Changes in component 'nf-core/cat/fastq'
'modules/nf-core/cat/fastq/meta.yml' is unchanged
Changes in 'cat/fastq/main.nf':
--- modules/nf-core/cat/fastq/main.nf
+++ modules/nf-core/cat/fastq/main.nf
@@ -23,7 +23,13 @@
     if (meta.single_end) {
         if (readList.size >= 1) {
             """
-            cat ${readList.join(' ')} > ${prefix}.merged.fastq.gz
+            for f in ${readList.join(' ')}; do
+                if [ \$(echo \$f | grep '.gz\$') ]; then
+                    cat \$f >> ${prefix}.merged.fastq.gz
+                else
+                    gzip -c \$f >> ${prefix}.merged.fastq.gz
+                fi
+            done
 
             cat <<-END_VERSIONS > versions.yml
             "${task.process}":
@@ -40,8 +46,21 @@
             def read2 = []
             readList.eachWithIndex { v, ix -> (ix & 1 ? read2 : read1) << v }
             """
-            cat ${read1.join(' ')} > ${prefix}_1.merged.fastq.gz
-            cat ${read2.join(' ')} > ${prefix}_2.merged.fastq.gz
+            for f in ${read1.join(' ')}; do
+                if [ \$(echo \$f | grep '.gz\$') ]; then
+                    cat \$f >> ${prefix}_1.merged.fastq.gz
+                else
+                    gzip -c \$f >> ${prefix}_1.merged.fastq.gz
+                fi
+            done
+
+            for f in ${read2.join(' ')}; do
+                if [ \$(echo \$f | grep '.gz\$') ]; then
+                    cat \$f >> ${prefix}_2.merged.fastq.gz
+                else
+                    gzip -c \$f >> ${prefix}_2.merged.fastq.gz
+                fi
+            done
 
             cat <<-END_VERSIONS > versions.yml
             "${task.process}":

'modules/nf-core/cat/fastq/environment.yml' is unchanged
'modules/nf-core/cat/fastq/tests/main.nf.test.snap' is unchanged
'modules/nf-core/cat/fastq/tests/main.nf.test' is unchanged
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