### Example Params File Configuration

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

This is an example of a params file in YAML format that can be used with the -params-file argument. It specifies input, output directory, and genome reference.

```yaml
input: './samplesheet.csv'
outdir: './results/'
genome: 'GATK.GRCh38'
<...>
```

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

### Start with Annotation (VCF input)

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

Use this format when starting from the annotation step. The CSV must include 'patient', 'sample', and 'vcf' columns. Input VCFs must be sorted and compressed (bgzip/tabix).

```bash
patient,sample,vcf
patient1,test_sample,test.vcf.gz
```

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

### Run Sarek Pipeline Quickstart

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

This is the typical command for running the pipeline. Ensure you replace placeholders like <VERSION>, <PROFILE>, and <TOOLS> with your specific values. The -profile argument is mandatory.

```bash
nextflow run nf-core/sarek -r <VERSION> -profile <PROFILE> --input ./samplesheet.csv --outdir ./results --genome GATK.GRCh38 --tools <TOOLS>
```

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

### Sarek Configuration for Local Cache

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

Example of how to specify SnpEff and VEP cache locations using command-line arguments for a local storage setup. Ensure the paths provided match your cache directory structure.

```bash
nextflow run nf-core/sarek \
    --igenomes_base /data/igenomes/ \
    --snpeff_cache /data/cache/snpeff_cache/ \
    --vep_cache /data/cache/vep_cache/ \
    ...
```

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

### Full Samplesheet for Annotation

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

This example shows a full samplesheet for annotation, including optional 'variantcaller' information per sample.

```bash
patient,sample,variantcaller,vcf
test,sample3,strelka,sample3.variants.vcf.gz
test,sample4_vs_sample3,manta,sample4_vs_sample3.diploid_sv.vcf.gz
test,sample4_vs_sample3,manta,sample4_vs_sample3.somatic_sv.vcf.gz
```

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

### Full Samplesheet for Prepare Recalibration (CRAM input)

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

This example demonstrates a full samplesheet for preparing recalibration tables with CRAM input, including optional 'sex' and 'status' columns.

```bash
patient,sex,status,sample,cram,crai
patient1,XX,0,normal_sample,test_md.cram,test_md.cram.crai
patient1,XX,1,tumor_sample,test2_md.cram,test2_md.cram.crai
patient1,XX,1,relapse_sample,test3_md.cram,test3_md.cram.crai
```

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

### Full Samplesheet for Prepare Recalibration (BAM input)

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

This example demonstrates a full samplesheet for preparing recalibration tables with BAM input, including optional 'sex' and 'status' columns.

```bash
patient,sex,status,sample,bam,bai
patient1,XX,0,test_sample,test_md.bam,test_md.bam.bai
patient1,XX,1,tumor_sample,test2_md.bam,test2_md.bam.bai
patient1,XX,1,relapse_sample,test3_md.bam,test3_md.bam.bai
```

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

### Full Samplesheet for Recalibration (CRAM input)

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

This example shows a full samplesheet for recalibration with CRAM input, including optional 'sex' and 'status' columns.

```bash
patient,sex,status,sample,cram,crai,table
patient1,XX,0,test_sample,test_mapped.cram,test_mapped.cram.crai,test.table
patient1,XX,1,tumor_sample,test2_mapped.cram,test2_mapped.cram.crai,test2.table
patient1,XX,1,relapse_sample,test3_mapped.cram,test3_mapped.cram.crai,test3.table
```

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

### Full Samplesheet with BAM Input

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

An example of a comprehensive samplesheet including patient sex and status information, used for BAM input. This allows for detailed sample tracking and processing.

```csv
patient,sex,status,sample,bam,bai
patient1,XX,0,test_sample,test_mapped.bam,test_mapped.bam.bai
patient1,XX,1,tumor_sample,test2_mapped.bam,test2_mapped.bam.bai
patient1,XX,1,relapse_sample,test3_mapped.bam,test3_mapped.bam.bai
```

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

### Start with Base Quality Score Recalibration (CRAM input)

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

Use this format when starting from base quality score recalibration with CRAM input. The CSV must include 'patient', 'sample', 'cram', 'crai', and 'table' columns.

```bash
patient,sample,cram,crai,table
patient1,test_sample,test_mapped.cram,test_mapped.cram.crai,test.table
```

