mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
Merge branch 'master' into motus_profile
This commit is contained in:
James A. Fellows Yates
GitHub
commit
8a83ad0518
22 changed files with 1001 additions and 311 deletions
84
modules/busco/main.nf
Normal file
84
modules/busco/main.nf
Normal file
|
|
@ -0,0 +1,84 @@
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|
process BUSCO {
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tag "$meta.id"
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label 'process_medium'
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|
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conda (params.enable_conda ? "bioconda::busco=5.3.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/busco:5.3.2--pyhdfd78af_0':
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|
'quay.io/biocontainers/busco:5.3.2--pyhdfd78af_0' }"
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|
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input:
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tuple val(meta), path('tmp_input/*')
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each lineage // Required: lineage to check against, "auto" enables --auto-lineage instead
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path busco_lineages_path // Recommended: path to busco lineages - downloads if not set
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path config_file // Optional: busco configuration file
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output:
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tuple val(meta), path("*-busco.batch_summary.txt"), emit: batch_summary
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tuple val(meta), path("short_summary.*.txt") , emit: short_summaries_txt, optional: true
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tuple val(meta), path("short_summary.*.json") , emit: short_summaries_json, optional: true
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tuple val(meta), path("*-busco") , emit: busco_dir
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}-${lineage}"
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def busco_config = config_file ? "--config $config_file" : ''
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def busco_lineage = lineage.equals('auto') ? '--auto-lineage' : "--lineage_dataset ${lineage}"
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def busco_lineage_dir = busco_lineages_path ? "--offline --download_path ${busco_lineages_path}" : ''
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"""
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|
# Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
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# Check for container variable initialisation script and source it.
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if [ -f "/usr/local/env-activate.sh" ]; then
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set +u # Otherwise, errors out because of various unbound variables
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. "/usr/local/env-activate.sh"
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set -u
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fi
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||||||
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# If the augustus config directory is not writable, then copy to writeable area
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if [ ! -w "\${AUGUSTUS_CONFIG_PATH}" ]; then
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# Create writable tmp directory for augustus
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AUG_CONF_DIR=\$( mktemp -d -p \$PWD )
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cp -r \$AUGUSTUS_CONFIG_PATH/* \$AUG_CONF_DIR
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export AUGUSTUS_CONFIG_PATH=\$AUG_CONF_DIR
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echo "New AUGUSTUS_CONFIG_PATH=\${AUGUSTUS_CONFIG_PATH}"
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|
fi
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# Ensure the input is uncompressed
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INPUT_SEQS=input_seqs
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mkdir "\$INPUT_SEQS"
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cd "\$INPUT_SEQS"
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for FASTA in ../tmp_input/*; do
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if [ "\${FASTA##*.}" == 'gz' ]; then
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gzip -cdf "\$FASTA" > \$( basename "\$FASTA" .gz )
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|
else
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ln -s "\$FASTA" .
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|
fi
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|
done
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|
cd ..
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|
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|
busco \\
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|
--cpu $task.cpus \\
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--in "\$INPUT_SEQS" \\
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--out ${prefix}-busco \\
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|
$busco_lineage \\
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$busco_lineage_dir \\
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|
$busco_config \\
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|
$args
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|
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|
# clean up
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|
rm -rf "\$INPUT_SEQS"
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|
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# Move files to avoid staging/publishing issues
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|
mv ${prefix}-busco/batch_summary.txt ${prefix}-busco.batch_summary.txt
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|
mv ${prefix}-busco/*/short_summary.*.{json,txt} . || echo "Short summaries were not available: No genes were found."
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|
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|
cat <<-END_VERSIONS > versions.yml
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|
"${task.process}":
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|
busco: \$( busco --version 2>&1 | sed 's/^BUSCO //' )
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|
END_VERSIONS
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|
"""
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}
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69
modules/busco/meta.yml
Normal file
69
modules/busco/meta.yml
Normal file
|
|
@ -0,0 +1,69 @@
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|
name: busco
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|
description: Benchmarking Universal Single Copy Orthologs
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keywords:
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- quality control
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- genome
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|
- transcriptome
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- proteome
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|
tools:
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|
- busco:
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|
description: BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
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|
homepage: https://busco.ezlab.org/
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|
documentation: https://busco.ezlab.org/busco_userguide.html
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|
tool_dev_url: https://gitlab.com/ezlab/busco
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|
doi: "10.1007/978-1-4939-9173-0_14"
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|
licence: ["MIT"]
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||||||
|
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|
input:
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||||||
|
- meta:
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type: map
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|
description: |
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|
Groovy Map containing sample information
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|
e.g. [ id:'test', single_end:false ]
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- fasta:
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|
type: file
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|
description: Nucleic or amino acid sequence file in FASTA format.
