1. Operator Tour¶

In this chapter, we take a curated tour of the Nextflow operators. Commonly used and well understood operators are not covered here - only those that we've seen could use more attention or those where the usage could be more elaborate. These set of operators have been chosen to illustrate tangential concepts and Nextflow features.

1.1 map¶

1.1.1 Basics¶

Map is certainly the most commonly used of the operators covered here. It's a way to supply a closure through which each element in the channel is passed. The return value of the closure is emitted as an element in a new output channel. A canonical example is a closure that multiplies two numbers:

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workflow {
    Channel.of( 1, 2, 3, 4, 5 )
    | map { it * it }
    | view
}

The code above is available in a starter main.nf file available at advanced/operators/main.nf. It is recommended to open and edit this file to follow along with the examples given in the rest of this chapter. The workflow can be executed with:

cd operators
nextflow run .

By default, the element being passed to the closure is given the default name it. If you would prefer a more informative variable name, it can be named by using the -> notation:

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workflow {
    Channel.of( 1, 2, 3, 4, 5 )
    | map { num -> num * num }
    | view
}

Groovy is an optionally typed language, and it is possible to specify the type of the argument passed to the closure.

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workflow {
    Channel.of( 1, 2, 3, 4, 5 )
    | map { Integer num -> num * num }
    | view
}

1.1.2 Named Closures¶

If you find yourself re-using the same closure multiple times in your pipeline, the closure can be named and referenced:

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def squareIt = { Integer num -> num * num }

workflow {
    Channel.of( 1, 2, 3, 4, 5 )
    | map( squareIt )
    | view
}

If you have these re-usable closures defined, you can compose them together.

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def squareIt = { it * it }
def addTwo = { it + 2 }

workflow {
    Channel.of( 1, 2, 3, 4, 5 )
    | map( squareIt >> addTwo )
    | view
}

N E X T F L O W  ~  version 23.04.1
Launching `./main.nf` [focused_borg] DSL2 - revision: f3c3e751fe
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The above is the same as writing:

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def squareIt = { it * it }
def addTwo = { it + 2 }

workflow {
    Channel.of( 1, 2, 3, 4, 5 )
    | map( squareIt )
    | map( addTwo )
    | view
}

For those inclined towards functional programming, you'll be happy to know that closures can be curried:

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def timesN = { multiplier, it -> it * multiplier }
def timesTen = timesN.curry(10)

workflow {
    Channel.of( 1, 2, 3, 4, 5 )
    | map( timesTen )
    | view
}

1.2 view¶

In addition to the argument-less usage of view as shown above, this operator can also take a closure to customize the stdout message. We can create a closure to print the value of the elements in a channel as well as their type, for example:

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def timesN = { multiplier, it -> it * multiplier }
def timesTen = timesN.curry(10)

workflow {
    Channel.of( 1, 2, 3, 4, 5 )
    | map( timesTen )
    | view { "Found '$it' (${it.getClass()})"}
}

1.3 splitCsv¶

A common Nextflow pattern is for a simple samplesheet to be passed as primary input into a workflow. We'll see some more complicated ways to manage these inputs later on in the workshop, but the splitCsv (docs) is an excellent tool to have in a pinch. This operator will parse a csv/tsv and return a channel where each item is a row in the csv/tsv:

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workflow {
    Channel.fromPath("data/samplesheet.csv")
    | splitCsv( header: true )
    | view
}

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process FastQC {
    input:
    tuple val(id), path(fastqs)
    // ... rest of the process

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workflow {
    Channel.fromPath("data/samplesheet.csv")
    | splitCsv( header: true )
    | map { row ->
        [row.id, [file(row.fastq1), file(row.fastq2)]]
    }
    | view
}

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workflow {
    Channel.fromPath("data/samplesheet.csv")
    | splitCsv( header: true )
    | map { row ->
        metaMap = [id: row.id, type: row.type, repeat: row.repeat]
        [metaMap, [file(row.fastq1), file(row.fastq2)]]
    }
    | view
}

1.4 multiMap¶

The multiMap (documentation) operator is a way of taking a single input channel and emitting into multiple channels for each input element.

