remove if statement

nf-core · Aug 24, 2023 · 011addc · 011addc
1 parent 82fa500
commit 011addc
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Showing 2 changed files with 99 additions and 106 deletions.
diff --git a/conf/modules/sra.config b/conf/modules/sra.config
@@ -13,80 +13,76 @@
 //
 //  Process options for the SRA workflow
 //
-if (params.input_type == 'sra') {
+process {
 
-    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: SRA_IDS_TO_RUNINFO {
+        publishDir = [
+            path: { "${params.outdir}/metadata" },
+            enabled: false
+        ]
+    }
 
-        withName: SRATOOLS_PREFETCH {
-            publishDir = [
-                path: { "${params.outdir}/sra" },
-                enabled: false
-            ]
-        }
+    withName: SRA_RUNINFO_TO_FTP {
+        publishDir = [
+            path: { "${params.outdir}/metadata" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 
-        withName: SRATOOLS_FASTERQDUMP {
-            ext.args = '--split-files --include-technical'
-            publishDir = [
+    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: SRA_TO_SAMPLESHEET {
-            publishDir = [
-                path: { "${params.outdir}/samplesheet" },
-                enabled: false
-            ]
-        }
+    withName: SRATOOLS_PREFETCH {
+        publishDir = [
+            path: { "${params.outdir}/sra" },
+            enabled: false
+        ]
+    }
 
-        withName: SRA_MERGE_SAMPLESHEET {
-            publishDir = [
-                path: { "${params.outdir}/samplesheet" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
+    withName: SRATOOLS_FASTERQDUMP {
+        ext.args = '--split-files --include-technical'
+        publishDir = [
+            path: { "${params.outdir}/fastq" },
+            mode: params.publish_dir_mode,
+            pattern: "*.fastq.gz"
+        ]
+    }
 
-        withName: MULTIQC_MAPPINGS_CONFIG {
-            publishDir = [
-                path: { "${params.outdir}/samplesheet" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
+    withName: SRA_TO_SAMPLESHEET {
+        publishDir = [
+            path: { "${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 }
+        ]
     }
 
 }
diff --git a/conf/modules/synapse.config b/conf/modules/synapse.config
@@ -13,57 +13,54 @@
 //
 //  Process options for the Synapse workflow
 //
-if (params.input_type == 'synapse') {
 
-    process {
+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: { "${params.outdir}/fastq/md5" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.md5"
-                ]
-            ]
-        }
+    withName: SYNAPSE_LIST {
+        ext.args = '--long'
+        publishDir = [
+            path: { "${params.outdir}/metadata" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 
-        withName: SYNAPSE_SHOW {
-            publishDir = [
-                path: { "${params.outdir}/metadata" },
+    withName: SYNAPSE_GET {
+        publishDir = [
+            [
+                path: { "${params.outdir}/fastq" },
+                mode: params.publish_dir_mode,
+                pattern: "*.fastq.gz"
+            ],
+            [
+                path: { "${params.outdir}/fastq/md5" },
                 mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                pattern: "*.md5"
             ]
-        }
+        ]
+    }
 
-        withName: SYNAPSE_TO_SAMPLESHEET {
-            publishDir = [
-                path: { "${params.outdir}/samplesheet" },
-                enabled: false
-            ]
-        }
+    withName: SYNAPSE_SHOW {
+        publishDir = [
+            path: { "${params.outdir}/metadata" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 
-        withName: SYNAPSE_MERGE_SAMPLESHEET {
-            publishDir = [
-                path: { "${params.outdir}/samplesheet" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
+    withName: SYNAPSE_TO_SAMPLESHEET {
+        publishDir = [
+            path: { "${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 }
+        ]
     }
 
 }