Nextflow

Walkthrough

The analysis using kallisto and bustools uses directory as outputs and inputs to downstream processes which we have not encountered before.

To call files in the directory, use parameter expansion: ${variable}

Append a forward slash /, treating the variable as a directory: ${variable}/file.txt

Save the below script as test.nf and run nextflow run test.nf

#!/usr/bin/env nextflow

/*
 * Use process to create output directory
 * with some files in it.
 */

process create_dir{

    output:
        file("bus_output") into dir_out

    script:
    """
    mkdir -p bus_output
    touch bus_output/output.bus
    touch bus_output/matrix.ec
    touch bus_output/transcripts.txt
    """
}

process stage_files{

    echo true

    input:
        file(bus_output) from dir_out

    output:
        stdout to out

    script:
    """
    printf "\n"
    printf "Ouput BUS file: ${bus_output}/output.bus \n"
    printf "Matrix file: ${bus_output}/matrix.ec \n"
    printf "Transcripts file: ${bus_output}/transcripts.txt \n"
    """
}

Exercise

Complete the scRNA-Seq pipeline below. Refer to the pipeline section of this weeks tutorial to check process requirements.

This is a very staright forward pipeline as all variables are hard coded within the script.

Save the below script as kallisto_bustools.nf and run in your directory:

nextflow -bg \
run kallisto_bustools.nf \
-with-singularity /data/MSc/2020/MA5112/scRNA-Seq/container/scRNA.img

N.B I’ve tweaked the output directories slightly, all output files will end up in bus_output/ which is slightly different from the interactive shell session we ran previously.

#!/usr/bin/env nextflow

reads = Channel.fromFilePairs("/data/MSc/2020/MA5112/scRNA-Seq/reads/*_R{1,2}_*")
index = Channel.value(file("/data/MSc/2020/MA5112/scRNA-Seq/reference/Homo_sapiens.cDNA.idx"))
whitelist = Channel.value(file("/data/MSc/2020/MA5112/scRNA-Seq/assets/10xv3_whitelist.txt"))
chemistry = "10xv3"
outdir = "."


process kallisto_bus{

    publishDir "${outdir}", mode:'copy'

    input:

    output:

    script:
    """
    kallisto bus \
    """
}

process bustools_correct{

    publishDir "${outdir}/bus_output", mode:'copy'

    input:

    output:

    script:
    """
    bustools correct \
    """
}


process bustools_sort{

    publishDir "${outdir}/bus_output", mode:'copy'

    input:

    output:

    script:
    """
    mkdir -p tmp

    bustools sort \
    """
}


process bustools_text{

    publishDir "${outdir}/bus_output", mode:'copy'

    input:

    output:

    script:
    """
    bustools text \
    """
}

Genomic Data Analysis II

Nextflow

Walkthrough

Exercise