Cannot run HiSat2 (nf4-science(rnaseq) training)

Training
,
1

I have 2 questions:

  1. Regarding nf4-science (RNA-seq) in this process of HiSat2
    modules/hisat2_align.nf
#!/usr/bin/env nextflow

process HISAT2_ALIGN {

    container "community.wave.seqera.io/library/hisat2_samtools:5e49f68a37dc010e"
    publishDir "results/align", mode: 'copy'

    input:
    path reads
    path index_zip

    output:
    path "${reads.simpleName}.bam", emit: bam
    path "${reads.simpleName}.hisat2.log", emit: log

    script:
    """
    tar -xzvf $index_zip
    hisat2 -x ${index_zip.simpleName} -U $reads \
        --new-summary --summary-file ${reads.simpleName}.hisat2.log | \
        samtools view -bS -o ${reads.simpleName}.bam
    """
}

and this main pipeline (rnaseq.nf)

/*
 * Pipeline parameters
 */
params.hisat2_index_zip = "data/genome_index.tar.gz"

The code import index_zip as an input, however, I cannot do so. I have chack GitHub repo, i can’t find genome_index.tar.gz

=========================
2. I entry the training because I want to modify nf-core/chipseq for my own analysis (start from .bam instead of .fastq). After finish nf4-science (rna-seq) and open up the nfcore/rnaseq and nfcore/chipseq code, I still feel that it is quite a lot complicate. The question is which training modules or where should I take the skill to fulfill my purpose?

Thank you for your answer,
Namthip

2

Hi @KuchikiNamthip, happy to help!

  1. You’re meant to create that file in Part 1: 2.3. Create the Hisat2 genome index files. If you skipped running through Part 1 (working interactively with the tools in docker containers) you will need to go and do that step in order to move forward with the pipeline.

  2. You’re correct that there’s quite a difference in complexity between the beginner training and the nf-core pipelines. We are working on some training to fill that gap; in the meantime you can start with this training module: Introduction to nf-core - training.nextflow.io

Good luck and don’t hesitate to reach out if there’s anything else we can do to help.

3

Thank you so much, @GeraldineVdA
That help me a lot.
The training module: Introduction to nf-core - training.nextflow.io also help a lot to understand nf-core.
It is recent update in version the latest version (2.1.3). I passed this point since version 2.1.1, I will back and try it! encourage you all to make training to fill this gap!

Thank a lot and waiting for further training

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