==============
Short tutorial
==============

Here a short toturial is provided for BALSAMIC (**version** = 7.0.2). 

Running a test sample
---------------------

Given the 

::

  balsamic config case \
    --tumor tests/test_data/fastq/S1_R_1.fastq.gz \
    --normal tests/test_data/fastq/S2_R_1.fastq.gz \
    --case-id demo_run_balsamic \
    --analysis-dir demo/ \
    --panel-bed tests/test_data/references/panel/panel.bed \
    --balsamic-cache ~/balsamic_cache \
    --quiet


Notes:

- If you want to test tumor_only mode, remove the ``--normal tests/test_data/fastq/S2_R_1.fastq.gz`` line.
- ``--output-config demo_run_balsamic.json`` is also optional

Let's try a dry run and see everything is in place:

::

  balsamic run analysis --sample-config demo/demo_run_balsamic/demo_run_balsamic.json

Command above should exit a similar output as below:

::

  Job counts:
  count jobs
  1 BaseRecalibrator
  1 CollectAlignmentSummaryMetrics
  1 CollectHsMetrics
  1 CollectInsertSizeMetrics
  1 IndelRealigner
  1 MarkDuplicates
  1 RealignerTargetCreator
  1 all
  1 bwa_mem
  1 cnvkit_single
  1 fastp
  1 fastqc
  13  haplotypecaller
  1 haplotypecaller_merge
  1 manta_germline
  1 manta_tumor_only
  1 mergeBam_tumor
  1 mergeBam_tumor_gatk
  1 multiqc
  1 mutect2_merge
  13  mutect2_tumor_only
  1 sambamba_exon_depth
  1 sambamba_panel_depth
  1 samtools_sort_index
  1 somatic_snv_indel_vcf_merge
  1 split_bed_by_chrom
  1 strelka_germline
  1 vardict_merge
  13  vardict_tumor_only
  7 vep
  72
  This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.
 
And now run balsamic through SLURM. Make sure you set your SLURM project account using ``--account`` if your local
settings require it:

::

  balsamic run analysis --sample-config demo/demo_run_balsamic/demo_run_balsamic.json \
    --profile slurm --qos low --account development --run-analysis

And now run balsamic through QSUB. Make sure you set your QSUB project account using ``--account`` if your local
settings require it: 

::

  balsamic run analysis --sample-config demo/demo_run_balsamic/demo_run_balsamic.json \
    --profile qsub --qos low --account development --run-analysis


And running workflow without submitting jobs. Set number of cores by passing an argument to snakemake as seen below:

::

  balsamic run analysis --sample-config demo/demo_run_balsamic/demo_run_balsamic.json \
    --run-mode local --snakemake-opt "--cores 8" --run-analysis