Added fasta_explore_search_plot_tidk subworkflow

modules.json

@@ -54,6 +54,40 @@
                         "branch": "master",
                         "git_sha": "3a5fef109d113b4997c9822198664ca5f2716208",
                         "installed_by": ["modules"]
+                    },
+                    "seqkit/seq": {
+                        "branch": "master",
+                        "git_sha": "687ad41c14008d3d55cf7c2ffacebe6a057211a4",
+                        "installed_by": ["fasta_explore_search_plot_tidk"]
+                    },
+                    "seqkit/sort": {
+                        "branch": "master",
+                        "git_sha": "ffcdfb354f8c8e59bdccc1a4249f0f3b232c2a3d",
+                        "installed_by": ["fasta_explore_search_plot_tidk"]
+                    },
+                    "tidk/explore": {
+                        "branch": "master",
+                        "git_sha": "fad335b31b32d78f89a8340373d3ccfc0f2b18b5",
+                        "installed_by": ["fasta_explore_search_plot_tidk"]
+                    },
+                    "tidk/plot": {
+                        "branch": "master",
+                        "git_sha": "d54cd1d823f151854825da8ffe7289bcbf77206b",
+                        "installed_by": ["fasta_explore_search_plot_tidk"]
+                    },
+                    "tidk/search": {
+                        "branch": "master",
+                        "git_sha": "669a329f4aa37f5b7f03776c2ed1cd0ef122c626",
+                        "installed_by": ["fasta_explore_search_plot_tidk"]
+                    }
+                }
+            },
+            "subworkflows": {
+                "nf-core": {
+                    "fasta_explore_search_plot_tidk": {
+                        "branch": "master",
+                        "git_sha": "2b21fbeb20ad9f17612f4a3dd7b12971513f08d5",
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }

modules/local/busco.nf

@@ -2,10 +2,10 @@ process BUSCO {
     tag "${asm_tag}:${lineage_dataset}"
     label 'process_high'
 
-    conda "bioconda::busco=5.2.2"
+    conda "bioconda::busco=5.6.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/busco:5.2.2--pyhdfd78af_0':
-        'quay.io/biocontainers/busco:5.2.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/busco:5.6.1--pyhdfd78af_0':
+        'biocontainers/busco:5.6.1--pyhdfd78af_0' }"
 
     input:
     tuple val(asm_tag), path(fasta_file)
@@ -17,6 +17,9 @@ process BUSCO {
     path "${asm_tag}/short_summary.specific.${lineage_dataset}.${asm_tag}_${lineage_initials}.txt"  , emit: summary
     path "versions.yml"                                                                             , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def lineages_path   = download_path ? "--download_path ${download_path}" : ''
     lineage_initials    = "${lineage_dataset}".split("_")[0]

modules/local/busco_plot.nf

@@ -2,27 +2,41 @@ process BUSCO_PLOT {
     tag 'all summaries'
     label 'process_single'
 
-    conda "bioconda::busco=5.2.2"
+    conda "bioconda::busco=5.6.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/busco:5.2.2--pyhdfd78af_0':
-        'quay.io/biocontainers/busco:5.2.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/busco:5.6.1--pyhdfd78af_0':
+        'biocontainers/busco:5.6.1--pyhdfd78af_0' }"
 
     input:
     path "short_summary.*", stageAs: 'busco/*'
 
     output:
-    path 'busco/*.png', emit: png
+    path 'busco/*.png'  , emit: png
+    path "versions.yml" , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
 
     script:
     """
     generate_plot.py \\
         -wd ./busco
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        busco: \$( busco --version 2>&1 | sed 's/^BUSCO //' )
+    END_VERSIONS
     """
 
     stub:
     """
     mkdir -p busco
 
     touch busco/summary_plot.png
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        busco: \$( busco --version 2>&1 | sed 's/^BUSCO //' )
+    END_VERSIONS
     """
 }