Let's assume we've been given a samplesheet that has tumor/normal pairs bundled together on the same row. View the example samplesheet with:

cd operators
cat data/samplesheet.ugly.csv

Using the splitCsv operator would give us one entry that would contain all four fastq files. Let's consider that we wanted to split these fastqs into separate channels for tumor and normal. In other words, for every row in the samplesheet, we would like to emit an entry into two new channels. To do this, we can use the multiMap operator:

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workflow {
    Channel.fromPath("data/samplesheet.ugly.csv")
    | splitCsv( header: true )
    | multiMap { row ->
        tumor:
            metamap = [id: row.id, type:'tumor', repeat:row.repeat]
            [metamap, file(row.tumor_fastq_1), file(row.tumor_fastq_2)]
        normal:
            metamap = [id: row.id, type:'normal', repeat:row.repeat]
            [metamap, file(row.normal_fastq_1), file(row.normal_fastq_2)]
    }
    | set { samples }

    samples.tumor | view { "Tumor: $it"}
    samples.normal | view { "Normal: $it"}
}

1.5 branch¶

The branch operator (documentation) is a way of taking a single input channel and emitting a new element into one (and only one) of a selection of output channels.

In the example above, the multiMap operator was necessary because we were supplied with a samplesheet that combined two pairs of fastq per row and we wanted to turn each row into new elements in multiple channels. If we were to use the neater samplesheet that had tumor/normal pairs on separate rows, we could use the branch operator to achieve the same result as we are routing each input element into a single output channel.

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workflow {
    Channel.fromPath("data/samplesheet.csv")
    | splitCsv( header: true )
    | map { row -> [[id: row.id, repeat: row.repeat, type: row.type], [file(row.fastq1), file(row.fastq2)]] }
    | branch { meta, reads ->
        tumor: meta.type == "tumor"
        normal: meta.type == "normal"
    }
    | set { samples }

    samples.tumor | view { "Tumor: $it"}
    samples.normal | view { "Normal: $it"}
}

An element is only emitted to the first channel were the test condition is met. If an element does not meet any of the tests, it is not emitted to any of the output channels. You can 'catch' any such samples by specifying true as a condition. If we knew that all samples would be either tumor or normal and no third 'type', we could write

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branch { meta, reads ->
    tumor: meta.type == "tumor"
    normal: true
}

We may want to emit a slightly different element than the one passed as input. The branch operator can (optionally) return a new element to an channel. For example, to add an extra key in the meta map of the tumor samples, we add a new line under the condition and return our new element. In this example, we modify the first element of the List to be a new list that is the result of merging the existing meta map with a new map containing a single key:

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branch { meta, reads ->
    tumor: meta.type == "tumor"
        return [meta + [newKey: 'myValue'], reads]
    normal: true
}

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branch { meta, reads ->
    tumor: meta.type == "tumor"
        return [meta + [type: 'abnormal'], reads]
    normal: true
}

1.5.1 Multi-channel Objects¶

Some Nextflow operators return objects that contain multiple channels. The multiMap and branch operators are excellent examples. In most instances, the output is assigned to a variable and then addressed by name:

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numbers = Channel.of( 1, 2, 3, 4, 5 )
| multiMap {
    small: it
    large: it * 10
}
numbers.small | view { num -> "Small: $num"}
numbers.large | view { num -> "Large: $num"}

or by using the set operator (documentation):

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Channel.of( 1, 2, 3, 4, 5 )
| multiMap {
    small: it
    large: it * 10
}
| set { numbers }

numbers.small | view { num -> "Small: $num"}
numbers.large | view { num -> "Large: $num"}

A more interesting situation occurs when given a process that takes multiple channels as input:

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process MultiInput {
    debug true
    input:
    val(smallNum)
    val(bigNum)

    "echo -n small is $smallNum and big is $bigNum"
}

You can either provide the channels individually:

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Channel.of( 1, 2, 3, 4, 5 )
| multiMap {
    small: it
    large: it * 10
}
| set { numbers }

MultiInput(numbers.small, numbers.large)

or you can provide the multichannel as a single input:

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Channel.of( 1, 2, 3, 4, 5)
| multiMap {
    small: it
    large: it * 10
}
| set { numbers }

MultiInput(numbers)

For an even cleaner solution, you can skip the now-redundant set operator:

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Channel.of( 1, 2, 3, 4, 5 )
| multiMap {
    small: it
    large: it * 10
}
| MultiInput

If you have processes that output multiple channels and input multiple channels and the cardinality matches, they can be chained together in the same manner.

