Migrate template to nf-core-utils plugin

nf_core/pipeline-template/main.nf

@@ -23,6 +23,22 @@ include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_{{ s
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
 {%- if igenomes %}
 include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_{{ short_name }}_pipeline'
+{%- endif %}
+
+// Import nf-core-utils plugin functions
+include { getWorkflowVersion      } from 'plugin/nf-core-utils'
+include { dumpParametersToJSON    } from 'plugin/nf-core-utils'
+include { checkCondaChannels      } from 'plugin/nf-core-utils'
+{%- if email %}
+include { completionEmail         } from 'plugin/nf-core-utils'
+{%- endif %}
+include { completionSummary       } from 'plugin/nf-core-utils'
+{%- if adaptivecard or slackreport %}
+include { imNotification          } from 'plugin/nf-core-utils'
+{%- endif %}
+include { checkConfigProvided     } from 'plugin/nf-core-utils'
+include { checkProfileProvided    } from 'plugin/nf-core-utils'
+{%- if igenomes %}
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

nf_core/pipeline-template/modules.json

@@ -13,30 +13,14 @@
                     }{% endif %}{%- if multiqc %}{% if fastqc %},{% endif %}
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b",
+                        "git_sha": "c9a31c472ef2d86802eb44f27322955849859361",
                         "installed_by": ["modules"]
                     }
                     {%- endif %}
                 }
             },
             "subworkflows": {
-                "nf-core": {
-                    "utils_nextflow_pipeline": {
-                        "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
-                        "installed_by": ["subworkflows"]
-                    },
-                    "utils_nfcore_pipeline": {
-                        "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
-                        "installed_by": ["subworkflows"]
-                    }{% if nf_schema %},
-                    "utils_nfschema_plugin": {
-                        "branch": "master",
-                        "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd",
-                        "installed_by": ["subworkflows"]
-                    }{% endif %}
-                }
+                "nf-core": {}
             }
         }
     }

nf_core/pipeline-template/nextflow.config

@@ -322,6 +322,7 @@ manifest {
 // Nextflow plugins
 plugins {
     id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id '[email protected]' // Utility functions for nf-core pipelines
 }
 
 validation {

nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf

@@ -8,19 +8,25 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-{% if nf_schema %}include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
+{% if nf_schema %}include { paramsSummaryLog          } from 'plugin/nf-schema'
+include { validateParameters        } from 'plugin/nf-schema'
 include { paramsSummaryMap          } from 'plugin/nf-schema'
 include { samplesheetToList         } from 'plugin/nf-schema'
 include { paramsHelp                } from 'plugin/nf-schema'{% endif %}
 {%- if email %}
-include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
+include { completionEmail           } from 'plugin/nf-core-utils'
 {%- endif %}
-include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
+include { completionSummary         } from 'plugin/nf-core-utils'
 {%- if adaptivecard or slackreport %}
-include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
+include { imNotification            } from 'plugin/nf-core-utils'
 {%- endif %}
-include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
-include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
+include { checkConfigProvided       } from 'plugin/nf-core-utils'
+include { checkProfileProvided      } from 'plugin/nf-core-utils'
+include { getWorkflowVersion        } from 'plugin/nf-core-utils'
+include { dumpParametersToJSON      } from 'plugin/nf-core-utils'
+include { checkCondaChannels        } from 'plugin/nf-core-utils'
+include { processVersionsFromFile   } from 'plugin/nf-core-utils'
+include { workflowVersionToChannel  } from 'plugin/nf-core-utils'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -48,58 +54,36 @@ workflow PIPELINE_INITIALISATION {
     //
     // Print version and exit if required and dump pipeline parameters to JSON file
     //
-    UTILS_NEXTFLOW_PIPELINE (
-        version,
-        true,
-        outdir,
-        workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
-    )
+    if (version) {
+        log.info("${workflow.manifest.name} ${getWorkflowVersion(workflow.manifest.version, workflow.commitId)}")
+        System.exit(0)
+    }
+
+    if (outdir) {
+        dumpParametersToJSON(outdir, params)
+    }
+
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        checkCondaChannels()
+    }
 
