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https://github.com/MillironX/taxprofiler.git
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Merge pull request #223 from nf-core/multiqc-tweaks
MultiQC Tweaks after full-test experiments
This commit is contained in:
commit
1d7da61801
5 changed files with 52 additions and 34 deletions
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@ -268,35 +268,13 @@ table_columns_visible:
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non-primary_alignments: False
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reads_MQ0_percent: False
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error_rate: False
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Kraken:
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"% Unclassified": False
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"% Top 5": False
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Bracken:
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"% Unclassified": False
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"% Top 5": False
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Kraken: False
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Bracken: False
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Centrifuge: False
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DIAMOND:
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queries_aligned: False
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Kaiju:
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assigned: False
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"% Assigned": False
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"% Unclassified": False
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MALT:
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"Num. of queries": False
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Total reads: False
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Mappability: False
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Assig. Taxonomy: False
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Taxonomic assignment success: False
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motus:
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Total number of reads: False
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Number of reads after filtering: False
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Total number of inserts: False
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Unique mappers: False
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Multiple mappers: False
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Ignored multiple mapper without unique hit: False
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"Number of ref-mOTUs": False
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"Number of meta-mOTUs": False
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"Number of ext-mOTUs": False
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DIAMOND: False
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Kaiju: False
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MALT: False
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motus: False
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table_columns_name:
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FastQC (pre-Trimming):
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@ -158,7 +158,7 @@ process {
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[
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path: { "${params.outdir}/porechop" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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pattern: '*_porechopped.fastq.gz',
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enabled: params.save_preprocessed_reads
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],
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[
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@ -350,7 +350,7 @@ process {
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withName: KRAKEN2_KRAKEN2 {
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ext.args = params.kraken2_save_minimizers ? { "${meta.db_params} --report-minimizer-data" } : { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { meta.tool == "bracken" ? "${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}_${meta.db_name}.kraken" }
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ext.prefix = params.perform_runmerging ? { meta.tool == "bracken" ? "${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}_${meta.db_name}.kraken2" }
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publishDir = [
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path: { "${params.outdir}/kraken2/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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@ -179,7 +179,8 @@
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"porechop/porechop": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": ["modules"],
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"patch": "modules/nf-core/porechop/porechop/porechop-porechop.diff"
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},
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"prinseqplusplus": {
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"branch": "master",
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11
modules/nf-core/porechop/porechop/main.nf
generated
11
modules/nf-core/porechop/porechop/main.nf
generated
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@ -11,7 +11,7 @@ process PORECHOP_PORECHOP {
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path("*.fastq.gz"), emit: reads
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tuple val(meta), path("*_porechopped.fastq.gz"), emit: reads
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tuple val(meta), path("*.log") , emit: log
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path "versions.yml" , emit: versions
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@ -22,12 +22,17 @@ process PORECHOP_PORECHOP {
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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## To ensure ID matches rest of pipeline based on meta.id rather than input file name
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[[ -f ${prefix}.fastq.gz ]] || ln -s $reads ${prefix}.fastq.gz
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porechop \\
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-i $reads \\
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-i ${prefix}.fastq.gz \\
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-t $task.cpus \\
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$args \\
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-o ${prefix}.fastq.gz \\
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-o ${prefix}_porechopped.fastq.gz \\
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> ${prefix}.log
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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porechop: \$( porechop --version )
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34
modules/nf-core/porechop/porechop/porechop-porechop.diff
generated
Normal file
34
modules/nf-core/porechop/porechop/porechop-porechop.diff
generated
Normal file
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@ -0,0 +1,34 @@
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Changes in module 'nf-core/porechop/porechop'
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--- modules/nf-core/porechop/porechop/main.nf
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+++ modules/nf-core/porechop/porechop/main.nf
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@@ -11,7 +11,7 @@
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tuple val(meta), path(reads)
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output:
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- tuple val(meta), path("*.fastq.gz"), emit: reads
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+ tuple val(meta), path("*_porechopped.fastq.gz"), emit: reads
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tuple val(meta), path("*.log") , emit: log
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path "versions.yml" , emit: versions
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@@ -22,12 +22,17 @@
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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+ ## To ensure ID matches rest of pipeline based on meta.id rather than input file name
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+
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+ [[ -f ${prefix}.fastq.gz ]] || ln -s $reads ${prefix}.fastq.gz
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+
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porechop \\
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- -i $reads \\
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+ -i ${prefix}.fastq.gz \\
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-t $task.cpus \\
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$args \\
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- -o ${prefix}.fastq.gz \\
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+ -o ${prefix}_porechopped.fastq.gz \\
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> ${prefix}.log
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+
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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porechop: \$( porechop --version )
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************************************************************
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