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|
pattern: "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}"
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|
- lineage:
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|
type: value
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|
description: The BUSCO lineage to use, or "auto" to automatically select lineage
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|
- busco_lineages_path:
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|
type: directory
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|
description: Path to local BUSCO lineages directory.
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- config_file:
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|
type: file
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|
description: Path to BUSCO config file.
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|
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|
output:
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||||||
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- meta:
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||||||
|
type: map
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||||||
|
description: |
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||||||
|
Groovy Map containing sample information
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||||||
|
e.g. [ id:'test', single_end:false ]
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|
- batch_summary:
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|
type: file
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|
description: Summary of all sequence files analyzed
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|
pattern: "*-busco.batch_summary.txt"
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- short_summaries_txt:
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type: file
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|
description: Short Busco summary in plain text format
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pattern: "short_summary.*.txt"
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|
- short_summaries_json:
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type: file
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||||||
|
description: Short Busco summary in JSON format
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||||||
|
pattern: "short_summary.*.json"
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||||||
|
- busco_dir:
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|
type: directory
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||||||
|
description: BUSCO lineage specific output
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|
pattern: "*-busco"
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|
- versions:
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|
type: file
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||||||
|
description: File containing software versions
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||||||
|
pattern: "versions.yml"
|
||||||
|
|
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|
authors:
|
||||||
|
- "@priyanka-surana"
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||||||
|
- "@charles-plessy"
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||||||
|
- "@mahesh-panchal"
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||||||
|
- "@muffato"
|
||||||
|
- "@jvhagey"
|
||||||
|
|
@ -1,4 +1,4 @@
|
||||||
process SNAPALIGNER_PAIRED {
|
process SNAPALIGNER_ALIGN {
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||||||
tag '$meta.id'
|
tag '$meta.id'
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label 'process_high'
|
label 'process_high'
|
||||||
|
|
||||||
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|
@ -21,15 +21,16 @@ process SNAPALIGNER_PAIRED {
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||||||
script:
|
script:
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||||||
def args = task.ext.args ?: ''
|
def args = task.ext.args ?: ''
