add nextflow d30e48d

nextflow/docs/snippets/.gitignore

@@ -0,0 +1,2 @@
+.nextflow*
+work

nextflow/docs/snippets/branch-criteria.nf

@@ -0,0 +1,12 @@
+def criteria = branchCriteria { v ->
+    small: v < 10
+    large: v > 10
+}
+
+channel.of(1, 2, 30).branch(criteria).set { ch1 }
+channel.of(10, 20, 3).branch(criteria).set { ch2 }
+
+ch1.small.view { v -> "$v is small" }
+ch1.large.view { v -> "$v is large" }
+ch2.small.view { v -> "$v is small" }
+ch2.large.view { v -> "$v is large" }

nextflow/docs/snippets/branch-criteria.out

@@ -0,0 +1,5 @@
+1 is small
+2 is small
+3 is small
+20 is large
+30 is large

nextflow/docs/snippets/branch-with-fallback.nf

@@ -0,0 +1,11 @@
+channel.of(1, 2, 3, 40, 50)
+    .branch { v ->
+        small: v < 10
+        large: v < 50
+        other: true
+    }
+    .set { result }
+
+result.small.view { v -> "$v is small" }
+result.large.view { v -> "$v is large" }
+result.other.view { v -> "$v is other" }

nextflow/docs/snippets/branch-with-fallback.out

@@ -0,0 +1,5 @@
+1 is small
+2 is small
+3 is small
+40 is large
+50 is other

nextflow/docs/snippets/branch-with-mapper.nf

@@ -0,0 +1,16 @@
+channel.of(1, 2, 3, 40, 50)
+    .branch { v ->
+        alpha: v < 10
+            return v + 2
+
+        beta: v < 50
+            return v - 2
+
+        other: true
+            return 0
+    }
+    .set { result }
+
+result.alpha.view { v -> "$v is alpha" }
+result.beta.view { v -> "$v is beta" }
+result.other.view { v -> "$v is other" }

nextflow/docs/snippets/branch-with-mapper.out

@@ -0,0 +1,5 @@
+3 is alpha
+4 is alpha
+5 is alpha
+38 is beta
+0 is other

nextflow/docs/snippets/branch.nf

@@ -0,0 +1,9 @@
+channel.of(1, 2, 3, 40, 50)
+    .branch { v ->
+        small: v < 10
+        large: v > 10
+    }
+    .set { result }
+
+result.small.view { v -> "$v is small" }
+result.large.view { v -> "$v is large" }

nextflow/docs/snippets/branch.out

@@ -0,0 +1,5 @@
+1 is small
+2 is small
+3 is small
+40 is large
+50 is large

nextflow/docs/snippets/buffer-with-closing.nf

@@ -0,0 +1,3 @@
+channel.of( 1, 2, 3, 1, 2, 3 )
+    .buffer { v -> v == 2 }
+    .view()

nextflow/docs/snippets/buffer-with-closing.out

@@ -0,0 +1,2 @@
+[1, 2]
+[3, 1, 2]

nextflow/docs/snippets/buffer-with-opening-closing.nf

@@ -0,0 +1,4 @@
+// emits bundles starting with `2` and ending with `4`
+channel.of( 1, 2, 3, 4, 5, 1, 2, 3, 4, 5, 1, 2 )
+    .buffer( 2, 4 )
+    .view()

nextflow/docs/snippets/buffer-with-opening-closing.out

@@ -0,0 +1,2 @@
+[2, 3, 4]
+[2, 3, 4]

nextflow/docs/snippets/buffer-with-size-remainder.nf

@@ -0,0 +1,3 @@
+channel.of( 1, 2, 3, 1, 2, 3, 1 )
+    .buffer( size: 2, remainder: true )
+    .view()

nextflow/docs/snippets/buffer-with-size-remainder.out

@@ -0,0 +1,4 @@
+[1, 2]
+[3, 1]
+[2, 3]
+[1]

nextflow/docs/snippets/buffer-with-size-skip.nf

@@ -0,0 +1,3 @@
+channel.of( 1, 2, 3, 4, 5, 1, 2, 3, 4, 5, 1, 2 )
+    .buffer( size: 3, skip: 2 )
+    .view()