1.6 groupTuple¶

A common operation is to group elements from a single channel where those elements share a common key. Take this example samplesheet as an example:

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workflow {
    Channel.fromPath("data/samplesheet.csv")
    | splitCsv(header: true)
    | map { row ->
        meta = [id: row.id, type: row.type]
        [meta, row.repeat, [row.fastq1, row.fastq2]]
    }
    | view
}

We see that there are multiple rows where the first element in the item emitted by the channel is the Map [id:sampleA, type:normal] and items in the channel where the first element is the Map [id:sampleA, type:tumor].

The groupTuple operator allows us to combine elements that share a common key:

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workflow {
    Channel.fromPath("data/samplesheet.csv")
    | splitCsv(header: true)
    | map { row ->
        meta = [id: row.id, type: row.type]
        [meta, row.repeat, [row.fastq1, row.fastq2]]
    }
    | groupTuple
    | view
}

1.7 transpose¶

The transpose operator is often misunderstood. It can be thought of as the inverse of the groupTuple operator. Give the following workflow, the groupTuple and transpose operators cancel each other out. Removing lines 8 and 9 returns the same result.

Given a workflow that returns one element per sample, where we have grouped the samplesheet lines on a meta containing only id and type:

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workflow {
    Channel.fromPath("data/samplesheet.csv")
    | splitCsv(header: true)
    | map { row ->
        meta = [id: row.id, type: row.type]
        [meta, row.repeat, [row.fastq1, row.fastq2]]
    }
    | groupTuple
    | view
}

N E X T F L O W  ~  version 23.04.1
Launching `./main.nf` [spontaneous_rutherford] DSL2 - revision: 7dc1cc0039
[[id:sampleA, type:normal], [1, 2], [[data/reads/sampleA_rep1_normal_R1.fastq.gz, data/reads/sampleA_rep1_normal_R2.fastq.gz], [data/reads/sampleA_rep2_normal_R1.fastq.gz, data/reads/sampleA_rep2_normal_R2.fastq.gz]]]
[[id:sampleA, type:tumor], [1, 2], [[data/reads/sampleA_rep1_tumor_R1.fastq.gz, data/reads/sampleA_rep1_tumor_R2.fastq.gz], [data/reads/sampleA_rep2_tumor_R1.fastq.gz, data/reads/sampleA_rep2_tumor_R2.fastq.gz]]]
[[id:sampleB, type:normal], [1], [[data/reads/sampleB_rep1_normal_R1.fastq.gz, data/reads/sampleB_rep1_normal_R2.fastq.gz]]]
[[id:sampleB, type:tumor], [1], [[data/reads/sampleB_rep1_tumor_R1.fastq.gz, data/reads/sampleB_rep1_tumor_R2.fastq.gz]]]
[[id:sampleC, type:normal], [1], [[data/reads/sampleC_rep1_normal_R1.fastq.gz, data/reads/sampleC_rep1_normal_R2.fastq.gz]]]
[[id:sampleC, type:tumor], [1], [[data/reads/sampleC_rep1_tumor_R1.fastq.gz, data/reads/sampleC_rep1_tumor_R2.fastq.gz]]]

If we add in a transpose, each repeat number is matched back to the appropriate list of reads:

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workflow {
    Channel.fromPath("data/samplesheet.csv")
    | splitCsv(header: true)
    | map { row ->
        meta = [id: row.id, type: row.type]
        [meta, row.repeat, [row.fastq1, row.fastq2]]
    }
    | groupTuple
    | transpose
    | view
}

