Tweaks to MultiQC based on full test experiments

assets/multiqc_config.yml

@@ -268,12 +268,8 @@ table_columns_visible:
     non-primary_alignments: False
     reads_MQ0_percent: False
     error_rate: False
-  Kraken:
-    "% Unclassified": False
-    "% Top 5": False
-  Bracken:
-    "% Unclassified": False
-    "% Top 5": False
+  Kraken: False
+  Bracken: False
   Centrifuge: False
   DIAMOND:
     queries_aligned: False

conf/modules.config

@@ -158,7 +158,7 @@ process {
             [
                 path: { "${params.outdir}/porechop" },
                 mode: params.publish_dir_mode,
-                pattern: '*.fastq.gz',
+                pattern: '*_porechopped.fastq.gz',
                 enabled: params.save_preprocessed_reads
             ],
             [

modules.json

@@ -179,7 +179,8 @@
                     "porechop/porechop": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/porechop/porechop/porechop-porechop.diff"
                     },
                     "prinseqplusplus": {
                         "branch": "master",

modules/nf-core/porechop/porechop/main.nf

@@ -22,12 +22,16 @@ process PORECHOP_PORECHOP {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
+    ## To ensure ID matches rest of pipeline based on meta.id rather than input file name
+    mv $reads ${prefix}.fastq.gz
+
     porechop \\
         -i $reads \\
         -t $task.cpus \\
         $args \\
-        -o ${prefix}.fastq.gz \\
+        -o ${prefix}_porechopped.fastq.gz \\
         > ${prefix}.log
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         porechop: \$( porechop --version )

modules/nf-core/porechop/porechop/porechop-porechop.diff

@@ -0,0 +1,23 @@
+Changes in module 'nf-core/porechop/porechop'
+--- modules/nf-core/porechop/porechop/main.nf
++++ modules/nf-core/porechop/porechop/main.nf
+@@ -22,12 +22,16 @@
+     def args = task.ext.args ?: ''
+     def prefix = task.ext.prefix ?: "${meta.id}"
+     """
++    ## To ensure ID matches rest of pipeline based on meta.id rather than input file name
++    mv $reads ${prefix}.fastq.gz
++
+     porechop \\
+         -i $reads \\
+         -t $task.cpus \\
+         $args \\
+-        -o ${prefix}.fastq.gz \\
++        -o ${prefix}_porechopped.fastq.gz \\
+         > ${prefix}.log
++
+     cat <<-END_VERSIONS > versions.yml
+     "${task.process}":
+         porechop: \$( porechop --version )
+
+************************************************************