add nextflow d30e48d

nextflow/tests/collect-record.nf

@@ -0,0 +1,69 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.types = true
+
+/*
+ * fake alignment step producing a BAM and BAI files
+ */
+process align {
+    debug true
+
+    input:
+    record(
+        barcode: String,
+        seq_id: String
+    )
+
+    output:
+    record(
+        barcode: barcode,
+        seq_id: seq_id,
+        bam: file('bam'),
+        bai: file('bai')
+    )
+
+    script:
+    """
+    echo BAM ${seq_id} - ${barcode} > bam
+    echo BAI ${seq_id} - ${barcode} > bai
+    """
+}
+
+/*
+ * Finally merge the BAMs and BAIs with the same 'barcode'
+ */
+process merge {
+    debug true
+
+    input:
+    tuple(barcode: String, samples: Bag<Record>)
+
+    stage:
+    stageAs samples*.bam, 'bam?'
+    stageAs samples*.bai, 'bai?'
+
+    script:
+    """
+    echo barcode: ${barcode}
+    echo seq_ids: ${samples*.seq_id.join(' ')}
+    echo bam    : ${samples*.bam.join(' ')}
+    echo bai    : ${samples*.bai.join(' ')}
+    """
+}
+
+/*
+ * main flow
+ */
+workflow {
+    ch_barcode = channel.of('alpha', 'gamma')
+    ch_seq = channel.of('one', 'two', 'three')
+    ch_inputs = ch_barcode
+        .combine(ch_seq)
+        .map { barcode, seq_id -> record(barcode: barcode, seq_id: seq_id) }
+
+    ch_aligned = align( ch_inputs )
+        .map { r -> tuple(r.barcode, r) }
+        .groupBy()
+
+    merge( ch_aligned )
+}