Editing the CAT/CAT module to handle single files (#1196)

* Removed if-statement to only run on more than 1 file, now it will run on single files as well.

* Added a test for running the cat_cat module on a single file.

* Created a new test.yml with nf-core modules create-test-yml -t cat/cat

* Edited test.yml to not include paths and md5sums for versions.yml, and also removed sometimes variable md5sums

modules/cat/cat/main.nf

@@ -18,30 +18,28 @@ process CAT_CAT {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def file_list = files_in.collect { it.toString() }
-    if (file_list.size > 1) {
 
-        // | input     | output     | command1 | command2 |
+    // | input     | output     | command1 | command2 |
-        // |-----------|------------|----------|----------|
+    // |-----------|------------|----------|----------|
-        // | gzipped   | gzipped    | cat      |          |
+    // | gzipped   | gzipped    | cat      |          |
-        // | ungzipped | ungzipped  | cat      |          |
+    // | ungzipped | ungzipped  | cat      |          |
-        // | gzipped   | ungzipped  | zcat     |          |
+    // | gzipped   | ungzipped  | zcat     |          |
-        // | ungzipped | gzipped    | cat      | pigz     |
+    // | ungzipped | gzipped    | cat      | pigz     |
 
-        def in_zip   = file_list[0].endsWith('.gz')
+    def in_zip   = file_list[0].endsWith('.gz')
-        def out_zip  = file_out.endsWith('.gz')
+    def out_zip  = file_out.endsWith('.gz')
-        def command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
+    def command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
-        def command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
+    def command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
-        """
+    """
-        $command1 \\
+    $command1 \\
-            $args \\
+        $args \\
-            ${file_list.join(' ')} \\
+        ${file_list.join(' ')} \\
-            $command2 \\
+        $command2 \\
-            > $file_out
+        > $file_out
 
-        cat <<-END_VERSIONS > versions.yml
+    cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
+    "${task.process}":
-            pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
+        pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
-        END_VERSIONS
+    END_VERSIONS
-        """
+    """
-    }
 }

tests/modules/cat/cat/main.nf

@@ -43,3 +43,12 @@ workflow test_cat_unzipped_zipped {
 
     CAT_CAT ( input, 'cat.txt.gz' )
 }
+
+workflow test_cat_one_file_unzipped_zipped {
+
+    input = [
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+    ]
+
+    CAT_CAT ( input, 'cat.txt.gz' )
+}

tests/modules/cat/cat/test.yml

@@ -31,3 +31,11 @@
     - cat/cat
   files:
     - path: output/cat/cat.txt.gz
+
+- name: cat one file unzipped zipped
+  command: nextflow run ./tests/modules/cat/cat -entry test_cat_one_file_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
+  tags:
+    - cat
+    - cat/cat
+  files:
+    - path: output/cat/cat.txt.gz