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

### Run Sarek Pipeline with Params File

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

Use a params file to specify settings for multiple runs instead of listing each flag in the command. This example uses a YAML file.

```bash
nextflow run nf-core/sarek -params-file params.yaml
```

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

### Start with Base Quality Score Recalibration (BAM input)

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

Use this format when starting from base quality score recalibration with BAM input. The CSV must include 'patient', 'sample', 'bam', 'bai', and 'table' columns.

```bash
patient,sample,bam,bai,table
patient1,test_sample,test_mapped.cram,test_mapped.cram.crai,test.table
```

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

### Full Samplesheet with CRAM Input

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

An example of a comprehensive samplesheet including patient sex and status information, used for CRAM input. This allows for detailed sample tracking and processing.

```csv
patient,sex,status,sample,cram,crai
patient1,XX,0,normal_sample,test_mapped.cram,test_mapped.cram.crai
patient1,XX,1,tumor_sample,test2_mapped.cram,test2_mapped.cram.crai
patient1,XX,1,relapse_sample,test3_mapped.cram,test3_mapped.cram.crai
```

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

### Prepare Recalibration Tables (BAM input)

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

Use this format when starting with BAM files for preparing recalibration tables. Ensure the CSV includes 'patient', 'sample', 'bam', and 'bai' columns.

```bash
patient,sample,bam,bai
patient1,test_sample,test_md.bam,test_md.bam.bai
```

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

### Input CSV for Duplicate Marking (BAM)

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

Provide a CSV file with BAM and BAI file paths to start the pipeline from the duplicate marking step. Ensure columns like `patient`, `sample`, `bam`, and `bai` are present.

```csv
patient,sample,bam,bai
patient1,test_sample,test_mapped.bam,test_mapped.bam.bai
```

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

### Prepare Recalibration Tables (CRAM input)

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

Use this format when starting with CRAM files for preparing recalibration tables. Ensure the CSV includes 'patient', 'sample', 'cram', and 'crai' columns.

```bash
patient,sample,cram,crai
patient1,test_sample,test_md.cram,test_md.cram.crai
```

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

### Input CSV for Duplicate Marking (CRAM)

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

Provide a CSV file with CRAM and CRAI file paths to start the pipeline from the duplicate marking step. Ensure columns like `patient`, `sample`, `cram`, and `crai` are present.

```csv
patient,sample,cram,crai
patient1,test_sample,test_mapped.cram,test_mapped.cram.crai
```

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

### Set up Sentieon License (File)

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

Use this command to set the SENTIEON_LICENSE_BASE64 secret with a Sentieon license file. The file content must be base64 encoded.

```bash
nextflow secrets set SENTIEON_LICENSE_BASE64 $(cat <sentieon_license_file.lic> | base64 -w 0)
```

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

### Minimal Config for FastQ Files

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

Use this format for a single-lane sample with gzipped FastQ files.

```bash
patient,sample,lane,fastq_1,fastq_2
patient1,test_sample,lane_1,test_1.fastq.gz,test_2.fastq.gz
```

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

### Minimal Config for SPRING Compressed Files (Single)

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

Use this format for a single-lane sample with SPRING compressed FastQ files.

```bash
patient,sample,lane,spring_1
patient1,test_sample,lane_1,test_R1_and_R2.fastq.gz.spring
```

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

### Full Samplesheet Config with FastQ Files

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

Includes all possible columns for multiple samples and lanes, with additional metadata like sex and status.

```bash
patient,sex,status,sample,lane,fastq_1,fastq_2
patient1,XX,0,normal_sample,lane_1,test_L001_1.fastq.gz,test_L001_2.fastq.gz
patient1,XX,0,normal_sample,lane_2,test_L002_1.fastq.gz,test_L002_2.fastq.gz
patient1,XX,0,normal_sample,lane_3,test_L003_1.fastq.gz,test_L003_2.fastq.gz
patient1,XX,1,tumor_sample,lane_1,test2_L001_1.fastq.gz,test2_L001_2.fastq.gz
patient1,XX,1,tumor_sample,lane_2,test2_L002_1.fastq.gz,test2_L002_2.fastq.gz
patient1,XX,1,relapse_sample,lane_1,test3_L001_1.fastq.gz,test3_L001_2.fastq.gz
```

