Move long read preprocessing into a subworkflow

assets/multiqc_config.yml

@@ -25,6 +25,8 @@ run_modules:
   - quast
   - kraken
   - prokka
+  - porechop
+  - filtlong
 
 ## Module order
 top_modules:
@@ -35,6 +37,7 @@ top_modules:
   - "fastp"
   - "adapterRemoval"
   - "porechop"
+  - "filtlong"
   - "fastqc":
       name: "FastQC: after preprocessing"
       info: "After trimming and, if requested, contamination removal."

conf/modules.config

@@ -177,14 +177,30 @@ process {
         ext.prefix = { "${meta.id}_run${meta.run}_trimmed" }
     }
 
+    withName: PORECHOP_ABI {
+        publishDir = [
+                path: { "${params.outdir}/QC_longreads/porechop" },
+                mode: params.publish_dir_mode,
+                pattern: "*_trimmed.fastq",
+                enabled: params.save_porechop_reads
+            ]
+        ext.prefix = { "${meta.id}_run${meta.run}_trimmed" }
+    }
+
     withName: FILTLONG {
+        ext.args = [
+            "--min_length ${params.longreads_min_length}",
+            "--keep_percent ${params.longreads_keep_percent}",
+            "--trim",
+            "--length_weight ${params.longreads_length_weight}"
+        ].join(' ').trim()
         publishDir = [
-            path: { "${params.outdir}/QC_longreads/Filtlong" },
-            mode: params.publish_dir_mode,
-            pattern: "*_lr_filtlong.fastq.gz",
-            enabled: params.save_filtlong_reads
-        ]
-        ext.prefix = { "${meta.id}_run${meta.run}_lengthfiltered" }
+                path: { "${params.outdir}/QC_longreads/Filtlong" },
+                mode: params.publish_dir_mode,
+                pattern: "*_lr_filtlong.fastq.gz",
+                enabled: params.save_filtlong_reads
+            ]
+        ext.prefix = { "${meta.id}_run${meta.run}_lr_filtlong" }
     }
 
     withName: NANOLYSE {

modules.json

@@ -62,6 +62,11 @@
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
+                    "chopper": {
+                        "branch": "master",
+                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
+                        "installed_by": ["modules"]
+                    },
                     "concoct/concoct": {
                         "branch": "master",
                         "git_sha": "baa30accc6c50ea8a98662417d4f42ed18966353",
@@ -107,6 +112,11 @@
                         "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
                         "installed_by": ["modules"]
                     },
+                    "filtlong": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "freebayes": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
@@ -202,6 +212,11 @@
                         "git_sha": "3135090b46f308a260fc9d5991d7d2f9c0785309",
                         "installed_by": ["modules"]
                     },
+                    "porechop/abi": {
+                        "branch": "master",
+                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
+                        "installed_by": ["modules"]
+                    },
                     "porechop/porechop": {
                         "branch": "master",
                         "git_sha": "1d68c7f248d1a480c5959548a9234602b771199e",