N E X T F L O W  ~  version 23.04.1
Launching `./main.nf` [elegant_rutherford] DSL2 - revision: 2c5476b133
[[id:sampleA, type:normal], 1, [data/reads/sampleA_rep1_normal_R1.fastq.gz, data/reads/sampleA_rep1_normal_R2.fastq.gz]]
[[id:sampleA, type:normal], 2, [data/reads/sampleA_rep2_normal_R1.fastq.gz, data/reads/sampleA_rep2_normal_R2.fastq.gz]]
[[id:sampleA, type:tumor], 1, [data/reads/sampleA_rep1_tumor_R1.fastq.gz, data/reads/sampleA_rep1_tumor_R2.fastq.gz]]
[[id:sampleA, type:tumor], 2, [data/reads/sampleA_rep2_tumor_R1.fastq.gz, data/reads/sampleA_rep2_tumor_R2.fastq.gz]]
[[id:sampleB, type:normal], 1, [data/reads/sampleB_rep1_normal_R1.fastq.gz, data/reads/sampleB_rep1_normal_R2.fastq.gz]]
[[id:sampleB, type:tumor], 1, [data/reads/sampleB_rep1_tumor_R1.fastq.gz, data/reads/sampleB_rep1_tumor_R2.fastq.gz]]
[[id:sampleC, type:normal], 1, [data/reads/sampleC_rep1_normal_R1.fastq.gz, data/reads/sampleC_rep1_normal_R2.fastq.gz]]
[[id:sampleC, type:tumor], 1, [data/reads/sampleC_rep1_tumor_R1.fastq.gz, data/reads/sampleC_rep1_tumor_R2.fastq.gz]]

1.8 flatMap¶

As the name suggests, the flatMap operator allows you to modify the elements in a channel and then flatten the resulting collection. This is useful if you need to "expand" elements in a channel an incoming element can turn into zero or more elements in the output channel. For example:

workflow {
    numbers = Channel.of(1, 2)

    numbers
    | flatMap { n -> [ n, n*10, n*100 ] }
    | view
}

The input channel has two elements. For each element in the input channel, we return a List of length three. The List is flattened and each element in our returned list is emitted independently into the output channel:

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workflow {
    numbers = Channel.of(1, 2)

    numbers
    | flatMap { n -> [ n, [n*10, n*100] ] }
    | view
}

mkdir -p data/datfiles/sample{1,2}
touch data/datfiles/sample1/data.{1,2,3,4,5,6,7}.dat
touch data/datfiles/sample2/data.{1,2,3,4}.dat
tree data/datfiles

workflow {
    Channel.fromPath("data/datfiles/sample*/*.dat")
    | map { [it.getParent().name, it] }
    | groupTuple
    | view
}

[sample2, [sample2/data.1.dat, sample2/data.3.dat, sample2/data.2.dat, sample2/data.4.dat]]
[sample1, [sample1/data.1.dat, sample1/data.3.dat, sample1/data.2.dat, sample1/data.6.dat, sample1/data.5.dat, sample1/data.4.dat]]

[sample1, [sample1/data.1.dat, sample1/data.3.dat, sample1/data.2.dat]]
[sample1, [sample1/data.6.dat, sample1/data.5.dat, sample1/data.4.dat]]
[sample2, [sample2/data.1.dat, sample2/data.3.dat, sample2/data.2.dat]]
[sample2, [sample2/data.4.dat]]

workflow {
    Channel.fromPath("data/datfiles/sample*/*.dat")
    | map { [it.getParent().name, it] }
    | groupTuple
    | flatMap { id, files -> files.collate(3).collect { chunk -> [id, chunk] } }
    | view
}

1.9 collectFile¶

The collectFile operator allows you to write one or more new files based on the contents of a channel.

1.9.1 Writing strings to a single file¶

At its most basic, this operator writes the contents of the elements of a channel directly into a file. If the objecting being passed into the collectFile operator is a string, the strings are written to the collected file:

workflow {
    characters = Channel.of(
        ['name': 'Jake', 'title': 'Detective'],
        ['name': 'Rosa', 'title': 'Detective'],
        ['name': 'Terry', 'title': 'Sergeant'],
        ['name': 'Amy', 'title': 'Detective'],
        ['name': 'Charles', 'title': 'Detective'],
        ['name': 'Gina', 'title': 'Administrator'],
        ['name': 'Raymond', 'title': 'Captain'],
        ['name': 'Michael', 'title': 'Detective'],
        ['name': 'Norm', 'title': 'Detective']
    )

    characters
    | map { it.name }
    | collectFile
    | view
}

The operator returns a channel containing a new file collect-file.data:

N E X T F L O W  ~  version 23.10.1
Launching `./main.nf` [distracted_ritchie] DSL2 - revision: 1e5061406d
work/tmp/57/8052c566f657c59679f07958031231/collect-file.data

If we view the contents of this file, we see the strings written (without delimiter) to a single file:

RaymondTerryNormRosaCharlesJakeGinaMichaelAmy

We can supply arguments name and newLine to the collectFile operator to return a file with a more informative name and newlines separating each entry:

characters
| map { it.name }
| collectFile(name: 'people.txt', newLine: true)
| view

