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

MultiQC Tweaks after full-test experiments
This commit is contained in:
James A. Fellows Yates 2023-01-30 11:25:28 +01:00 committed by GitHub
commit 1d7da61801
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5 changed files with 52 additions and 34 deletions

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@ -268,35 +268,13 @@ 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
Kaiju:
assigned: 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
DIAMOND: False
Kaiju: False
MALT: False
motus: False
table_columns_name:
FastQC (pre-Trimming):

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@ -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,

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@ -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",

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@ -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 )

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@ -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 )
************************************************************