renamed output in entrezdirect/esummary: xml (#1928)

* renamed output: xml

* removed tail -n+3 from output

* removed comment

* removed blank space

* removed blank space

* updated test

modules/entrezdirect/esummary/main.nf

@@ -12,7 +12,7 @@ process ENTREZDIRECT_ESUMMARY {
     val database
 
     output:
-    tuple val(meta), path("*.xml"), emit: xml_esummary
+    tuple val(meta), path("*.xml"), emit: xml
     path "versions.yml"           , emit: versions
 
     when:
@@ -24,12 +24,11 @@ process ENTREZDIRECT_ESUMMARY {
     input = uids_file ? "-input ${uids_file}" : "-id ${uid}"
     if (!uid && !uids_file) error "No input. Valid input: an identifier or a .txt file with identifiers"
     if (uid && uids_file) error "Only one input is required: a single identifier or a .txt file with identifiers"
-    // use of 'tail -n+3' is to ensure a clean XML file. Otherwise an irrelevant Perl compilation error ends up in the XML
     """
     esummary \\
         $args \\
         -db $database \\
-        $input | tail -n+3 > ${prefix}.xml
+        $input > ${prefix}.xml
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/entrezdirect/esummary/meta.yml

@@ -48,7 +48,7 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  - xml_esummary:
+  - xml:
       type: file
       description: Query result in XML format
       pattern: "*.xml"

tests/modules/entrezdirect/esummary/main.nf

@@ -14,7 +14,6 @@ workflow test_entrezdirect_esummary_sra {
         uid = '5135484',
         []
     ]
-
     database = 'sra'
 
     ENTREZDIRECT_ESUMMARY ( input, database )
@@ -30,7 +29,6 @@ workflow test_entrezdirect_esummary_genome {
         uid = '768',
         []
     ]
-
     database = 'genome'
 
     ENTREZDIRECT_ESUMMARY ( input, database )
@@ -46,7 +44,6 @@ workflow test_entrezdirect_esummary_assembly {
         uid = '191021',
         []
     ]
-
     database = 'assembly'
 
     ENTREZDIRECT_ESUMMARY ( input, database )

tests/modules/entrezdirect/esummary/nextflow.config

@@ -1,5 +1,3 @@
 process {
-
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
 }

tests/modules/entrezdirect/esummary/test.yml

@@ -5,7 +5,7 @@
     - entrezdirect/esummary
   files:
     - path: output/entrezdirect/test_sra.xml
-      md5sum: aeb7f5710a5447a8de89b9e6fc464606
+      md5sum: bc4bc7f3c53af5961bc8592225959363
 
 - name: entrezdirect esummary test_entrezdirect_esummary_genome
   command: nextflow run ./tests/modules/entrezdirect/esummary -entry test_entrezdirect_esummary_genome -c ./tests/config/nextflow.config  -c ./tests/modules/entrezdirect/esummary/nextflow.config
@@ -14,7 +14,7 @@
     - entrezdirect/esummary
   files:
     - path: output/entrezdirect/test_genome.xml
-      md5sum: 2abea497bcef9312105b23ed78b72f62
+      md5sum: af6242f231bdc147d6197edfd0954585
 
 - name: entrezdirect esummary test_entrezdirect_esummary_assembly
   command: nextflow run ./tests/modules/entrezdirect/esummary -entry test_entrezdirect_esummary_assembly -c ./tests/config/nextflow.config  -c ./tests/modules/entrezdirect/esummary/nextflow.config
@@ -23,4 +23,4 @@
     - entrezdirect/esummary
   files:
     - path: output/entrezdirect/test_assembly.xml
-      md5sum: 01c962bc82d3b3bcb9d4da5b0b6b408a
+      md5sum: 32f81147eea61df5814e87c2df1092a9