nextflow/docs/snippets/buffer-with-size-skip.out

@@ -0,0 +1,2 @@
+[3, 4, 5]
+[3, 4, 5]

nextflow/docs/snippets/buffer-with-size.nf

@@ -0,0 +1,3 @@
+channel.of( 1, 2, 3, 1, 2, 3, 1 )
+    .buffer( size: 2 )
+    .view()

nextflow/docs/snippets/buffer-with-size.out

@@ -0,0 +1,3 @@
+[1, 2]
+[3, 1]
+[2, 3]

nextflow/docs/snippets/collate-with-no-remainder.nf

@@ -0,0 +1,3 @@
+channel.of(1, 2, 3, 1, 2, 3, 1)
+    .collate( 3, false )
+    .view()

nextflow/docs/snippets/collate-with-no-remainder.out

@@ -0,0 +1,2 @@
+[1, 2, 3]
+[1, 2, 3]

nextflow/docs/snippets/collate-with-step.nf

@@ -0,0 +1,3 @@
+channel.of(1, 2, 3, 4)
+    .collate( 3, 1 )
+    .view()

nextflow/docs/snippets/collate-with-step.out

@@ -0,0 +1,4 @@
+[1, 2, 3]
+[2, 3, 4]
+[3, 4]
+[4]

nextflow/docs/snippets/collate.nf

@@ -0,0 +1,3 @@
+channel.of(1, 2, 3, 1, 2, 3, 1)
+    .collate( 3 )
+    .view()

nextflow/docs/snippets/collate.out

@@ -0,0 +1,3 @@
+[1, 2, 3]
+[1, 2, 3]
+[1]

nextflow/docs/snippets/collect-with-mapper.nf

@@ -0,0 +1,3 @@
+channel.of( 'hello', 'ciao', 'bonjour' )
+    .collect { v -> v.length() }
+    .view()

nextflow/docs/snippets/collect-with-mapper.out

@@ -0,0 +1 @@
+[5, 4, 7]

nextflow/docs/snippets/collect.nf

@@ -0,0 +1,3 @@
+channel.of( 1, 2, 3, 4 )
+    .collect()
+    .view()

nextflow/docs/snippets/collect.out

@@ -0,0 +1 @@
+[1, 2, 3, 4]

nextflow/docs/snippets/collectfile-closure.nf

@@ -0,0 +1,8 @@
+channel.of('Hola', 'Ciao', 'Hello', 'Bonjour', 'Halo')
+    .collectFile { item ->
+        [ "${item[0]}.txt", item + '\n' ]
+    }
+    .subscribe { file ->
+        println "File '${file.name}' contains:"
+        println file.text
+    }

nextflow/docs/snippets/collectfile-closure.out

@@ -0,0 +1,11 @@
+File 'B.txt' contains:
+Bonjour
+
+File 'C.txt' contains:
+Ciao
+
+File 'H.txt' contains:
+Halo
+Hola
+Hello
+

nextflow/docs/snippets/collectfile.nf

@@ -0,0 +1,6 @@
+channel.of('alpha', 'beta', 'gamma')
+    .collectFile(name: 'sample.txt', newLine: true)
+    .subscribe { file ->
+        println "Entries are saved to file: $file"
+        println "File content is: ${file.text}"
+    }

nextflow/docs/snippets/combine-by.nf

@@ -0,0 +1,4 @@
+source = channel.of( [1, 'alpha'], [2, 'beta'] )
+target = channel.of( [1, 'x'], [1, 'y'], [1, 'z'], [2, 'p'], [2, 'q'], [2, 't'] )
+
+source.combine(target, by: 0).view()

nextflow/docs/snippets/combine-by.out

@@ -0,0 +1,6 @@
+[1, alpha, x]
+[1, alpha, y]
+[1, alpha, z]
+[2, beta, p]
+[2, beta, q]
+[2, beta, t]

nextflow/docs/snippets/combine.nf

@@ -0,0 +1,6 @@
+numbers = channel.of(1, 2, 3)
+words = channel.of('hello', 'ciao')
+
+numbers
+    .combine(words)
+    .view()

