fix save_filtered_longreads parameter

nf-core · Nov 1, 2024 · 7ec9a74 · 7ec9a74
1 parent bfa5e06
commit 7ec9a74
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Showing 3 changed files with 17 additions and 7 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -190,7 +190,7 @@ process {
             path: { "${params.outdir}/QC_longreads/Filtlong" },
             mode: params.publish_dir_mode,
             pattern: "*_filtlong.fastq.gz",
-            enabled: params.save_filtlong_reads
+            enabled: params.save_filtered_longreads
         ]
         ext.prefix = { "${meta.id}_run${meta.run}_filtlong" }
     }
@@ -206,7 +206,7 @@ process {
             path: { "${params.outdir}/QC_longreads/Nanoq" },
             mode: params.publish_dir_mode,
             pattern: "*_nanoq_filtered.fastq.gz",
-            enabled: params.save_filtered_reads
+            enabled: params.save_filtered_longreads
             ],
             [
                 path: { "${params.outdir}/QC_longreads/Nanoq" },
@@ -218,7 +218,17 @@ process {
     }
 
     withName: NANOLYSE {
-        publishDir = [[path: { "${params.outdir}/QC_longreads/NanoLyse" }, mode: params.publish_dir_mode, pattern: "*.log"], [path: { "${params.outdir}/QC_longreads/NanoLyse" }, mode: params.publish_dir_mode, pattern: "*_nanolyse.fastq.gz", enabled: params.save_lambdaremoved_reads]]
+        publishDir = [
+            [
+                path: { "${params.outdir}/QC_longreads/NanoLyse" },
+                mode: params.publish_dir_mode, pattern: "*.log"
+            ],
+            [
+                path: { "${params.outdir}/QC_longreads/NanoLyse" },
+                mode: params.publish_dir_mode, pattern: "*_nanolyse.fastq.gz",
+                enabled: params.save_lambdaremoved_reads
+            ]
+        ]
         ext.prefix = { "${meta.id}_run${meta.run}_lambdafiltered" }
     }
 
@@ -237,7 +247,7 @@ process {
                 path: { "${params.outdir}/QC_longreads/Chopper" },
                 mode: params.publish_dir_mode,
                 pattern: "*_chopper.fastq.gz",
-                enabled: params.save_lambdaremoved_reads
+                enabled: params.save_lambdaremoved_reads || params.save_filtered_longreads
             ]
         ]
         ext.prefix =  { "${meta.id}_run${meta.run}_chopper" }

diff --git a/nextflow.config b/nextflow.config
@@ -111,7 +111,7 @@ params {
     lambda_reference                     = "${baseDir}/assets/data/GCA_000840245.1_ViralProj14204_genomic.fna.gz"
     save_lambdaremoved_reads             = false
     save_porechop_reads                  = false
-    save_filtered_reads                  = false
+    save_filtered_longreads                  = false
 
     // binning options
     skip_metabat2                   = false

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -424,9 +424,9 @@
                     "type": "boolean",
                     "description": "Specify to save the resulting clipped FASTQ files to --outdir."
                 },
-                "save_filtered_reads": {
+                "save_filtered_longreads": {
                     "type": "boolean",
-                    "description": "Specify to save the resulting length filtered FASTQ files to --outdir."
+                    "description": "Specify to save the resulting length filtered long read FASTQ files to --outdir."
                 },
                 "longread_adaptertrimming_tool": {
                     "type": "string",