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Tweaks to MultiQC based on full test experiments
This commit is contained in:
parent
e7d7affcd0
commit
a993300099
5 changed files with 33 additions and 9 deletions
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@ -268,12 +268,8 @@ table_columns_visible:
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non-primary_alignments: False
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non-primary_alignments: False
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reads_MQ0_percent: False
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reads_MQ0_percent: False
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error_rate: False
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error_rate: False
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Kraken:
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Kraken: False
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"% Unclassified": False
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Bracken: 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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Centrifuge: False
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Centrifuge: False
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DIAMOND:
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DIAMOND:
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queries_aligned: False
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queries_aligned: False
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@ -158,7 +158,7 @@ process {
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[
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[
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path: { "${params.outdir}/porechop" },
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path: { "${params.outdir}/porechop" },
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mode: params.publish_dir_mode,
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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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enabled: params.save_preprocessed_reads
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],
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],
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[
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[
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@ -179,7 +179,8 @@
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"porechop/porechop": {
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"porechop/porechop": {
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"branch": "master",
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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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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},
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"prinseqplusplus": {
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"prinseqplusplus": {
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"branch": "master",
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"branch": "master",
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6
modules/nf-core/porechop/porechop/main.nf
generated
6
modules/nf-core/porechop/porechop/main.nf
generated
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@ -22,12 +22,16 @@ process PORECHOP_PORECHOP {
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def args = task.ext.args ?: ''
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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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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mv $reads ${prefix}.fastq.gz
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porechop \\
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porechop \\
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-i $reads \\
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-i $reads \\
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-t $task.cpus \\
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-t $task.cpus \\
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$args \\
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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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> ${prefix}.log
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cat <<-END_VERSIONS > versions.yml
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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"${task.process}":
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porechop: \$( porechop --version )
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porechop: \$( porechop --version )
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23
modules/nf-core/porechop/porechop/porechop-porechop.diff
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23
modules/nf-core/porechop/porechop/porechop-porechop.diff
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@ -0,0 +1,23 @@
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Changes in module 'nf-core/porechop/porechop'
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--- modules/nf-core/porechop/porechop/main.nf
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+++ modules/nf-core/porechop/porechop/main.nf
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@@ -22,12 +22,16 @@
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${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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+ mv $reads ${prefix}.fastq.gz
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+
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porechop \\
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-i $reads \\
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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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