update with latest review

src/pear/config.vsh.yaml

@@ -10,7 +10,7 @@ functionality:
     repository: https://github.com/tseemann/PEAR
     documentation: https://cme.h-its.org/exelixis/web/software/pear/doc.html
     reference: doi:10.1093/bioinformatics/btt593
-    licence: "['Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported']"
+    licence: "CC-BY-NC-SA-3.0"
   requirements:
     commands: [ pear , gzip ]
   argument_groups:
@@ -161,5 +161,6 @@ platforms:
     setup:
       - type: docker
         run: |
-          pear -h | grep 'PEAR v' | sed 's/PEAR v//' | sed 's/ .*//' > /var/software_versions.txt
+          version=$(pear -h | grep 'PEAR v' | sed 's/PEAR v//' | sed 's/ .*//') && \
+          echo "pear: $version" > /var/software_versions.txt
   - type: nextflow

src/pear/script.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 ## VIASH START
-## VIASh END
+## VIASH END
 
 [[ "$par_emperical_freqs" == "false" ]] && unset par_emperical_freqs
 [[ "$par_nbase" == "false" ]] && unset par_nbase
@@ -15,12 +15,12 @@ if [[ "${par_reverse_fastq##*.}" == "gz" ]]; then
   par_reverse_fastq=${par_reverse_fastq%.*}
 fi
 
-par_output="pear_output"
+output_dir=$(mktemp -d -p "$meta_temp_dir" "pear.XXXXXX")
 
 pear \
   -f "$par_forward_fastq" \
   -r "$par_reverse_fastq" \
-  -o "$par_output" \
+  -o "$output_dir" \
   ${par_p_value:+-p "${par_p_value}"} \
   ${par_min_overlap:+-v "${par_min_overlap}"} \
   ${par_max_assembly_length:+-m "${par_max_assembly_length}"} \
@@ -39,25 +39,25 @@ pear \
 
 
 if [[ "${par_assembled##*.}" == "gz" ]]; then
-  gzip -9 -c ${par_output}.assembled.fastq > ${par_assembled}
+  gzip -9 -c ${output_dir}.assembled.fastq > ${par_assembled}
 else
-  mv ${par_output}.assembled.fastq ${par_assembled}
+  mv ${output_dir}.assembled.fastq ${par_assembled}
 fi
 
 if [[ "${par_unassembled_forward##*.}" == "gz" ]]; then
-  gzip -9 -c ${par_output}.unassembled.forward.fastq > ${par_unassembled_forward}
+  gzip -9 -c ${output_dir}.unassembled.forward.fastq > ${par_unassembled_forward}
 else
-  mv ${par_output}.unassembled.forward.fastq ${par_unassembled_forward}
+  mv ${output_dir}.unassembled.forward.fastq ${par_unassembled_forward}
 fi
 
 if [[ "${par_unassembled_reverse##*.}" == "gz" ]]; then
-  gzip -9 -c ${par_output}.unassembled.reverse.fastq > ${par_unassembled_reverse}
+  gzip -9 -c ${output_dir}.unassembled.reverse.fastq > ${par_unassembled_reverse}
 else
-  mv ${par_output}.unassembled.reverse.fastq ${par_unassembled_reverse}
+  mv ${output_dir}.unassembled.reverse.fastq ${par_unassembled_reverse}
 fi
 
 if [[ "${par_discarded##*.}" == "gz" ]]; then
-  gzip -9 -c ${par_output}.discarded.fastq > ${par_discarded}
+  gzip -9 -c ${output_dir}.discarded.fastq > ${par_discarded}
 else
-  mv ${par_output}.discarded.fastq ${par_discarded}
+  mv ${output_dir}.discarded.fastq ${par_discarded}
 fi