Expected output

Before running the workflow, you have to specify the top output directory in the config.yaml file. All output files will be generated in this directory. If the full workflow is executed, the output directory will have the following structure:

outputdir
    |--benchmarks
    |    |--fastqc_sample1_R1.txt
    |    |--...
    |--FastQC
    |    |--sample1_R1_fastqc.html
    |    |--...
    |--FASTQtrimmed
    |    |--sample1_R1_val_1.fq.gz
    |    |--sample1_R1.fastq.gz_trimming_report.txt
    |    |--...
    |--logs
    |    |--fastqc_sample1_R1.log
    |    |--...
    |--MultiQC
    |    |--multiqc_report.html
    |    |--multiqc_data/
    |--outputR
    |    |--edgeR_dge.html
    |    |--DRIMSeq_dtu.hml
    |    |--prepare_shiny.html
    |    |--shiny_sce.rds
    |    |--...
    |--Rout
    |    |--install_pkgs.Rout
    |    |--...
    |--salmon
    |    |--sample1
    |    |    |--aux_info/
    |    |    |--cmd_info.json
    |    |    |--lib_format_counts.json
    |    |    |--libParams/
    |    |    |--logs/
    |    |    |--quant.sf
    |    |--...
    |--STAR
    |    |--sample1
    |    |    |--sample1_Aligned.sortedByCoord.out.bam
    |    |    |--sample1_Aligned.sortedByCoord.out.bam.bai
    |    |    |--sample1_Log.final.out
    |    |    |--sample1_Log.out
    |    |    |--sample1_Log.progress.out
    |    |    |--sample1_SJ.out.tab
    |    |--...
    |--STARbigwig
    |    |--sample1_Aligned.sortedByCoord.out.bw
    |    |--...