nextflow/docs/snippets/combine.out

@@ -0,0 +1,6 @@
+[1, hello]
+[2, hello]
+[3, hello]
+[1, ciao]
+[2, ciao]
+[3, ciao]

nextflow/docs/snippets/concat.nf

@@ -0,0 +1,5 @@
+a = channel.of( 'a', 'b', 'c' )
+b = channel.of( 1, 2, 3 )
+c = channel.of( 'p', 'q' )
+
+c.concat( b, a ).view()

nextflow/docs/snippets/concat.out

@@ -0,0 +1,8 @@
+p
+q
+1
+2
+3
+a
+b
+c

nextflow/docs/snippets/count-with-filter-closure.nf

@@ -0,0 +1,3 @@
+channel.of('a', 'c', 'c', 'q', 'b')
+    .count { v -> v <= 'c' }
+    .view()

nextflow/docs/snippets/count-with-filter-closure.out

@@ -0,0 +1 @@
+4

nextflow/docs/snippets/count-with-filter-number.nf

@@ -0,0 +1,3 @@
+channel.of(4, 1, 7, 1, 1)
+    .count(1)
+    .view()

nextflow/docs/snippets/count-with-filter-number.out

@@ -0,0 +1 @@
+3

nextflow/docs/snippets/count-with-filter-regex.nf

@@ -0,0 +1,3 @@
+channel.of('a', 'c', 'c', 'q', 'b')
+    .count( ~/c/ )
+    .view()

nextflow/docs/snippets/count-with-filter-regex.out

@@ -0,0 +1 @@
+2

nextflow/docs/snippets/count.nf

@@ -0,0 +1,3 @@
+channel.of(9, 1, 7, 5)
+    .count()
+    .view()

nextflow/docs/snippets/count.out

@@ -0,0 +1 @@
+4

nextflow/docs/snippets/cross-with-mapper.nf

@@ -0,0 +1,4 @@
+source = channel.of( [1, 'alpha'], [2, 'beta'] )
+target = channel.of( [1, 'a'], [1, 'b'], [2, 'a'], [2, 'b'] )
+
+source .cross(target) { v -> v[1][0] } .view()

nextflow/docs/snippets/cross-with-mapper.out

@@ -0,0 +1,4 @@
+[[1, alpha], [1, a]]
+[[1, alpha], [2, a]]
+[[2, beta], [1, b]]
+[[2, beta], [2, b]]

nextflow/docs/snippets/cross.nf

@@ -0,0 +1,4 @@
+source = channel.of( [1, 'alpha'], [2, 'beta'] )
+target = channel.of( [1, 'x'], [1, 'y'], [1, 'z'], [2, 'p'], [2, 'q'], [2, 't'] )
+
+source.cross(target).view()

nextflow/docs/snippets/cross.out

@@ -0,0 +1,6 @@
+[[1, alpha], [1, x]]
+[[1, alpha], [1, y]]
+[[1, alpha], [1, z]]
+[[2, beta], [2, p]]
+[[2, beta], [2, q]]
+[[2, beta], [2, t]]

nextflow/docs/snippets/distinct-with-mapper.nf

@@ -0,0 +1,3 @@
+channel.of( 1, 1, 2, 2, 2, 3, 1, 1, 2, 4, 6 )
+    .distinct { v -> v % 2 }
+    .view()

nextflow/docs/snippets/distinct-with-mapper.out

@@ -0,0 +1,4 @@
+1
+2
+3
+2

nextflow/docs/snippets/distinct.nf

@@ -0,0 +1,3 @@
+channel.of( 1, 1, 2, 2, 2, 3, 1, 1, 2, 2, 3 )
+    .distinct()
+    .view()

nextflow/docs/snippets/distinct.out

@@ -0,0 +1,6 @@
+1
+2
+3
+1
+2
+3

nextflow/docs/snippets/dump.nf

@@ -0,0 +1,7 @@
+channel.of( 1, 2, 3 )
+    .map { v -> v + 1 }
+    .dump(tag: 'plus1')
+
+channel.of( 1, 2, 3 )
+    .map { v -> v ** 2 }
+    .dump(tag: 'exp2')