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||||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
def prefix = task.ext.prefix ?: "${meta.id}"
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||||||
|
def subcmd = meta.single_end ? "single" : "paired"
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||||||
|
|
||||||
"""
|
"""
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mkdir -p index
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mkdir -p index
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mv $index index/
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mv $index index/
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||||||
|
|
||||||
snap-aligner paired \\
|
snap-aligner ${subcmd} \\
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||||||
index \\
|
index \\
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||||||
${reads.join(" ")} \\
|
${reads.join(" ")} \\
|
||||||
-o -bam ${prefix}.bam \\
|
-o ${prefix}.bam \\
|
||||||
-t ${task.cpus} \\
|
-t ${task.cpus} \\
|
||||||
$args
|
$args
|
||||||
|
|
||||||
|
|
@ -1,5 +1,5 @@
|
||||||
name: "snapaligner_paired"
|
name: "snapaligner_align"
|
||||||
description: Performs paired end fastq alignment to a fasta reference using SNAP
|
description: Performs fastq alignment to a fasta reference using SNAP
|
||||||
keywords:
|
keywords:
|
||||||
- alignment
|
- alignment
|
||||||
- map
|
- map
|
||||||
|
|
@ -22,7 +22,7 @@ input:
|
||||||
e.g. [ id:'test', single_end:false ]
|
e.g. [ id:'test', single_end:false ]
|
||||||
- reads:
|
- reads:
|
||||||
type: file
|
type: file
|
||||||
description: List of input fastq files of size 2 for fastq or 1 for bam
|
description: List of input fastq files of size 2 for paired fastq or 1 for bam or single fastq
|
||||||
pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}"
|
pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}"
|
||||||
- index:
|
- index:
|
||||||
type: file
|
type: file
|
||||||
|
|
@ -1,41 +0,0 @@
|
||||||
process SNAPALIGNER_SINGLE {
|
|
||||||
tag '$meta.id'
|
|
||||||
label 'process_high'
|
|
||||||
|
|
||||||
conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null)
|
|
||||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
||||||
'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.1--hd03093a_1':
|
|
||||||
'quay.io/biocontainers/snap-aligner:2.0.1--hd03093a_1' }"
|
|
||||||
|
|
||||||
input:
|
|
||||||
tuple val(meta), path(reads)
|
|
||||||
path index
|
|
||||||
|
|
||||||
output:
|
|
||||||
tuple val(meta), path("*.bam"), emit: bam
|
|
||||||
path "versions.yml" , emit: versions
|
|
||||||
|
|
||||||
when:
|
|
||||||
task.ext.when == null || task.ext.when
|
|
||||||
|
|
||||||
script:
|
|
||||||
def args = task.ext.args ?: ''
|
|
||||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
||||||
|
|
||||||
"""
|
|
||||||
mkdir -p index
|
|
||||||
mv $index index/
|
|
||||||
|
|
||||||
snap-aligner single \\
|
|
||||||
index \\
|
|
||||||
${reads.join(" ")} \\
|
|
||||||
-o -bam ${prefix}.bam \\
|
|
||||||
-t ${task.cpus} \\
|
|
||||||
$args
|
|
||||||
|
|
||||||
cat <<-END_VERSIONS > versions.yml
|
|
||||||
"${task.process}":
|
|
||||||
snapaligner: \$(snap-aligner 2>&1| head -n 1 | sed 's/^.*version //;s/.\$//')
|
|
||||||
END_VERSIONS
|
|
||||||
"""
|
|
||||||
}
|
|
||||||
|
|
@ -1,48 +0,0 @@
|
||||||
name: "snapaligner_single"
|
|
||||||
description: Performs single end fastq alignment to a fasta reference using SNAP
|
|
||||||
keywords:
|
|
||||||
- alignment
|
|
||||||
- map
|
|
||||||
- fastq
|
|
||||||
- bam
|
|
||||||
- sam
|
|
||||||
tools:
|
|
||||||
- "snapaligner":
|
|
||||||
description: "Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data"
|
|
||||||
homepage: "http://snap.cs.berkeley.edu"
|
|
||||||
documentation: "https://1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug"
|
|
||||||
tool_dev_url: "https://github.com/amplab/snap"
|
|
||||||
doi: "10.1101/2021.11.23.469039"
|
|
||||||
licence: "['Apache v2']"
|
|
||||||
input:
|
|
||||||
- meta:
|
|
||||||
type: map
|
|
||||||
description: |
|
|
||||||
Groovy Map containing sample information
