MultiQC searches a directory tree for summary output or logs of many well known bioinformatics tools and compiles them into a single html report across all detected samples and tools.
The tools MultiQC knows about fall into three groups:
$MULTIQC_TEST_DATAAllocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive salloc.exe: Pending job allocation 46116226 salloc.exe: job 46116226 queued and waiting for resources salloc.exe: job 46116226 has been allocated resources salloc.exe: Granted job allocation 46116226 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn3144 are ready for job [user@cn3144 ~]$ module load multiqc [+] Loading multiqc 1.9 [user@cn3144 ~]$ cp -r $MULTIQC_TEST_DATA/wgs . [user@cn3144 ~]$ multiqc --title 'WGS_test' wgs [INFO ] multiqc : This is MultiQC v1.9 [INFO ] multiqc : Template : default [INFO ] multiqc : Report title: WGS_test [INFO ] multiqc : Searching : wgs Searching 1346 files.. [####################################] 100% [INFO ] qualimap : Found 12 BamQC reports [INFO ] snpeff : Found 6 reports [INFO ] varianteval : Found 6 VariantEval reports [INFO ] picard : Found 6 MarkDuplicates reports [INFO ] fastq_screen : Found 12 reports [INFO ] fastqc : Found 12 reports [INFO ] multiqc : Compressing plot data [INFO ] multiqc : Report : WGS_test_multiqc_report.html [INFO ] multiqc : Data : WGS_test_multiqc_report_data [INFO ] multiqc : MultiQC complete [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
This generates a comprehensive report with a number of metrics summarized across all samples.
Create a batch input file (e.g. multiqc.sh), which uses the input file 'multiqc.in'. For example:
#!/bin/bash module load multiqc || exit 1 multiqc --title 'tenure here i come' /path/to/awsome/project
Submit this job using the Slurm sbatch command.
sbatch --cpus-per-task=2 --mem=4g multiqc.sh