add nextflow d30e48d

nextflow/tests-v1/publish-dir.nf

@@ -0,0 +1,75 @@
+#!/usr/bin/env nextflow
+/*
+ * Copyright 2013-2024, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+process align {
+    publishDir 'data', mode: 'copy'
+
+    input:
+    val(x)
+
+    output:
+    path("*.bam")
+    path("${x}.bai")
+
+    """
+    echo ${x} > ${x}.bam
+    echo ${x} | rev > ${x}.bai
+    """
+}
+
+process my_combine {
+    publishDir 'data'
+    publishDir 'more/data', mode: 'copy'
+
+    input:
+    path(bamfile)
+    path(baifile)
+
+    output:
+    path 'result.txt'
+
+    """
+    cat $bamfile > result.txt
+    cat $baifile >> result.txt
+    """
+}
+
+process foo {
+  publishDir 'data', mode: 'link'
+  output:
+  file 'xxx'
+
+  '''
+  mkdir xxx
+  touch xxx/A
+  touch xxx/B
+  touch xxx/C
+  '''
+}
+
+workflow {
+  def input = Channel.of('alpha','beta','delta')
+  align(input)
+
+  def bam = align.out[0].toSortedList { it.name }
+  def bai = align.out[1].toSortedList { it.name }
+  my_combine( bam, bai )
+  my_combine.out.view{ it.text }
+
+  foo()
+}