nf-core · Pranjal-Bioinfo · Jan 16, 2025 · Jan 16, 2025 · Jan 16, 2025 · Jan 16, 2025
diff --git a/assets/nf-core-mag_logo_light.png b/assets/nf-core-mag_logo_light.png
diff --git a/conf/modules.config b/conf/modules.config
@@ -47,6 +47,25 @@ process {
         tag        = { "${meta.id}_run${meta.run}" }
     }
 
+  withName: TRIMMOMATIC {
+        ext.args   = "LEADING:30 TRAILING:30 SLIDINGWINDOW:4:20 MINLEN:35"
+        publishDir = [
+            [
+                path: { "${params.outdir}/QC_shortreads/trimmomatic/${meta.id}" },
+                mode: params.publish_dir_mode,
+                pattern: "*_trim.log"
+            ],
+            [
+                path: { "${params.outdir}/QC_shortreads/trimmomatic/${meta.id}" },
+                mode: params.publish_dir_mode,
+                pattern: "*.fastq.gz",
+                enabled: params.save_clipped_reads
+            ]
+        ]
+        ext.prefix = { "${meta.id}_run${meta.run}_trimmomatic" }
+        tag        = { "${meta.id}_run${meta.run}" }
+    }
+
     withName: ADAPTERREMOVAL_PE {
         ext.args   = [
             "--minlength ${params.reads_minlength}",
@@ -620,6 +639,9 @@ process {
         ]
     }
 
+    withName: 'CONCOCT_CUTUPFASTA' {
+        ext.args = '-c 10000 -o 0 --merge_last'
+    }
     withName: 'CONCOCT_.*' {
         publishDir = [
             [

diff --git a/docs/images/nf-core-mag_logo_light.png b/docs/images/nf-core-mag_logo_light.png
diff --git a/modules.json b/modules.json
@@ -282,6 +282,11 @@
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
+                    "trimmomatic": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "untar": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",

diff --git a/modules/nf-core/trimmomatic/environment.yml b/modules/nf-core/trimmomatic/environment.yml
diff --git a/modules/nf-core/trimmomatic/main.nf b/modules/nf-core/trimmomatic/main.nf
diff --git a/modules/nf-core/trimmomatic/meta.yml b/modules/nf-core/trimmomatic/meta.yml
diff --git a/modules/nf-core/trimmomatic/tests/main.nf.test b/modules/nf-core/trimmomatic/tests/main.nf.test