Merge pull request #223 from nf-core/multiqc-tweaks

MultiQC Tweaks after full-test experiments

assets/multiqc_config.yml

@@ -268,35 +268,13 @@ table_columns_visible:
     non-primary_alignments: False
     reads_MQ0_percent: False
     error_rate: False
-  Kraken:
+  Kraken: False
-    "% Unclassified": False
+  Bracken: False
-    "% Top 5": False
-  Bracken:
-    "% Unclassified": False
-    "% Top 5": False
   Centrifuge: False
-  DIAMOND:
+  DIAMOND: False
-    queries_aligned: False
+  Kaiju: False
-  Kaiju:
+  MALT: False
-    assigned: False
+  motus: False
-    "% Assigned": False
-    "% Unclassified": False
-  MALT:
-    "Num. of queries": False
-    Total reads: False
-    Mappability: False
-    Assig. Taxonomy: False
-    Taxonomic assignment success: False
-  motus:
-    Total number of reads: False
-    Number of reads after filtering: False
-    Total number of inserts: False
-    Unique mappers: False
-    Multiple mappers: False
-    Ignored multiple mapper without unique hit: False
-    "Number of ref-mOTUs": False
-    "Number of meta-mOTUs": False
-    "Number of ext-mOTUs": False
 
 table_columns_name:
   FastQC (pre-Trimming):

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
             ],
             [
@@ -350,7 +350,7 @@ process {
 
     withName: KRAKEN2_KRAKEN2 {
         ext.args = params.kraken2_save_minimizers ? { "${meta.db_params} --report-minimizer-data" } : { "${meta.db_params}" }
-        ext.prefix = params.perform_runmerging ? { meta.tool == "bracken" ? "${meta.id}_${meta.db_name}.bracken" : "${meta.id}_${meta.db_name}.kraken" } : { meta.tool == "bracken" ? "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" : "${meta.id}_${meta.run_accession}_${meta.db_name}.kraken" }
+        ext.prefix = params.perform_runmerging ? { meta.tool == "bracken" ? "${meta.id}_${meta.db_name}.bracken" : "${meta.id}_${meta.db_name}.kraken2" } : { meta.tool == "bracken" ? "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" : "${meta.id}_${meta.run_accession}_${meta.db_name}.kraken2" }
         publishDir = [
             path: { "${params.outdir}/kraken2/${meta.db_name}/" },
             mode: params.publish_dir_mode,

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

@@ -11,7 +11,7 @@ process PORECHOP_PORECHOP {
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path("*.fastq.gz"), emit: reads
+    tuple val(meta), path("*_porechopped.fastq.gz"), emit: reads
     tuple val(meta), path("*.log")     , emit: log
     path "versions.yml"                , emit: versions
 
@@ -22,12 +22,17 @@ 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
+    
+    [[ -f ${prefix}.fastq.gz   ]] || ln -s $reads ${prefix}.fastq.gz
+
     porechop \\
-        -i $reads \\
+        -i ${prefix}.fastq.gz \\
         -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 +1,34 @@
+Changes in module 'nf-core/porechop/porechop'
+--- modules/nf-core/porechop/porechop/main.nf
++++ modules/nf-core/porechop/porechop/main.nf
+@@ -11,7 +11,7 @@
+     tuple val(meta), path(reads)
+ 
+     output:
+-    tuple val(meta), path("*.fastq.gz"), emit: reads
++    tuple val(meta), path("*_porechopped.fastq.gz"), emit: reads
+     tuple val(meta), path("*.log")     , emit: log
+     path "versions.yml"                , emit: versions
+ 
+@@ -22,12 +22,17 @@
+     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
++    
++    [[ -f ${prefix}.fastq.gz   ]] || ln -s $reads ${prefix}.fastq.gz
++
+     porechop \\
+-        -i $reads \\
++        -i ${prefix}.fastq.gz \\
+         -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 )
+
+************************************************************