nextflow/docs/snippets/filter-closure.nf

@@ -0,0 +1,3 @@
+channel.of( 1, 2, 3, 4, 5 )
+    .filter { v -> v % 2 == 1 }
+    .view()

nextflow/docs/snippets/filter-closure.out

@@ -0,0 +1,3 @@
+1
+3
+5

nextflow/docs/snippets/filter-regex.nf

@@ -0,0 +1,3 @@
+channel.of( 'a', 'b', 'aa', 'bc', 3, 4.5 )
+    .filter( ~/^a.*/ )
+    .view()

nextflow/docs/snippets/filter-regex.out

@@ -0,0 +1,2 @@
+a
+aa

nextflow/docs/snippets/filter-type.nf

@@ -0,0 +1,3 @@
+channel.of( 'a', 'b', 'aa', 'bc', 3, 4.5 )
+    .filter( Number )
+    .view()

nextflow/docs/snippets/filter-type.out

@@ -0,0 +1,2 @@
+3
+4.5

nextflow/docs/snippets/first.nf

@@ -0,0 +1,19 @@
+// no condition is specified, emits the very first item: 1
+channel.of( 1, 2, 3 )
+    .first()
+    .view()
+
+// emits the first item matching the regular expression: 'aa'
+channel.of( 'a', 'aa', 'aaa' )
+    .first( ~/aa.*/ )
+    .view()
+
+// emits the first String value: 'a'
+channel.of( 1, 2, 'a', 'b', 3 )
+    .first( String )
+    .view()
+
+// emits the first item for which the predicate evaluates to true: 4
+channel.of( 1, 2, 3, 4, 5 )
+    .first { v -> v > 3 }
+    .view()

nextflow/docs/snippets/first.out

@@ -0,0 +1,4 @@
+1
+a
+aa
+4

nextflow/docs/snippets/flatmap-list.nf

@@ -0,0 +1,3 @@
+channel.of( 1, 2, 3 )
+    .flatMap { n -> [ n, n*2, n*3 ] }
+    .view()

nextflow/docs/snippets/flatmap-list.out

@@ -0,0 +1,9 @@
+1
+2
+3
+2
+4
+6
+3
+6
+9

nextflow/docs/snippets/flatmap-map.nf

@@ -0,0 +1,3 @@
+channel.of( 1, 2, 3 )
+    .flatMap { n -> [ number: n, square: n*n, cube: n*n*n ] }
+    .view { entry -> "${entry.key}: ${entry.value}" }

nextflow/docs/snippets/flatmap-map.out

@@ -0,0 +1,9 @@
+number: 1
+square: 1
+cube: 1
+number: 2
+square: 4
+cube: 8
+number: 3
+square: 9
+cube: 27

nextflow/docs/snippets/flatten.nf

@@ -0,0 +1,3 @@
+channel.of( [1, [2, 3]], 4, [5, [6]] )
+    .flatten()
+    .view()

nextflow/docs/snippets/flatten.out

@@ -0,0 +1,6 @@
+1
+2
+3
+4
+5
+6

nextflow/docs/snippets/groupby-size.nf

@@ -0,0 +1,13 @@
+channel.of(
+        tuple('chr1', ['/path/to/region1_chr1.vcf', '/path/to/region2_chr1.vcf']),
+        tuple('chr2', ['/path/to/region1_chr2.vcf', '/path/to/region2_chr2.vcf', '/path/to/region3_chr2.vcf']),
+    )
+    .flatMap { chr, vcfs ->
+        vcfs.collect { vcf ->
+            tuple(chr, vcfs.size(), vcf)    // preserve group size
+        }
+    }
+    .view { v -> "scattered: ${v}" }
+    .groupBy()
+    .map { key, values -> tuple(key, values.toSorted()) }
+    .view { v -> "gathered: ${v}" }

