Nextflow: How to format input tuple for STAR_ALIGN process with STAR index directory

Question

[DdogBoss]

Hi all,

I am trying to pass the output of a STAR genome index process to a STAR alignment process in Nextflow, but I keep running into tuple/variable issues. Here’s a minimal reproducible example of my setup.

STAR index process

    process STAR {
    publishDir params.outdir, mode: "copy"
    label 'process_high'

    input:
        tuple path(reference), path(gtf)

    output:
         path 'STAR_index/' emit: index_dir

    script:
    """
    mkdir -p STAR_index
    STAR --runThreadN $task.cpus \
         --runMode genomeGenerate \
         --genomeDir STAR_index \
         --genomeFastaFiles $reference \
         --sjdbGTFfile $gtf
    """
    }

Workflow snippet

    // Channel with sample reads
    Channel.fromFilePairs(params.reads)
    | set { align_ch }
    // STAR index
    star_index_result = STAR(star_index_ch)
    // Flatten reads and prepare tuples
    pre_aligned_input_ch = align_ch.map { sample, reads ->
    tuple(sample, reads.toArray())   
    }
    aligned_input = pre_aligned_input_ch.combine(star_index_result.index_dir) { sample_tuple, index_dir ->
    def sample = sample_tuple[0]
    def reads  = sample_tuple[1]
    tuple(index_dir, sample, *reads)  
    }
    STAR_ALIGN(aligned_input)

align_ch returns tuples like [sample_name, [read1, read2]]. I want aligned_input tuples to look like [index_dir, sample1, read1, read2].

Reads are structured like *_{R1,R2}.subset.fastq.gz where the wildcard is the sample name.

STAR align process

    process STAR_ALIGN {
    publishDir params.outdir, mode: "copy"
    label 'process_high'

    input:
    tuple path(index_dir), val(sample), path(reads)

    output:
    tuple val(sample), path("*.bam"), emit: bam
    tuple val(sample), path("*.Log.final.out"), emit: log

    script:
    """
    STAR \
        --runThreadN $task.cpus \
        --genomeDir ${index_dir} \
        --readFilesIn ${reads.join(' ')} \
        --readFilesCommand zcat \
        --outFileNamePrefix ${sample}_ \
        --outSAMtype BAM SortedByCoordinate \
        2> ${sample}.Log.final.out
    """
    }

Problem The tuples I am feeding into the STAR align process are not valid, and I either get this error:

    ERROR ~ No such variable: path -- Check script 'modules/star/main.nf' at line: 12 or see '.nextflow.log' file for more details

or a DataflowVariable error, or not a valid path.

My goal is to massage the input to STAR_ALIGN so that it receives a tuple like this:

    [index_dir, sample_name, [read1, read2]]

Current attempts with .combine() and *reads either throw a DataflowVariable error or the path variable is missing.

Question How can I properly construct a Nextflow channel/tuple so that each sample is paired with the STAR index directory and the list of reads, in a format acceptable for the STAR_ALIGN process input:

tuple path(index_dir), val(sample), path(reads)

Answer 1

[Pierre Lindenbaum]

align_ch returns tuples like [sample_name, [read1, read2]]. I want aligned_input tuples to look like [index_dir, sample1, read1, read2].

STAR_ALIGN(
   star_index_result.combine(
     align_ch.map{sn,reads->[sn,reads[0],reads[1]]}
        ) )

and STAR_ALIGN :

input:
   tuple path(index_dir), val(sample), path(R1),path(R2)