Merge pull request #146 from SantiagoSanchezF/chore/combinegenecaller_add_params_to_support_tool_version_strings

chore(combinegenecaller): Add params to support tool version strings

Author: mberacochea

modules/ebi-metagenomics/combinedgenecaller/merge/main.nf

@@ -2,10 +2,12 @@ process COMBINEDGENECALLER_MERGE {
     tag "${meta.id}"
     label 'process_single'
 
-    container "microbiome-informatics/mgnify-pipelines-toolkit:1.4.12"
+    container "microbiome-informatics/mgnify-pipelines-toolkit:1.4.17"
 
     input:
     tuple val(meta), path(pyrodigal_gff, stageAs: "pyrodigal/"), path(pyrodigal_ffn, stageAs: "pyrodigal/"), path(pyrodigal_faa, stageAs: "pyrodigal/"), path(fgs_gff, stageAs: "fgsrs/"), path(fgs_ffn, stageAs: "fgsrs/"), path(fgs_faa, stageAs: "fgsrs/"), path(mask)
+    val(pyrodigal_version)
+    val(fgsrs_version)
 
     output:
     tuple val(meta), path("*.faa.gz"), emit: faa
@@ -42,6 +44,9 @@ process COMBINEDGENECALLER_MERGE {
         is_mask_compressed = mask.name.endsWith(".gz")
         mask_parameter = "--mask ${mask.name.replace(".gz", "")} "
     }
+
+    def pyrodigal_version_parameter = pyrodigal_version ? "--pyrodigal-version ${pyrodigal_version} " : ""
+    def fgsrs_version_parameter = fgsrs_version ? "--fgsrs-version ${fgsrs_version} " : ""
     """
     if [ "${is_prod_gff_compressed}" == "true" ]; then
         gzip -d -c ${pyrodigal_gff} > ${pyrodigal_gff_file}
@@ -73,7 +78,9 @@ process COMBINEDGENECALLER_MERGE {
         --pyrodigal-faa ${pyrodigal_faa_file} \\
         --fgsrs-gff ${fgs_gff_file} \\
         --fgsrs-ffn ${fgs_ffn_file} \\
-        --fgsrs-faa ${fgs_faa_file} ${mask_parameter}
+        --fgsrs-faa ${fgs_faa_file} ${mask_parameter} \\
+        ${pyrodigal_version_parameter} \\
+        ${fgsrs_version_parameter}
 
     gzip -n ${prefix}.{faa,ffn,gff}
 

modules/ebi-metagenomics/combinedgenecaller/merge/meta.yml

@@ -53,6 +53,12 @@ input:
         type: file
         description: sequence mask file (tblout files generated by Infernal cmscan or cmsearch)
         pattern: "*.*"
+    - pyrodigal_version:
+        type: string
+        description: version string for Pyrodigal tool (optional)
+    - fgsrs_version:
+        type: string
+        description: version string for FragGeneScanRS tool (optional)
 output:
   - faa:
       - meta:

modules/ebi-metagenomics/combinedgenecaller/merge/tests/main.nf.test

@@ -9,7 +9,7 @@ nextflow_process {
     tag "combinedgenecaller"
     tag "combinedgenecaller/merge"
 
-    test("combinedgenecaller merge without a maskfile") {
+    test("combinedgenecaller merge without a maskfile and without tool version strings") {
 
         when {
             process {
@@ -24,6 +24,8 @@ nextflow_process {
                     file(params.mgnify_pipelines_toolkit_testdata + '/combined_gene_caller_merge/input_fgsrs.faa', checkIfExists: true),
                     []
                 ]
+                input[1] = ''
+                input[2] = ''
                 """
             }
         }
@@ -36,7 +38,7 @@ nextflow_process {
         }
     }
 
-    test("combinedgenecaller merge with a maskfile") {
+    test("combinedgenecaller merge with a maskfile and tool version strings") {
 
         when {
             process {
@@ -49,8 +51,10 @@ nextflow_process {
                     file(params.mgnify_pipelines_toolkit_testdata + '/combined_gene_caller_merge/input_fgsrs.gff', checkIfExists: true),
                     file(params.mgnify_pipelines_toolkit_testdata + '/combined_gene_caller_merge/input_fgsrs.ffn', checkIfExists: true),
                     file(params.mgnify_pipelines_toolkit_testdata + '/combined_gene_caller_merge/input_fgsrs.faa', checkIfExists: true),
-                    file(params.mgnify_pipelines_toolkit_testdata + '/combined_gene_caller_merge/cmsearch.all.tblout.deoverlapped', checkIfExists: true),
+                    file(params.mgnify_pipelines_toolkit_testdata + '/combined_gene_caller_merge/cmsearch.all.tblout.deoverlapped', checkIfExists: true)
                 ]
+                input[1] = '2.0.0'
+                input[2] = '1.1.0'
                 """
             }
         }

subworkflows/ebi-metagenomics/combined_gene_caller/main.nf

@@ -7,8 +7,10 @@ include { COMBINEDGENECALLER_MERGE } from '../../../modules/ebi-metagenomics/com
 workflow COMBINED_GENE_CALLER {
 
     take:
-    ch_assembly  // channel: [ val(meta), [ fasta ] ]
-    ch_mask_file // channel: [ val(meta), [.out | .txt] ]
+    ch_assembly          // channel: [ val(meta), [ fasta ] ]
+    ch_mask_file         // channel: [ val(meta), [.out | .txt] ]
+    pyrodigal_version    // string: optional version string for pyrodigal
+    fgsrs_version        // string: optional version string for fraggenescanrs
 
     main:
 
@@ -49,7 +51,7 @@ workflow COMBINED_GENE_CALLER {
         ]
     }
 
-    COMBINEDGENECALLER_MERGE( ch_merge )
+    COMBINEDGENECALLER_MERGE( ch_merge, pyrodigal_version, fgsrs_version )
 
     ch_versions = ch_versions.mix(COMBINEDGENECALLER_MERGE.out.versions)
 

subworkflows/ebi-metagenomics/combined_gene_caller/tests/main.nf.test

@@ -33,6 +33,8 @@ nextflow_workflow {
                     file("${moduleDir}/tests/data/test_assembly.fasta.gz", checkIfExists: true)
                 ]
                 input[1] = channel.empty()
+                input[2] = ''
+                input[3] = ''
             """
             }
         }
@@ -67,6 +69,8 @@ nextflow_workflow {
                     [ id:'test', single_end:false ],
                     file("${moduleDir}/tests/data/test_tblout.deoverlapped", checkIfExists: true)
                 ])
+                input[2] = ''
+                input[3] = ''
             """
             }
         }
@@ -106,6 +110,8 @@ nextflow_workflow {
                     file("${moduleDir}/tests/data/test_assembly.fasta.gz", checkIfExists: true)
                 ]
                 input[1] = channel.empty()
+                input[2] = ''
+                input[3] = ''
             """
             }
         }