|
|
||||||
e.g. [ id:'test', single_end:false ]
|
|
||||||
- reads:
|
|
||||||
type: file
|
|
||||||
description: List of single end input files
|
|
||||||
pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}"
|
|
||||||
- index:
|
|
||||||
type: file
|
|
||||||
description: List of SNAP genome index files
|
|
||||||
pattern: "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}"
|
|
||||||
|
|
||||||
output:
|
|
||||||
- meta:
|
|
||||||
type: map
|
|
||||||
description: |
|
|
||||||
Groovy Map containing sample information
|
|
||||||
e.g. [ id:'test', single_end:false ]
|
|
||||||
- versions:
|
|
||||||
type: file
|
|
||||||
description: File containing software versions
|
|
||||||
pattern: "versions.yml"
|
|
||||||
- bam:
|
|
||||||
type: file
|
|
||||||
description: Aligned BAM file
|
|
||||||
pattern: "*.{bam}"
|
|
||||||
|
|
||||||
authors:
|
|
||||||
- "@matthdsm"
|
|
||||||
|
|
@ -1,43 +1,26 @@
|
||||||
process SRATOOLS_PREFETCH {
|
process SRATOOLS_PREFETCH {
|
||||||
tag "$id"
|
tag "$id"
|
||||||
label 'process_low'
|
label 'process_low'
|
||||||
label 'error_retry'
|
|
||||||
|
|
||||||
conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
|
conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
|
||||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||||
'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5262h314213e_0' :
|
'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' :
|
||||||
'quay.io/biocontainers/sra-tools:2.11.0--pl5262h314213e_0' }"
|
'quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
|
||||||
|
|
||||||
input:
|
input:
|
||||||
tuple val(meta), val(id)
|
tuple val(meta), val(id)
|
||||||
|
|
||||||
output:
|
output:
|
||||||
tuple val(meta), path("$id"), emit: sra
|
tuple val(meta), path(id), emit: sra
|
||||||
path "versions.yml" , emit: versions
|
path "versions.yml" , emit: versions
|
||||||
|
|
||||||
when:
|
when:
|
||||||
task.ext.when == null || task.ext.when
|
task.ext.when == null || task.ext.when
|
||||||
|
|
||||||
script:
|
shell:
|
||||||
def args = task.ext.args ?: ''
|
args = task.ext.args ?: ''
|
||||||
def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
|
args2 = task.ext.args2 ?: '5 1 100' // <num retries> <base delay in seconds> <max delay in seconds>
|
||||||
"""
|
config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
|
||||||
eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
|
|
||||||
if [[ ! -f "\${NCBI_SETTINGS}" ]]; then
|
|
||||||
mkdir -p "\$(dirname "\${NCBI_SETTINGS}")"
|
|
||||||
printf '${config}' > "\${NCBI_SETTINGS}"
|
|
||||||
fi
|
|
||||||
|
|
||||||
prefetch \\
|
template 'retry_with_backoff.sh'
|
||||||
$args \\
|
|
||||||
--progress \\
|
|
||||||
$id
|
|
||||||
|
|
||||||
vdb-validate $id
|
|
||||||
|
|
||||||
cat <<-END_VERSIONS > versions.yml
|
|
||||||
"${task.process}":
|
|
||||||
sratools: \$(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
|
|
||||||
END_VERSIONS
|
|
||||||
"""
|
|
||||||
}
|
}
|
||||||
|
|
|
||||||
59
modules/sratools/prefetch/templates/retry_with_backoff.sh
Executable file
59
modules/sratools/prefetch/templates/retry_with_backoff.sh
Executable file
|
|
@ -0,0 +1,59 @@
|
||||||
|
#!/usr/bin/env bash
|
||||||
|
|
||||||
|
set -u
|
||||||
|
|
||||||
|
retry_with_backoff() {
|
||||||
|
local max_attempts=${1}
|
||||||
|
local delay=${2}
|
||||||
|
local max_time=${3}
|
||||||
|
local attempt=1
|
||||||
|
local output=
|
||||||
|
local status=
|
||||||
|
|
||||||
|
# Remove the first three arguments to this function in order to access
|
||||||
|
# the 'real' command with `${@}`.
|
||||||
|
shift 3
|
||||||
|
|
||||||
|
while [ ${attempt} -le ${max_attempts} ]; do
|
||||||
|
output=$("${@}")
|
||||||
|
status=${?}
|
||||||
|
|
||||||
|
if [ ${status} -eq 0 ]; then
|
||||||
|
break
|
||||||
|
fi
|
||||||
|
|
||||||
|
if [ ${attempt} -lt ${max_attempts} ]; then
|
||||||
|
echo "Failed attempt ${attempt} of ${max_attempts}. Retrying in ${delay} s." >&2
|
||||||
|
sleep ${delay}
|
||||||
|
elif [ ${attempt} -eq ${max_attempts} ]; then
|
||||||
|
echo "Failed after ${attempt} attempts." >&2
|
||||||
|
