SamStudio8 · July 28, 2021 17:00 · Jul 28, 2021
diff --git a/collect.nf b/collect.nf
@@ -0,0 +1,49 @@
+#!/usr/bin/env nextflow
+
+params.testdir = "/cephfs/covid/software/sam/nf-test/"
+
+params.fofn_single = [params.testdir, 'samples.csv'].join('/')
+single_manifest_ch = Channel
+    .fromPath(params.fofn_single)  // open say, a CSV
+    .splitCsv(header:true)         // split text stream into CSV records
+    .map { row-> file(row.path) }  // coerce the record and return a file for each line
+    .collect()                     // emit all items as one
+
+process echo_fofn_single {
+
+    input:
+    file '*.txt' from single_manifest_ch
+
+    output:
+    publishDir path: "${params.testdir}", pattern: "out", mode: "copy", overwrite: true
+    file "out"
+
+    script:
+    """
+    cat *.txt > out
+    """
+}
+
+
+params.fofn_group = [params.testdir, 'grouped_samples.tsv'].join('/')
+group_manifest_ch = Channel
+    .fromPath(params.fofn_group)
+    .splitCsv(header:true, sep:'\t')
+    .map { row-> tuple(row.group, file(row.path)) }  // coerce the record into a (group, file) tuple
+    .groupTuple()                                    // return tuples of (group, [file1, ...fileN])
+
+process echo_fofn_group {
+
+    input:
+    tuple(group, file(files)) from group_manifest_ch
+
+    output:
+    publishDir path: "${params.testdir}", pattern: "g*out", mode: "copy", overwrite: true
+    file "g${group}.out"
+
+    script:
+    """
+    cat ${files} > g${group}.out
+    """
+}
+
diff --git a/file1.txt b/file1.txt
@@ -0,0 +1 @@
+hello
diff --git a/file2.txt b/file2.txt
@@ -0,0 +1 @@
+world
diff --git a/file3.txt b/file3.txt
@@ -0,0 +1 @@
+hoot
diff --git a/file4.txt b/file4.txt
@@ -0,0 +1 @@
+meow
diff --git a/file5.txt b/file5.txt
@@ -0,0 +1 @@
+bang
diff --git a/g1.out b/g1.out
@@ -0,0 +1,2 @@
+hello
+world
diff --git a/g2.out b/g2.out
@@ -0,0 +1,2 @@
+hoot
+meow
diff --git a/g3.out b/g3.out
@@ -0,0 +1 @@
+bang
diff --git a/grouped_samples.tsv b/grouped_samples.tsv
@@ -0,0 +1,6 @@
+group	path
+1	/cephfs/covid/software/sam/nf-test/file1.txt
+1	/cephfs/covid/software/sam/nf-test/file2.txt
+2	/cephfs/covid/software/sam/nf-test/file3.txt
+2	/cephfs/covid/software/sam/nf-test/file4.txt
+3	/cephfs/covid/software/sam/nf-test/file5.txt
diff --git a/out b/out
@@ -0,0 +1,2 @@
+hello
+world
diff --git a/samples.csv b/samples.csv
@@ -0,0 +1,3 @@
+path
+/cephfs/covid/software/sam/nf-test/file1.txt
+/cephfs/covid/software/sam/nf-test/file2.txt
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