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Tweaks to MultiQC based on full test experiments

This commit is contained in:
James Fellows Yates 2023-01-24 15:06:42 +01:00
parent e7d7affcd0
commit a993300099
5 changed files with 33 additions and 9 deletions

View file

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

View file

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

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

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

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