nextflow/docs/snippets/groupby-size.out

@@ -0,0 +1,7 @@
+scattered: [chr1, 2, /path/to/region1_chr1.vcf]
+scattered: [chr1, 2, /path/to/region2_chr1.vcf]
+scattered: [chr2, 3, /path/to/region1_chr2.vcf]
+scattered: [chr2, 3, /path/to/region2_chr2.vcf]
+scattered: [chr2, 3, /path/to/region3_chr2.vcf]
+gathered: [chr1, [/path/to/region1_chr1.vcf, /path/to/region2_chr1.vcf]]
+gathered: [chr2, [/path/to/region1_chr2.vcf, /path/to/region2_chr2.vcf, /path/to/region3_chr2.vcf]]

nextflow/docs/snippets/groupby.nf

@@ -0,0 +1,4 @@
+channel.of( tuple(1, 'A'), tuple(1, 'B'), tuple(2, 'C'), tuple(3, 'B'), tuple(1, 'C'), tuple(2, 'A'), tuple(3, 'D') )
+    .groupBy()
+    .map { key, values -> tuple(key, values.toSorted()) }
+    .view()

nextflow/docs/snippets/groupby.out

@@ -0,0 +1,3 @@
+[1, [A, B, C]]
+[2, [A, C]]
+[3, [B, D]]

nextflow/docs/snippets/grouptuple-by.nf

@@ -0,0 +1,3 @@
+channel.of( [1, 'A'], [1, 'B'], [2, 'C'], [3, 'B'], [1, 'C'], [2, 'A'], [3, 'D'] )
+    .groupTuple(by: 1)
+    .view()

nextflow/docs/snippets/grouptuple-by.out

@@ -0,0 +1,4 @@
+[[1, 2], A]
+[[1, 3], B]
+[[2, 1], C]
+[[3], D]

nextflow/docs/snippets/grouptuple-groupkey.nf

@@ -0,0 +1,13 @@
+channel.of(
+        ['chr1', ['/path/to/region1_chr1.vcf', '/path/to/region2_chr1.vcf']],
+        ['chr2', ['/path/to/region1_chr2.vcf', '/path/to/region2_chr2.vcf', '/path/to/region3_chr2.vcf']],
+    )
+    .flatMap { chr, vcfs ->
+        vcfs.collect { vcf ->
+            tuple(groupKey(chr, vcfs.size()), vcf)              // preserve group size with key
+        }
+    }
+    .view { v -> "scattered: ${v}" }
+    .groupTuple()
+    .map { key, vcfs -> tuple(key.getGroupTarget(), vcfs) }     // unwrap group key
+    .view { v -> "gathered: ${v}" }

nextflow/docs/snippets/grouptuple-groupkey.out

@@ -0,0 +1,7 @@
+scattered: [chr1, /path/to/region1_chr1.vcf]
+scattered: [chr1, /path/to/region2_chr1.vcf]
+scattered: [chr2, /path/to/region1_chr2.vcf]
+scattered: [chr2, /path/to/region2_chr2.vcf]
+scattered: [chr2, /path/to/region3_chr2.vcf]
+gathered: [chr1, [/path/to/region1_chr1.vcf, /path/to/region2_chr1.vcf]]
+gathered: [chr2, [/path/to/region1_chr2.vcf, /path/to/region2_chr2.vcf, /path/to/region3_chr2.vcf]]

nextflow/docs/snippets/grouptuple.nf

@@ -0,0 +1,3 @@
+channel.of( [1, 'A'], [1, 'B'], [2, 'C'], [3, 'B'], [1, 'C'], [2, 'A'], [3, 'D'] )
+    .groupTuple()
+    .view()

nextflow/docs/snippets/grouptuple.out

@@ -0,0 +1,3 @@
+[1, [A, B, C]]
+[2, [C, A]]
+[3, [B, D]]

nextflow/docs/snippets/ifempty-1.nf

@@ -0,0 +1 @@
+channel.of(1, 2, 3).ifEmpty('Hello').view()

nextflow/docs/snippets/ifempty-1.out

@@ -0,0 +1,3 @@
+1
+2
+3

nextflow/docs/snippets/ifempty-2.nf

@@ -0,0 +1 @@
+channel.empty().ifEmpty('Hello').view()