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

### Example VCF Variant Line

Source: https://github.com/nf-core/sarek/blob/master/docs/usage/variantcalling/interpretation.md

This is an example of a VCF (Variant Call Format) line representing a specific genomic variant. It includes detailed annotations about the variant's position, alleles, quality metrics, and functional impact, such as predicted loss of function.

```bash
chr21   45989090        C       T       AC=1;AF=0.25;AN=4;BaseQRankSum=2.37;DP=86;ExcessHet=0;FS=0;MLEAC=1;MLEAF=0.25;MQ=60;MQRankSum=0;QD=2.99;ReadPosRankSum=-0.737;SOR=1.022;VQSLOD=9.09;culprit=QD;ANN=T|stop_gained|HIGH|COL6A1|ENSG00000142156|transcript|ENST00000361866.8|protein_coding|9/35|c.811C>T|p.Arg271*|892/4203|811/3087|271/1028||;LOF=(COL6A1|ENSG00000142156|1|1.00);NMD=(COL6A1|ENSG00000142156|1|1.00)     GT:AD:DP:GQ:PL       0/1:8,6:15:40:50,0,40   0/0:70,0:70:99:0,112,1494
```

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

### Minimal Config for SPRING Compressed Files (Paired)

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

Use this format for a single-lane sample with paired-end SPRING compressed FastQ files.

```bash
patient,sample,lane,spring_1,spring_2
patient1,test_sample,lane_1,test_R1.fastq.gz.spring,test_R2.fastq.gz.spring
```

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

### Set up Sentieon License (String)

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

Use this command to set the SENTIEON_LICENSE_BASE64 secret with a Sentieon license string (IP:Port). The license string must be base64 encoded.

```bash
nextflow secrets set SENTIEON_LICENSE_BASE64 $(echo -n <sentieon_license_string> | base64 -w 0)
```

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

### Minimal Config for BAM Files

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

Use this format for a single-lane sample with BAM files.

```bash
patient,sample,lane,bam
patient1,test_sample,lane_1,test.bam
```

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

### Multi-lane Config for FastQ Files

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

Configure samples multiplexed over multiple lanes using gzipped FastQ files.

```bash
patient,sample,lane,fastq_1,fastq_2
patient1,test_sample,lane_1,test_L001_1.fastq.gz,test_L001_2.fastq.gz
patient1,test_sample,lane_2,test_L002_1.fastq.gz,test_L002_2.fastq.gz
patient1,test_sample,lane_3,test_L003_1.fastq.gz,test_L003_2.fastq.gz
```

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

### Full Samplesheet Config with BAM Files

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

Includes all possible columns for multiple samples and lanes using BAM files, with additional metadata.

```bash
patient,sex,status,sample,lane,bam
patient1,XX,0,normal_sample,lane_1,test_L001.bam
patient1,XX,0,normal_sample,lane_2,test_L002.bam
patient1,XX,0,normal_sample,lane_3,test_L003.bam
patient1,XX,1,tumor_sample,lane_1,test2_L001.bam
patient1,XX,1,tumor_sample,lane_2,test2_L002.bam
patient1,XX,1,relapse_sample,lane_1,test3_L001.bam
```

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

### Run Pipeline with Trimming

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

Execute the pipeline with the `trim_fastq` profile for read trimming. Ensure the `test_cache` and `docker` profiles are also enabled.

```bash
nextflow run main.nf -profile test_cache,trim_fastq,docker
```

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

### Sarek Configuration for AWS S3 Cache

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

Example of how to specify SnpEff and VEP cache locations using command-line arguments for AWS S3 storage. Adjust the S3 bucket and paths according to your data organization.

```bash
nextflow run nf-core/sarek \
    --igenomes_base s3://my-reference-data/igenomes/ \
    --snpeff_cache s3://my-reference-data/cache/snpeff/ \
    --vep_cache s3://my-reference-data/cache/ensemblvep/ \
    ...
```

