Merge pull request #144 from EBI-Metagenomics/bbmap_reformat_standardise

Tidied up bbmap_reformat_standardise

Author: timrozday-mgnify

modules/ebi-metagenomics/bbmap/reformat_standardise/environment.yml

@@ -4,7 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  # TODO nf-core: List required Conda package(s).
-  #               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-  #               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
   - "bioconda::bbmap=39.33"

modules/ebi-metagenomics/bbmap/reformat_standardise/license.txt

@@ -14,8 +14,7 @@ process BBMAP_REFORMAT_STANDARDISE {
     output:
     tuple val(meta), path("*_reformated.${out_fmt}")       , emit: reformated
     tuple val(meta), path("${prefix}_singleton.${out_fmt}"), optional: true, emit: singleton
-    path  "versions.yml"                                      , emit: versions
-    path  "*.log"                                             , emit: log
+    path  "versions.yml"                                   , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -39,8 +38,7 @@ process BBMAP_REFORMAT_STANDARDISE {
         $interleaved_cmd \\
         $paired_cmd \\
         threads=${task.cpus} \\
-        ${args} \\
-        &> ${prefix}.reformat.sh.log
+        ${args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/ebi-metagenomics/bbmap/reformat_standardise/main.nf

@@ -14,7 +14,7 @@ tools:
       documentation: "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide"
       tool_dev_url: "https://sourceforge.net/projects/bbmap"
       doi: ""
-      licence: ["see licence.txt"]
+      licence: ["https://github.com/bbushnell/BBTools/blob/master/license.txt"]
       identifier: null
 
 input:
@@ -26,6 +26,8 @@ input:
       type: file
       description: "Input FASTQ file(s). Can be single-end or paired-end (as list). Paired-end reads can be interleaved (single file) or de-interleaved (two files)."
       pattern: "*.{fastq,fq,fastq.gz,fq.gz}"
+      ontologies:
+        - edam: http://edamontology.org/format_1930 # FASTQ
   - out_fmt:
       type: string
       description: "Output file format (e.g., 'fastq.gz', 'fasta.gz')"