============== Short tutorial ============== Here a short tutorial is provided for BALSAMIC (**version** = 14.0.1). Regarding fastq-inputs --------------------- Previous versions of BALSAMIC only accepted one fastq-pair per sample, which required concatenation of fastq-pairs if multiple existed. The current version BALSAMIC takes ``--fastq-path`` instead which is a path to a directory containing ALL fastq-files you want to include in the analysis, for tumor and normal (if it exists for the analysis). **NOTE**: The fastq-files in ``--fastq-path`` need to contain the names from ``--tumor-sample-name [sample_name]`` and ``--normal-sample-name [sample_name]`` as a sub-string in the fastq-names to correctly assign them to their respective sample. Running a test sample --------------------- Example config demo case: :: balsamic config case \ --analysis-dir demo/ --balsamic-cache ~/balsamic_cache --fastq-path tests/test_data/fastq/ --case-id demo_run_balsamic --gender female --analysis-workflow balsamic --genome-version hg19 --tumor-sample-name S1 --panel-bed tests/test_data/references/panel/panel.bed 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