Execute groovy inside nextflow process using process inputs

As you've already discovered, you can declare variables in the script block, before the command string. For example:

process alignment {

    input:
    tuple val(sample), path(fastq_files)

    output:
    tuple val(sample), path(output_file)

    script:
    output_file = "${sample}.bam"

    """
    >&2 echo "Aligning ${sample}..."
    touch "${output_file}"
    """
}

Note that these are global (within the process scope) unless you define them using the def keyword. If you don't need these elsewhere in your process definition, like in your example, a local variable (using def) is usually preferable. If, however, you need to access these in your output declaration, for example, then they will need to be global.

Note that the fromFilePairs factory method emits a tuple, where the first element is a group key and the second element is a list of files. The problem with just using val to declare the inputs is that the files in the second element will not be localized to the working directory when your script is run. To fix this, you can just change your input definition to something like:

input:
tuple val(sample), path(fastq_files)

The problem with this approach, is that we're unable to extract the parent directory name from the localized filenames. So you will need to pass this in somehow. Usually, you could just get the parent name from the first file in the tuple, using:

params.input_dir = './path/to/files'
params.pattern = '**_R{1,2}_00?.fastq.gz'


process alignment {

    debug true

    input:
    tuple val(sample), val(project), path(fastq_files)

    """
    echo "${sample}: ${project}: ${fastq_files}"
    """
}

workflow {

    Channel
        .fromFilePairs( "${params.input_dir}/${params.pattern}" )
        .map { sample, reads ->
            def project = reads[0].parent.name

            tuple( sample, project, reads )
        }
        .set { reads }

    alignment( reads )
}

But since the glob pattern has an additional wildcard, i.e. _00?, you may not necessarily get the results you expect. For example:

$ mkdir -p path/to/files/project{1,2,3}
$ touch path/to/files/project1/sample1_R{1,2}_00{1,2,3,4}.fastq.gz
$ touch path/to/files/project2/sample2_R{1,2}_00{1,2,3,4}.fastq.gz
$ touch path/to/files/project3/sample3_R{1,2}_00{1,2,3,4}.fastq.gz
$ nextflow run main.nf
N E X T F L O W  ~  version 22.04.0
Launching `main.nf` [determined_roentgen] DSL2 - revision: f80ab33ac8
executor >  local (12)
[a8/9235cc] process > alignment (12) [100%] 12 of 12 ✔
sample2: project2: sample2_R1_001.fastq.gz sample2_R1_004.fastq.gz

sample1: project1: sample1_R1_003.fastq.gz sample1_R2_001.fastq.gz

sample1: project1: sample1_R1_004.fastq.gz sample1_R2_003.fastq.gz

sample3: project3: sample3_R1_001.fastq.gz sample3_R2_001.fastq.gz

sample1: project1: sample1_R1_001.fastq.gz sample1_R2_004.fastq.gz

sample1: project1: sample1_R1_002.fastq.gz sample1_R2_002.fastq.gz

sample2: project2: sample2_R1_002.fastq.gz sample2_R2_002.fastq.gz

sample2: project2: sample2_R2_001.fastq.gz sample2_R2_004.fastq.gz

sample2: project2: sample2_R1_003.fastq.gz sample2_R2_003.fastq.gz

sample3: project3: sample3_R2_002.fastq.gz sample3_R2_004.fastq.gz

sample3: project3: sample3_R1_003.fastq.gz sample3_R1_004.fastq.gz

sample3: project3: sample3_R1_002.fastq.gz sample3_R2_003.fastq.gz

Fortunately, we can supply a custom file pair grouping strategy using a closure. This uses the readPrefix helper function:

workflow {

    Channel
        .fromFilePairs( "${params.input_dir}/${params.pattern}" ) { file ->
            prefix = Channel.readPrefix(file, params.pattern)
            suffix = file.simpleName.tokenize('_').last()

            "${file.parent.name}/${prefix}_${suffix}"
        }
        .map { key, reads ->
            def (project, sample) = key.tokenize('/')

            tuple( sample, project, reads )
        }
        .set { reads }

    alignment( reads )
}

Results:

$ nextflow run main.nf
N E X T F L O W  ~  version 22.04.0
Launching `main.nf` [loving_cantor] DSL2 - revision: 5a76ac712f
executor >  local (12)
[f4/74edbc] process > alignment (12) [100%] 12 of 12 ✔
sample1_003: project1: sample1_R1_003.fastq.gz sample1_R2_003.fastq.gz

sample2_002: project2: sample2_R1_002.fastq.gz sample2_R2_002.fastq.gz

sample1_002: project1: sample1_R1_002.fastq.gz sample1_R2_002.fastq.gz

sample2_003: project2: sample2_R1_003.fastq.gz sample2_R2_003.fastq.gz

sample2_004: project2: sample2_R1_004.fastq.gz sample2_R2_004.fastq.gz

sample2_001: project2: sample2_R1_001.fastq.gz sample2_R2_001.fastq.gz

sample1_001: project1: sample1_R1_001.fastq.gz sample1_R2_001.fastq.gz

sample1_004: project1: sample1_R1_004.fastq.gz sample1_R2_004.fastq.gz

sample3_001: project3: sample3_R1_001.fastq.gz sample3_R2_001.fastq.gz

sample3_004: project3: sample3_R1_004.fastq.gz sample3_R2_004.fastq.gz

sample3_002: project3: sample3_R1_002.fastq.gz sample3_R2_002.fastq.gz

sample3_003: project3: sample3_R1_003.fastq.gz sample3_R2_003.fastq.gz

I figured it out, if instead of just jumping into the shell script with the triple quotes, you can start specifying the process execution script with "script:" then run Groovy using the process inputs

process alignment {
    input:
        val files
    output:
        stdout
    script:
    test = (files[1][0] =~ '.+/test/([^/]+)/.+').findAll()[0][1]
    """
    echo $test
    """