Add chopper and nanoq options for longread preprocessing

conf/modules.config

@@ -192,17 +192,40 @@ process {
             "--min_length ${params.longreads_min_length}",
             "--keep_percent ${params.longreads_keep_percent}",
             "--trim",
-            "--length_weight ${params.longreads_length_weight}"
+            "--length_weight ${params.longreads_length_weight}",
+            params.longreads_min_quality ? "--min_mean_q ${params.longreads_min_quality}" : '',
         ].join(' ').trim()
         publishDir = [
                 path: { "${params.outdir}/QC_longreads/Filtlong" },
                 mode: params.publish_dir_mode,
                 pattern: "*_filtlong.fastq.gz",
-                enabled: params.save_filtlong_reads
+                enabled: params.save_filtered_reads
             ]
         ext.prefix = { "${meta.id}_run${meta.run}_filtlong" }
     }
 
+    withName: NANOQ {
+        ext.args = [
+            "--min-len ${params.longreads_min_length}",
+            params.longreads_min_quality ? "--min-qual ${params.longreads_min_quality}": '',
+            "-vv"
+        ].join(' ').trim()
+        publishDir = [
+            [
+            path: { "${params.outdir}/QC_longreads/Nanoq" },
+            mode: params.publish_dir_mode,
+            pattern: "*_nanoq_filtered.fastq.gz",
+            enabled: params.save_filtered_reads
+            ],
+            [
+                path: { "${params.outdir}/QC_longreads/Nanoq" },
+                mode: params.publish_dir_mode,
+                pattern: "*_nanoq_filtered.stats"
+            ]
+        ]
+        ext.prefix = { "${meta.id}_run${meta.run}_nanoq_filtered" }
+    }
+
     withName: NANOLYSE {
         publishDir = [
             [
@@ -220,6 +243,26 @@ process {
         ext.prefix = { "${meta.id}_run${meta.run}_lambdafiltered" }
     }
 
+    withName: CHOPPER {
+        ext.args2  = [
+            "--contam ${params.lambda_reference}"
+        ].join(' ').trim()
+        publishDir = [
+            [
+                path: { "${params.outdir}/QC_longreads/Chopper" },
+                mode: params.publish_dir_mode,
+                pattern: "*.log"
+            ],
+            [
+                path: { "${params.outdir}/QC_longreads/Chopper" },
+                mode: params.publish_dir_mode,
+                pattern: "*_chopper.fastq.gz",
+                enabled: params.save_lambdaremoved_reads
+            ]
+        ]
+        ext.prefix =  { "${meta.id}_run${meta.run}_chopper" }
+    }
+
     withName: NANOPLOT_RAW {
         ext.prefix = 'raw'
         ext.args   = {

modules.json

@@ -62,6 +62,11 @@
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
+                    "chopper": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "concoct/concoct": {
                         "branch": "master",
                         "git_sha": "baa30accc6c50ea8a98662417d4f42ed18966353",
@@ -207,6 +212,11 @@
                         "git_sha": "3135090b46f308a260fc9d5991d7d2f9c0785309",
                         "installed_by": ["modules"]
                     },
+                    "nanoq": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "porechop/abi": {
                         "branch": "master",
                         "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",