nextflow/docs/snippets/ifempty-2.out

@@ -0,0 +1 @@
+Hello

nextflow/docs/snippets/join-record-duplicates.nf

@@ -0,0 +1,4 @@
+left  = channel.of( record(id: 'X', a: 1), record(id: 'X', a: 3) )
+right = channel.of( record(id: 'X', b: 2), record(id: 'X', b: 4) )
+
+left.join(right, by: 'id').view()

nextflow/docs/snippets/join-record-duplicates.out

@@ -0,0 +1,4 @@
+[id:X, a:1, b:2]
+[id:X, a:1, b:4]
+[id:X, a:3, b:2]
+[id:X, a:3, b:4]

nextflow/docs/snippets/join-record-remainder.nf

@@ -0,0 +1,4 @@
+left  = channel.of( record(id: 'X', a: 1), record(id: 'Y', a: 2), record(id: 'Z', a: 3), record(id: 'P', a: 7) )
+right = channel.of( record(id: 'Z', b: 6), record(id: 'Y', b: 5), record(id: 'X', b: 4), record(id: 'Q', b: 8) )
+
+left.join(right, by: 'id', remainder: true).view()

nextflow/docs/snippets/join-record-remainder.out

@@ -0,0 +1,5 @@
+[id:Y, a:2, b:5]
+[id:Z, a:3, b:6]
+[id:X, a:1, b:4]
+[id:P, a:7]
+[id:Q, b:8]

nextflow/docs/snippets/join-record.nf

@@ -0,0 +1,4 @@
+left  = channel.of( record(id: 'X', a: 1), record(id: 'Y', a: 2), record(id: 'Z', a: 3), record(id: 'P', a: 7) )
+right = channel.of( record(id: 'Z', b: 6), record(id: 'Y', b: 5), record(id: 'X', b: 4) )
+
+left.join(right, by: 'id').view()

nextflow/docs/snippets/join-record.out

@@ -0,0 +1,3 @@
+[id:Z, a:3, b:6]
+[id:Y, a:2, b:5]
+[id:X, a:1, b:4]

nextflow/docs/snippets/join-tuple-remainder.nf

@@ -0,0 +1,4 @@
+left  = channel.of( ['X', 1], ['Y', 2], ['Z', 3], ['P', 7] )
+right = channel.of( ['Z', 6], ['Y', 5], ['X', 4] )
+
+left.join(right, remainder: true).view()

nextflow/docs/snippets/join-tuple-remainder.out

@@ -0,0 +1,4 @@
+[Y, 2, 5]
+[Z, 3, 6]
+[X, 1, 4]
+[P, 7, null]

nextflow/docs/snippets/join-tuple.nf

@@ -0,0 +1,4 @@
+left  = channel.of( ['X', 1], ['Y', 2], ['Z', 3], ['P', 7] )
+right = channel.of( ['Z', 6], ['Y', 5], ['X', 4] )
+
+left.join(right).view()

nextflow/docs/snippets/join-tuple.out

@@ -0,0 +1,3 @@
+[Z, 3, 6]
+[Y, 2, 5]
+[X, 1, 4]

nextflow/docs/snippets/last.nf

@@ -0,0 +1,3 @@
+channel.of( 1, 2, 3, 4, 5, 6 )
+    .last()
+    .view()

nextflow/docs/snippets/last.out

@@ -0,0 +1 @@
+6

nextflow/docs/snippets/map.nf

@@ -0,0 +1,3 @@
+channel.of( 1, 2, 3, 4, 5 )
+    .map { v -> v * v }
+    .view()

nextflow/docs/snippets/map.out

@@ -0,0 +1,5 @@
+1
+4
+9
+16
+25

nextflow/docs/snippets/max-with-comparator.nf

@@ -0,0 +1,4 @@
+// comparator function
+channel.of( "hello", "hi", "hey" )
+    .max { a, b -> a.length() <=> b.length() }
+    .view()

nextflow/docs/snippets/max-with-comparator.out

@@ -0,0 +1 @@
+hello

nextflow/docs/snippets/max-with-mapper.nf

@@ -0,0 +1,4 @@
+// mapping function
+channel.of( "hello", "hi", "hey" )
+    .max { v -> v.length() }
+    .view()