     {%- if nf_schema %}
 
     //
     // Validate parameters and generate parameter summary to stdout
     //
+    log.info paramsSummaryLog(workflow)
 
-    {%- if is_nfcore %}
-    before_text = """
--\033[2m----------------------------------------------------\033[0m-
-                                        \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
-\033[0;34m        ___     __   __   __   ___     \033[0;32m/,-._.--~\'\033[0m
-\033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
-\033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
-                                        \033[0;32m`._,._,\'\033[0m
-\033[0;35m  {{ name }} ${workflow.manifest.version}\033[0m
--\033[2m----------------------------------------------------\033[0m-
-"""
-    after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""}
-* The nf-core framework
-    https://doi.org/10.1038/s41587-020-0439-x
-
-* Software dependencies
-    https://github.com/{{ name }}/blob/{{ default_branch }}/CITATIONS.md
-"""{% endif %}
-    command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
-
-    UTILS_NFSCHEMA_PLUGIN (
-        workflow,
-        validate_params,
-        null,
-        help,
-        help_full,
-        show_hidden,
-        {% if is_nfcore -%}before_text{%- else %}""{%- endif %},
-        {% if is_nfcore -%}after_text{%- else %}""{%- endif %},
-        command
-    )
+    if (validate_params) {
+        validateParameters()
+    }
     {%- endif %}
 
     //
     // Check config provided to the pipeline
     //
-    UTILS_NFCORE_PIPELINE (
-        nextflow_cli_args
-    )
+    checkConfigProvided()
+    checkProfileProvided(nextflow_cli_args, monochrome_logs)
 
     {%- if igenomes %}
 
@@ -188,7 +172,7 @@ workflow PIPELINE_COMPLETION {
                 plaintext_email,
                 outdir,
                 monochrome_logs,
-                {% if multiqc %}multiqc_reports.getVal(),{% else %}[]{% endif %}
+                {% if multiqc %}multiqc_reports.getVal(){% else %}[]{% endif %}
             )
         }
         {%- endif %}
@@ -213,6 +197,57 @@ workflow PIPELINE_COMPLETION {
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
+//
+// Get channel of software versions used in pipeline in YAML format
+//
+def softwareVersionsToYAML(ch_versions) {
+    return ch_versions.unique()
+        .map { version -> processVersionsFromFile([version.toString()]) }
+        .unique()
+        .mix(Channel.fromList(workflowVersionToChannel(workflow.session)).map { it ->
+            """
+    Workflow:
+        ${it[1]}: ${it[2]}
+            """.stripIndent().trim()
+        })
+}
+
+{%- if multiqc %}
+//
+// Get workflow summary for MultiQC
+//
+def paramsSummaryMultiqc(summary_params) {
+    def summary_section = ''
+    summary_params
+        .keySet()
+        .each { group ->
+            def group_params = summary_params.get(group)
+            // This gets the parameters of that particular group
+            if (group_params) {
+                summary_section += "    <p style=\"font-size:110%\"><b>${group}</b></p>\n"
+                summary_section += "    <dl class=\"dl-horizontal\">\n"
+                group_params
+                    .keySet()
+                    .sort()
+                    .each { param ->
+                        summary_section += "        <dt>${param}</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
+                    }
+                summary_section += "    </dl>\n"
+            }
+        }
+
+    def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String
+    yaml_file_text     += "description: ' - this information is collected when the pipeline is started.'\n"
+    yaml_file_text     += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
+    yaml_file_text     += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
+    yaml_file_text     += "plot_type: 'html'\n"
+    yaml_file_text     += "data: |\n"
+    yaml_file_text     += "${summary_section}"
+
+    return yaml_file_text
+}
+{%- endif %}
+
 {%- if igenomes %}
 //
 // Check and validate pipeline parameters