by remove the 2>&1 to avoid the warning message.

modules/nf-core/genmap/index/main.nf

@@ -30,7 +30,7 @@ process GENMAP_INDEX {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        genmap: \$(genmap --version 2>&1 | sed 's/GenMap version: //; s/SeqAn.*\$//')
+        genmap: \$(genmap --version | sed 's/GenMap version: //; s/SeqAn.*\$//')
     END_VERSIONS
     """
 
@@ -42,7 +42,7 @@ process GENMAP_INDEX {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        genmap: \$(genmap --version 2>&1 | sed 's/GenMap version: //; s/SeqAn.*\$//')
+        genmap: \$(genmap --version | sed 's/GenMap version: //; s/SeqAn.*\$//')
     END_VERSIONS
     """
 }

modules/nf-core/genmap/map/main.nf

@@ -38,7 +38,7 @@ process GENMAP_MAP {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        genmap: \$(genmap --version 2>&1 | sed 's/GenMap version: //; s/SeqAn.*\$//')
+        genmap: \$(genmap --version | sed 's/GenMap version: //; s/SeqAn.*\$//')
     END_VERSIONS
     """
 
@@ -60,7 +60,7 @@ process GENMAP_MAP {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        genmap: \$(genmap --version 2>&1 | sed 's/GenMap version: //; s/SeqAn.*\$//')
+        genmap: \$(genmap --version | sed 's/GenMap version: //; s/SeqAn.*\$//')
     END_VERSIONS
     """
 }

modules/nf-core/pairtools/dedup/main.nf

@@ -32,7 +32,7 @@ process PAIRTOOLS_DEDUP {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        pairtools: \$(pairtools --version 2>&1 | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
+        pairtools: \$(pairtools --version | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
     END_VERSIONS
     """
 }

modules/nf-core/pairtools/flip/main.nf

@@ -33,7 +33,7 @@ process PAIRTOOLS_FLIP {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        pairtools: \$(pairtools --version 2>&1 | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
+        pairtools: \$(pairtools --version | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
     END_VERSIONS
     """
 }

modules/nf-core/pairtools/merge/main.nf

@@ -31,7 +31,7 @@ process PAIRTOOLS_MERGE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        pairtools: \$(pairtools --version 2>&1 | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
+        pairtools: \$(pairtools --version | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
     END_VERSIONS
     """
 }

modules/nf-core/pairtools/parse/main.nf

@@ -35,7 +35,7 @@ process PAIRTOOLS_PARSE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        pairtools: \$(pairtools --version 2>&1 | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
+        pairtools: \$(pairtools --version | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
     END_VERSIONS
     """
 }

modules/nf-core/pairtools/restrict/main.nf

@@ -33,7 +33,7 @@ process PAIRTOOLS_RESTRICT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        pairtools: \$(pairtools --version 2>&1 | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
+        pairtools: \$(pairtools --version | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
     END_VERSIONS
     """
 }

modules/nf-core/pairtools/select/main.nf

@@ -32,7 +32,7 @@ process PAIRTOOLS_SELECT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        pairtools: \$(pairtools --version 2>&1 | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
+        pairtools: \$(pairtools --version | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
     END_VERSIONS
     """
 }

modules/nf-core/pairtools/sort/main.nf

@@ -34,7 +34,7 @@ process PAIRTOOLS_SORT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        pairtools: \$(pairtools --version 2>&1 | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
+        pairtools: \$(pairtools --version | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
     END_VERSIONS
     """
 }

modules/nf-core/pairtools/split/main.nf

@@ -44,7 +44,7 @@ process PAIRTOOLS_SPLIT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        pairtools: \$(pairtools --version 2>&1 | sed 's/pairtools, version //')
+        pairtools: \$(pairtools --version | sed 's/pairtools, version //')
     END_VERSIONS
     """
 

modules/nf-core/pairtools/stats/main.nf

@@ -31,7 +31,7 @@ process PAIRTOOLS_STATS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        pairtools: \$(pairtools --version 2>&1 | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
+        pairtools: \$(pairtools --version | tr '\\n' ',' | sed 's/.*pairtools.*version //' | sed 's/,\$/\\n/')
     END_VERSIONS
     """
 }