: https://github.com/nf-core/oncoanalyser/blob/master/docs/usage.md

This section lists and describes various Nextflow profile options used to configure the execution environment for the oncoanalyser pipeline. Profiles specify how software dependencies are managed, such as using Docker, Singularity, Conda, or other containerization technologies, and can be combined for customized configurations.

```text
-profile docker
-profile singularity
-profile podman
-profile shifter
-profile charliecloud
-profile apptainer
-profile wave
-profile conda
-profile test,docker
```