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

### Multi-lane Config for BAM Files

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

Configure samples multiplexed over multiple lanes using BAM files.

```bash
patient,sample,lane,bam
patient1,test_sample,1,test_L001.bam
patient1,test_sample,2,test_L002.bam
patient1,test_sample,3,test_L003.bam
```

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

### Run Sarek Pipeline with Default Test Profile

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

Execute the Sarek pipeline using the 'test' profile and a specified container or institute profile. This command runs preprocessing and Strelka with default parameters. Ensure you have Nextflow installed and configured.

```bash
nextflow run nf-core/sarek -profile test,<container/institute> --outdir results
```

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

### Index FASTA with BWA

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

Use this command to create an index for a FASTA file using BWA.

```bash
bwa index -p bwa/${fasta.baseName} $fasta
```

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

### Define Input Samplesheet

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

A CSV file is used to define input data, with each row representing a pair of FASTQ files for a sample.

```csv
patient,sample,lane,fastq_1,fastq_2
ID1,S1,L002,ID1_S1_L002_R1_001.fastq.gz,ID1_S1_L002_R2_001.fastq.gz
```

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

### Run Annotation Test with Multiple Tools

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

This command executes the annotation test profile, enabling multiple annotation tools (snpeff, vep) and a merge step. It requires the test_cache, annotation, and docker profiles.

```bash
nextflow run main.nf -profile test_cache,annotation,docker --tools snpeff,vep,merge
```

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

### Run Annotation Test with Specific Tools

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

Use this command to run the annotation test with specified tools (snpeff) and the annotation step. Ensure you have the necessary container/institute profile configured.

```bash
nextflow run nf-core/sarek -profile test_cache,<container/institute> --outdir results --tools snpeff --step annotation
```

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

### Run Sarek with Pre-downloaded Cache

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

Execute Sarek using a previously downloaded cache. Specify the paths to the VEP and SnpEff cache directories using --vep_cache and --snpeff_cache parameters.

```bash
nextflow run nf-core/sarek --outdir results --vep_cache /path_to/my-own-cache/vep_cache --snpeff_cache /path_to/my-own-cache/snpeff_cache --tools vep,snpeff --input samplesheet_vcf.csv
```

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

### Build Hash Table with DragMap

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

Command to build a hash table for a reference FASTA file using DragMap.

```bash
dragen-os --build-hash-table true --ht-reference $fasta --output-directory dragmap
```

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

### Run Pipeline with UMI

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

Execute the pipeline with the `umi` profile for Unique Molecular Identifier processing. Ensure the `test_cache` and `docker` profiles are also enabled.

```bash
nextflow run main.nf -profile test_cache,umi,docker
```

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

### Run Pipeline with Somatic Strelka

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

Execute the pipeline with the `tools_somatic` profile and `strelka` tool. Ensure the `test_cache` and `docker` profiles are also enabled.

```bash
nextflow run main.nf -profile test_cache,tools_somatic,docker --tools strelka
```

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

### Run nf-core/sarek Pipeline

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

Execute the nf-core/sarek pipeline using Nextflow, specifying the profile, input samplesheet, and output directory.

```bash
nextflow run nf-core/sarek \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>
```

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

### Download Cache and Annotate with Sarek

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

Run Sarek to download the specified tool's cache (SnpEff and/or VEP) and then perform annotation. The cache is saved to the specified --outdir_cache location.

```bash
nextflow run nf-core/sarek --outdir results --outdir_cache /path_to/my-own-cache --tools vep,snpeff --download_cache --build_only_index --input false
```

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

### Navigate to VCF Directory

Source: https://github.com/nf-core/sarek/blob/master/docs/usage/variantcalling/interpretation.md

Change the current directory to the location of the VCF files for analysis.

```bash
cd /workspace/gitpod/training/annotation/haplotypecaller/joint_variant_calling
```

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

### Run Pipeline with GATK Spark

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

Execute the pipeline with the `use_gatk_spark` profile to utilize GATK with Spark. Ensure the `test_cache` and `docker` profiles are also enabled.

```bash
nextflow run main.nf -profile test_cache,use_gatk_spark,docker
```