Merge pull request #186 from maxulysse/split_configs

split up config files to be more modular

.nf-core.yml

@@ -1,13 +1,15 @@
 repository_type: pipeline
 lint:
+  actions_ci: false
+  files_exist:
+    - conf/modules.config
   files_unchanged:
     - .github/CONTRIBUTING.md
     - .github/ISSUE_TEMPLATE/bug_report.yml
     - assets/nf-core-fetchngs_logo_light.png
     - assets/sendmail_template.txt
     - lib/NfcoreTemplate.groovy
     - .gitattributes
-  actions_ci: false
   multiqc_config: false
   nextflow_config:
     - "params.validationShowHiddenParams"

conf/modules/base.config

@@ -0,0 +1,32 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+//
+// Generic process options for all workflows
+//
+process {
+
+    publishDir = [
+        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+    ]
+
+    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
+        publishDir = [
+            path: { "${params.outdir}/pipeline_info" },
+            mode: params.publish_dir_mode,
+            pattern: '*_versions.yml'
+        ]
+    }
+
+}

conf/modules/sra.config

@@ -0,0 +1,88 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+//
+//  Process options for the SRA workflow
+//
+process {
+
+    withName: SRA_IDS_TO_RUNINFO {
+        publishDir = [
+            path: { "${params.outdir}/metadata" },
+            enabled: false
+        ]
+    }
+
+    withName: SRA_RUNINFO_TO_FTP {
+        publishDir = [
+            path: { "${params.outdir}/metadata" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: SRA_FASTQ_FTP {
+        ext.args = '--retry 5 --continue-at - --max-time 1200'
+        publishDir = [
+            [
+                path: { "${params.outdir}/fastq" },
+                mode: params.publish_dir_mode,
+                pattern: "*.fastq.gz"
+            ],
+            [
+                path: { "${params.outdir}/fastq/md5" },
+                mode: params.publish_dir_mode,
+                pattern: "*.md5"
+            ]
+        ]
+    }
+
+    withName: SRATOOLS_PREFETCH {
+        publishDir = [
+            path: { "${params.outdir}/sra" },
+            enabled: false
+        ]
+    }
+
+    withName: SRATOOLS_FASTERQDUMP {
+        ext.args = '--split-files --include-technical'
+        publishDir = [
+            path: { "${params.outdir}/fastq" },
+            mode: params.publish_dir_mode,
+            pattern: "*.fastq.gz"
+        ]
+    }
+
+    withName: SRA_TO_SAMPLESHEET {
+        publishDir = [
+            path: { "${params.outdir}/samplesheet" },
+            enabled: false
+        ]
+    }
+
+    withName: SRA_MERGE_SAMPLESHEET {
+        publishDir = [
+            path: { "${params.outdir}/samplesheet" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: MULTIQC_MAPPINGS_CONFIG {
+        publishDir = [
+            path: { "${params.outdir}/samplesheet" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+}

conf/modules/synapse.config

@@ -0,0 +1,66 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+//
+//  Process options for the Synapse workflow
+//
+
+process {
+
+    withName: SYNAPSE_LIST {
+        ext.args = '--long'
+        publishDir = [
+            path: { "${params.outdir}/metadata" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: SYNAPSE_GET {
+        publishDir = [
+            [
+                path: { "${params.outdir}/fastq" },
+                mode: params.publish_dir_mode,
+                pattern: "*.fastq.gz"
+            ],
+            [
+                path: { "${params.outdir}/fastq/md5" },
+                mode: params.publish_dir_mode,
+                pattern: "*.md5"
+            ]
+        ]
+    }
+
+    withName: SYNAPSE_SHOW {
+        publishDir = [
+            path: { "${params.outdir}/metadata" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: SYNAPSE_TO_SAMPLESHEET {
+        publishDir = [
+            path: { "${params.outdir}/samplesheet" },
+            enabled: false
+        ]
+    }
+
+    withName: SYNAPSE_MERGE_SAMPLESHEET {
+        publishDir = [
+            path: { "${params.outdir}/samplesheet" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+}

nextflow.config

@@ -217,7 +217,13 @@ manifest {
 }
 
 // Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
+includeConfig 'conf/modules/base.config'
+if ( params.input_type == 'sra' ) {
+    includeConfig 'conf/modules/sra.config'
+}
+if ( params.input_type == 'synapse' ) {
+    includeConfig 'conf/modules/synapse.config'
+}
 
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit