Refactor pipeline outputs (#20)

* refactor: Restructure output directory * fix: Add missing curly brackets * refactor: Add bakta and move panaroo * fix: Remove deep nesting in annotation modules
beiko-lab · Feb 1, 2023 · ff53e97 · ff53e97
1 parent 4fd4843
commit ff53e97
Showing 1 changed file with 179 additions and 1 deletion.
diff --git a/conf/modules.config b/conf/modules.config
@@ -31,8 +31,186 @@ params {
     }
 }
 
-process{
+process {
+    //default: do not publish process results
+
+    publishDir = [
+        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        enabled: false
+    ]
+
+    // read_processing
+
+    withName: FASTQC {
+        publishDir = [
+            path: { "${params.outdir}/read_processing/raw_fastqc/${meta.id}" },
+            mode: params.publish_dir_mode,
+            pattern: "*.html",
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: TRIM_FASTQC {
+        publishDir = [
+            path: { "${params.outdir}/read_processing/trim_fastqc/${meta.id}" },
+            mode: params.publish_dir_mode,
+            pattern: "*.html",
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: FASTP {
+        publishDir = [
+            path: { "${params.outdir}/read_processing/fastp/${meta.id}" },
+            mode: params.publish_dir_mode,
+            pattern: "*.{html,json,gz}",
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: KRAKEN2_RUN {
+        publishDir = [
+            path: { "${params.outdir}/read_processing/kraken2/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    // assembly
+
+    withName: UNICYCLER {
+        publishDir = [
+            path: { "${params.outdir}/assembly/unicycler/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: QUAST {
+        publishDir = [
+            path: { "${params.outdir}/assembly/quast/" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: CHECKM_LINEAGEWF {
+        publishDir = [
+            path: { "${params.outdir}/assembly/checkm/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    // annotation
+
+    withName: PROKKA {
+        publishDir = [
+            path: { "${params.outdir}/annotation/prokka/" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: RGI {
+        publishDir = [
+            path: { "${params.outdir}/annotation/rgi" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: MOB_RECON {
+        publishDir = [
+            path: { "${params.outdir}/annotation/mob_recon/" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: BAKTA {
+        publishDir = [
+            path: { "${params.outdir}/annotation/bakta/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: DIAMOND_BLAST_CAZY {
+        publishDir = [
+            path: { "${params.outdir}/annotation/cazy/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: DIAMOND_BLAST_VFDB {
+        publishDir = [
+            path: { "${params.outdir}/annotation/vfdb/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: DIAMOND_BLAST_BACMET {
+        publishDir = [
+            path: { "${params.outdir}/annotation/bacmet/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    //  pangenomics
     withName: PANAROO_RUN {
         ext.args = "-a core --clean-mode strict --len_dif_percent 0.70 -c 0.7 -f 0.5"
+        publishDir = [
+            path: { "${params.outdir}/pangenomics/panaroo" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
     }
+
+    // phylogenomics
+    withName: IQTREE {
+        publishDir = [
+            path: { "${params.outdir}/phylogenomics/iqtree" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: FASTTREE {
+        publishDir = [
+            path: { "${params.outdir}/phylogenomics/fasttree" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: SNPSITES {
+        publishDir = [
+            path: { "${params.outdir}/phylogenomics/snpsites" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: MULTIQC {
+        publishDir = [
+            path: { "${params.outdir}/multiqc" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: GET_SOFTWARE_VERSIONS {
+        publishDir = [
+            path: { "${params.outdir}/pipeline_info" },
+            mode: params.publish_dir_mode,
+            pattern: '*_versions.yml'
+        ]
+    }
+
 }