diff --git a/modules.json b/modules.json
index 274c191..8f0fd8d 100644
--- a/modules.json
+++ b/modules.json
@@ -10,17 +10,17 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
-                    "fq/lint": {
-                        "branch": "master",
-                        "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
-                        "installed_by": ["modules"]
-                    },
                     "fastqscreen/fastqscreen": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff"
                     },
+                    "fq/lint": {
+                        "branch": "master",
+                        "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
+                        "installed_by": ["modules"]
+                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
index 2fbd94b..beef4a9 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
+++ b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
@@ -16,6 +16,7 @@ Changes in 'fastqscreen/fastqscreen/environment.yml':
 +  # - bwa
 +  # - bismark
 
+'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
 Changes in 'fastqscreen/fastqscreen/main.nf':
 --- modules/nf-core/fastqscreen/fastqscreen/main.nf
 +++ modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -36,11 +37,21 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
  
      output:
      tuple val(meta), path("*.txt")     , emit: txt
-@@ -24,31 +24,35 @@
+@@ -24,31 +24,45 @@
      script:
      def prefix = task.ext.prefix ?: "${meta.id}"
      def args = task.ext.args ?: ""
 +    def config_content = ref_names.withIndex().collect { name, i -> "DATABASE ${name} ./${ref_dirs[i]}/${ref_basenames[i]} ${ref_aligners[i]}" }.join('\n')
++    def num_reads     = reads instanceof List  ? reads.size() : 1
++    def mv_txt_cmd    = (num_reads == 1) ? 
++            "mv ${reads[0].simpleName}_screen.txt ${prefix}_screen.txt" : 
++            reads.collect { "mv ${it.simpleName}_screen.txt ${prefix}_${it.simpleName}_screen.txt" }.join(' && ')
++    def mv_html_cmd   = (num_reads == 1) ? 
++            "mv ${reads[0].simpleName}_screen.html ${prefix}_1_screen.html" : 
++            reads.collect { "mv ${it.simpleName}_screen.txt ${prefix}_${it.simpleName}_screen.txt" }.join(' && ')
++    def mv_png_cmd    = (num_reads == 1) ? 
++            "mv ${reads[0].simpleName}_screen.png ${prefix}_1_screen.png" : 
++            reads.collect { "mv ${it.simpleName}_screen.txt ${prefix}_${it.simpleName}_screen.txt" }.join(' && ')
 +    """
 +    echo '${config_content}' > fastq_screen.conf
  
@@ -59,9 +70,9 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
 -    "${task.process}":
 -        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
 -    END_VERSIONS
-+    mv *_screen.txt ${prefix}_screen.txt
-+    mv *_screen.html ${prefix}_screen.html
-+    mv *_screen.png ${prefix}_screen.png
++    $mv_txt_cmd
++    $mv_html_cmd
++    $mv_png_cmd
 +
 +    fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//')
 +    echo "\\\"${task.process}\\\":" > versions.yml
@@ -89,9 +100,8 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
  
  }
 
-'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
-'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged
 'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap' is unchanged
-'modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config' is unchanged
 'modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged
 ************************************************************
diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index 2eba839..9df8e27 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -25,6 +25,16 @@ process FASTQSCREEN_FASTQSCREEN {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def args = task.ext.args ?: ""
     def config_content = ref_names.withIndex().collect { name, i -> "DATABASE ${name} ./${ref_dirs[i]}/${ref_basenames[i]} ${ref_aligners[i]}" }.join('\n')
+    def num_reads     = reads instanceof List  ? reads.size() : 1
+    def mv_txt_cmd    = (num_reads == 1) ? 
+            "mv ${reads[0].simpleName}_screen.txt ${prefix}_screen.txt" : 
+            reads.collect { "mv ${it.simpleName}_screen.txt ${prefix}_${it.simpleName}_screen.txt" }.join(' && ')
+    def mv_html_cmd   = (num_reads == 1) ? 
+            "mv ${reads[0].simpleName}_screen.html ${prefix}_1_screen.html" : 
+            reads.collect { "mv ${it.simpleName}_screen.txt ${prefix}_${it.simpleName}_screen.txt" }.join(' && ')
+    def mv_png_cmd    = (num_reads == 1) ? 
+            "mv ${reads[0].simpleName}_screen.png ${prefix}_1_screen.png" : 
+            reads.collect { "mv ${it.simpleName}_screen.txt ${prefix}_${it.simpleName}_screen.txt" }.join(' && ')
     """
     echo '${config_content}' > fastq_screen.conf
 
@@ -34,9 +44,9 @@ process FASTQSCREEN_FASTQSCREEN {
         $reads \\
         $args
 
-    mv *_screen.txt ${prefix}_screen.txt
-    mv *_screen.html ${prefix}_screen.html
-    mv *_screen.png ${prefix}_screen.png
+    $mv_txt_cmd
+    $mv_html_cmd
+    $mv_png_cmd
 
     fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//')
     echo "\\\"${task.process}\\\":" > versions.yml