Allow compressed input for prodigal (#1200)

* Allow compressed input for prodigal

* use pigz instead of gzip

* fix typo

modules/prodigal/main.nf

@@ -2,10 +2,10 @@ process PRODIGAL {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::prodigal=2.6.3" : null)
+    conda (params.enable_conda ? "prodigal=2.6.3 pigz=2.6" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/prodigal:2.6.3--h516909a_2' :
-        'quay.io/biocontainers/prodigal:2.6.3--h516909a_2' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' :
+        'quay.io/biocontainers/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' }"
 
     input:
     tuple val(meta), path(genome)
@@ -22,7 +22,7 @@ process PRODIGAL {
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"
     """
-    prodigal -i "${genome}" \\
+    pigz -cdf ${genome} | prodigal \\
         $args \\
         -f $output_format \\
         -d "${prefix}.fna" \\
@@ -33,6 +33,7 @@ process PRODIGAL {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         prodigal: \$(prodigal -v 2>&1 | sed -n 's/Prodigal V\\(.*\\):.*/\\1/p')
+        pigz: \$(pigz -V 2>&1 | sed 's/pigz //g')
     END_VERSIONS
     """
 }

modules/prodigal/meta.yml

@@ -5,10 +5,10 @@ keywords:
 tools:
   - prodigal:
       description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program
-      homepage: {}
-      documentation: {}
+      homepage: {https://github.com/hyattpd/Prodigal}
+      documentation: {https://github.com/hyattpd/prodigal/wiki}
       tool_dev_url: {}
-      doi: ""
+      doi: "10.1186/1471-2105-11-119"
       licence: ["GPL v3"]
 
 input:
@@ -17,10 +17,12 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - bam:
+  - genome:
       type: file
-      description: BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
+      description: fasta/fasta.gz file
+  - output_format:
+      type: string
+      description: Output format ("gbk"/"gff"/"sqn"/"sco")
 
 output:
   - meta:
@@ -32,10 +34,22 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  - bam:
+  - nucleotide_fasta:
       type: file
-      description: Sorted BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
+      description: nucleotide sequences file
+      pattern: "*.{fna}"
+  - amino_acid_fasta:
+      type: file
+      description: protein translations file
+      pattern: "*.{faa}"
+  - all_gene_annotations:
+      type: file
+      description: complete starts file
+      pattern: "*.{_all.txt}"
+  - gene_annotations:
+      type: file
+      description: gene annotations in output_format given as input
+      pattern: "*.{output_format}"
 
 authors:
   - "@grst"