Raymond
Terry
Norm
Rosa
Charles
Jake
Gina
Michael
Amy

1.9.2 Collecting to a new location¶

By default, the collected file is written into the work directory, which makes it suitable for input into a downstream process. If the collected file is an output of the workflow instead of an intermediate, it can be written to a directory of your choosing using the storeDir argument:

characters
| map { it.name }
| collectFile(name: 'characters.txt', newLine: true, storeDir: 'results')
| view

1.9.3 Collecting file contents¶

If the contents of the input channel is a file, its contents are appended to the collected file. Here we make a small process WriteBio that generates a CSV from the Map object supplied as input:

process WriteBio {
    input: val(character)
    output: path('bio.txt')
    script:
    def article = character.title.toLowerCase() =~ ~/^[aeiou]/ ? 'an' : 'a'
    """
    echo ${character.name} is ${article} ${character.title} > bio.txt
    """
}

workflow {
    characters = Channel.of(
        ['name': 'Jake', 'title': 'Detective'],
        ['name': 'Rosa', 'title': 'Detective'],
        ['name': 'Terry', 'title': 'Sergeant'],
        ['name': 'Amy', 'title': 'Detective'],
        ['name': 'Charles', 'title': 'Detective'],
        ['name': 'Gina', 'title': 'Administrator'],
        ['name': 'Raymond', 'title': 'Captain'],
        ['name': 'Michael', 'title': 'Detective'],
        ['name': 'Norm', 'title': 'Detective']
    )

    characters
    | WriteBio
    | collectFile
    | view
}

... to produce the collected file

Charles is a Detective
Amy is a Detective
Norm is a Detective
Jake is a Detective
Rosa is a Detective
Raymond is a Captain
Gina is an Administrator
Terry is a Sergeant
Michael is a Detective

1.9.4 Collecting into multiple files¶

Instead of writing all entries to a single file, you can direct entries from the input channel to different files by supplying a closure to the collectFile operator. The closure must return a List of two entries where the two elements in the List are

1. the name of the file into which the data should be written, and
2. the data to write.

For example:

characters
| collectFile(newLine: true, storeDir: 'results') { character ->
    filename = "${character.title}s.txt"
    article = character.title.toLowerCase() =~ ~/^[aeiou]/ ? 'an' : 'a'
    text = "${character.name} is ${article} ${character.title}"
    [filename, text]
}
| view

The collectFile operator now returns a channel containing four files where we have the outputs grouped by the filename we specified.

Launching `./main.nf` [marvelous_legentil] DSL2 - revision: a571cfd449
results/Administrators.txt
results/Captains.txt
results/Detectives.txt
results/Sergeants.txt

1.9.5 Dealing with headers¶

Let's say we have a process that returns a CSV. In this example, we're going to create very small two-line CVSs, but the same approach is applicable to larger files as well.

process WriteBio {
    input: val(character)
    output: path('bio.csv')
    script:
    """
    echo "precinct,name,title" > bio.csv
    echo 99th,${character.name},${character.title} >> bio.csv
    """
}

If we run this with the same workflow as before:

characters
| WriteBio
| collectFile(name: 'characters.csv', storeDir: 'results')
| view

... the CSVs are simply concatenated with the header included each time:

precinct,name,title
99th,Jake,Detective
precinct,name,title
99th,Terry,Sergeant
precinct,name,title
99th,Rosa,Detective
...

To keep the header from only the first entry, we can use the keepHeader argument to collectFile:

characters
| WriteBio
| collectFile(name: 'characters.csv', storeDir: 'results', keepHeader: true)
| view

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process WriteBio {
    input: val(character)
    output: tuple val(character), path('bio.csv')
    script:
    """
    echo "precinct,name,title" > bio.csv
    echo 99th,${character.name},${character.title} >> bio.csv
    """
}

results
├── Administrators.csv
├── Captains.csv
├── Detectives.csv
└── Sergeants.csv

characters
| WriteBio
| collectFile(storeDir: 'results', keepHeader: true) { character, file ->
    ["${character.title}s.csv", file]
}
| view

characters
| WriteBio
| map { character, file -> ["${character.title}s.csv", file] }
| collectFile(storeDir: 'results', keepHeader: true)
| view