Fix: container updates docker manifest issues

CHANGELOG.md

@@ -9,10 +9,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- [#632](https://github.com/nf-core/mag/pull/632) - Use default NanoLyse log of just removed reads rather than custom (by @jfy133)
+
 ### `Fixed`
 
 ### `Dependencies`
 
+| Tool     | Previous version | New version |
+| -------- | ---------------- | ----------- |
+| Porechop | 0.2.3_seqan2.1.1 | 0.2.4       |
+| NanoPlot | 1.26.3           | 1.41.6      |
+| NanoLyse | 1.1.0            | 1.2.0       |
+
 ### `Deprecated`
 
 ## 3.0.1 [2024-06-10]

conf/base.config

@@ -77,7 +77,7 @@ process {
         memory = { check_max (8.GB * task.attempt, 'memory' ) }
         time   = { check_max (6.h  * task.attempt, 'time'   ) }
     }
-    withName: PORECHOP {
+    withName: PORECHOP_PORECHOP {
         cpus   = { check_max (4     * task.attempt, 'cpus'   ) }
         memory = { check_max (30.GB * task.attempt, 'memory' ) }
         time   = { check_max (4.h   * task.attempt, 'time'   ) }
@@ -93,7 +93,7 @@ process {
         memory = { check_max (64.GB * (2**(task.attempt-1)), 'memory' ) }
         time   = { check_max (24.h  * (2**(task.attempt-1)), 'time'   ) }
     }
-    withName: CENTRIFUGE {
+    withName: CENTRIFUGE_CENTRIFUGE {
         cpus   = { check_max (8     * task.attempt, 'cpus'   ) }
         memory = { check_max (40.GB * task.attempt, 'memory' ) }
         time   = { check_max (12.h  * task.attempt, 'time'   ) }
@@ -103,7 +103,7 @@ process {
         memory = { check_max (40.GB * task.attempt, 'memory' ) }
         time   = { check_max (12.h  * task.attempt, 'time'   ) }
     }
-    withName: KRONA {
+    withName: KRONA_KTIMPORTTAXONOMY {
         cpus   = { check_max (8     * task.attempt, 'cpus'   ) }
         memory = { check_max (20.GB * task.attempt, 'memory' ) }
         time   = { check_max (12.h  * task.attempt, 'time'   ) }

conf/modules.config

@@ -167,11 +167,11 @@ process {
         ]
     }
 
-    withName: PORECHOP {
+    withName: PORECHOP_PORECHOP {
         publishDir = [
                 path: { "${params.outdir}/QC_longreads/porechop" },
                 mode: params.publish_dir_mode,
-                pattern: "*_porechop.fastq",
+                pattern: "*_trimmed.fastq",
                 enabled: params.save_porechop_reads
             ]
         ext.prefix = { "${meta.id}_run${meta.run}_trimmed" }
@@ -206,6 +206,11 @@ process {
 
     withName: NANOPLOT_RAW {
         ext.prefix = 'raw'
+        ext.args = { [
+            "-p raw_",
+            "--title ${meta.id}_raw",
+            "-c darkblue",
+        ].join(' ').trim() }
         publishDir = [
             path: { "${params.outdir}/QC_longreads/NanoPlot/${meta.id}" },
             mode: params.publish_dir_mode,
@@ -214,7 +219,11 @@ process {
     }
 
     withName: NANOPLOT_FILTERED {
-        ext.prefix = 'filtered'
+        ext.args = { [
+            "-p filtered_",
+            "--title ${meta.id}_filtered",
+            "-c darkblue",
+        ].join(' ').trim() }
         publishDir = [
             path: { "${params.outdir}/QC_longreads/NanoPlot/${meta.id}" },
             mode: params.publish_dir_mode,

docs/output.md

@@ -105,7 +105,7 @@ The pipeline uses Nanolyse to map the reads against the Lambda phage and removes
 <summary>Output files</summary>
 
 - `QC_longreads/NanoLyse/`
-  - `[sample]_nanolyse.log`: Contains a brief log file indicating how many reads have been retained.
+  - `[sample]_[run]_lambdafiltered.nanolyse.log`: Contains a brief log file indicating how many reads have been removed.
 
 </details>
 

modules.json

@@ -197,6 +197,21 @@
                         "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
                         "installed_by": ["modules"]
                     },
+                    "nanolyse": {
+                        "branch": "master",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "installed_by": ["modules"]
+                    },
+                    "nanoplot": {
+                        "branch": "master",
+                        "git_sha": "3135090b46f308a260fc9d5991d7d2f9c0785309",
+                        "installed_by": ["modules"]
+                    },
+                    "porechop/porechop": {
+                        "branch": "master",
+                        "git_sha": "1d68c7f248d1a480c5959548a9234602b771199e",
+                        "installed_by": ["modules"]
+                    },
                     "prodigal": {
                         "branch": "master",
                         "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",

modules/local/nanolyse.nf

@@ -17,9 +17,9 @@ process NANOLYSE {
 
     script:
     """
-    cat ${reads} | NanoLyse --reference $nanolyse_db | gzip > ${meta.id}_nanolyse.fastq.gz
+    zcat ${reads} | NanoLyse --reference $nanolyse_db | gzip > ${meta.id}_nanolyse.fastq.gz
     echo "NanoLyse reference: $params.lambda_reference" >${meta.id}_nanolyse.log
-    cat ${reads} | echo "total reads before NanoLyse: \$((`wc -l`/4))" >>${meta.id}_nanolyse.log
+    zcat ${reads} | echo "total reads before NanoLyse: \$((`wc -l`/4))" >>${meta.id}_nanolyse.log
     gunzip -c ${meta.id}_nanolyse.fastq.gz | echo "total reads after NanoLyse: \$((`wc -l`/4))" >> ${meta.id}_nanolyse.log
 
     cat <<-END_VERSIONS > versions.yml