return ${status}
|
||||||
|
fi
|
||||||
|
|
||||||
|
attempt=$(( ${attempt} + 1 ))
|
||||||
|
delay=$(( ${delay} * 2 ))
|
||||||
|
if [ ${delay} -ge ${max_time} ]; then
|
||||||
|
delay=${max_time}
|
||||||
|
fi
|
||||||
|
done
|
||||||
|
|
||||||
|
echo "${output}"
|
||||||
|
}
|
||||||
|
|
||||||
|
eval "$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
|
||||||
|
if [[ ! -f "${NCBI_SETTINGS}" ]]; then
|
||||||
|
mkdir -p "$(dirname "${NCBI_SETTINGS}")"
|
||||||
|
printf '!{config}' > "${NCBI_SETTINGS}"
|
||||||
|
fi
|
||||||
|
|
||||||
|
retry_with_backoff !{args2} \
|
||||||
|
prefetch \
|
||||||
|
!{args} \
|
||||||
|
!{id}
|
||||||
|
|
||||||
|
vdb-validate !{id}
|
||||||
|
|
||||||
|
cat <<-END_VERSIONS > versions.yml
|
||||||
|
"!{task.process}":
|
||||||
|
sratools: $(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
|
||||||
|
END_VERSIONS
|
||||||
|
|
@ -337,6 +337,10 @@ bracken/bracken:
|
||||||
- modules/bracken/bracken/**
|
- modules/bracken/bracken/**
|
||||||
- tests/modules/bracken/bracken/**
|
- tests/modules/bracken/bracken/**
|
||||||
|
|
||||||
|
busco:
|
||||||
|
- modules/busco/**
|
||||||
|
- tests/modules/busco/**
|
||||||
|
|
||||||
bwa/aln:
|
bwa/aln:
|
||||||
- modules/bwa/aln/**
|
- modules/bwa/aln/**
|
||||||
- tests/modules/bwa/aln/**
|
- tests/modules/bwa/aln/**
|
||||||
|
|
@ -1767,13 +1771,9 @@ snapaligner/index:
|
||||||
- modules/snapaligner/index/**
|
- modules/snapaligner/index/**
|
||||||
- tests/modules/snapaligner/index/**
|
- tests/modules/snapaligner/index/**
|
||||||
|
|
||||||
snapaligner/paired:
|
snapaligner/align:
|
||||||
- modules/snapaligner/paired/**
|
- modules/snapaligner/align/**
|
||||||
- tests/modules/snapaligner/paired/**
|
- tests/modules/snapaligner/align/**
|
||||||
|
|
||||||
snapaligner/single:
|
|
||||||
- modules/snapaligner/single/**
|
|
||||||
- tests/modules/snapaligner/single/**
|
|
||||||
|
|
||||||
snpdists:
|
snpdists:
|
||||||
- modules/snpdists/**
|
- modules/snpdists/**
|
||||||
|
|
|
||||||
|
|
@ -125,6 +125,7 @@ params {
|
||||||
genome_gff3 = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gff3"
|
genome_gff3 = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gff3"
|
||||||
genome_gtf = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gtf"
|
genome_gtf = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gtf"
|
||||||
genome_interval_list = "${test_data_dir}/genomics/homo_sapiens/genome/genome.interval_list"
|
genome_interval_list = "${test_data_dir}/genomics/homo_sapiens/genome/genome.interval_list"
|
||||||
|
genome_multi_interval_bed = "${test_data_dir}/genomics/homo_sapiens/genome/genome.multi_intervals.bed"
|
||||||
genome_sizes = "${test_data_dir}/genomics/homo_sapiens/genome/genome.sizes"
|
genome_sizes = "${test_data_dir}/genomics/homo_sapiens/genome/genome.sizes"
|
||||||
genome_bed = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed"
|
genome_bed = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed"
|
||||||
genome_header = "${test_data_dir}/genomics/homo_sapiens/genome/genome.header"
|
genome_header = "${test_data_dir}/genomics/homo_sapiens/genome/genome.header"
|
||||||
|
|
@ -181,16 +182,16 @@ params {
|
||||||
vcfanno_toml = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml"
|
vcfanno_toml = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml"
|
||||||
}
|
}
|
||||||
'pangenome' {
|
'pangenome' {
|
||||||
pangenome_fa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa"
|
pangenome_fa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa"
|
||||||
pangenome_fa_gz = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa.gz"
|
pangenome_fa_gz = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa.gz"
|
||||||
pangenome_paf = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf"
|
pangenome_paf = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf"
|
||||||
pangenome_paf_gz = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf.gz"
|
pangenome_paf_gz = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf.gz"
|
||||||
pangenome_seqwish_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.seqwish.gfa"
|
pangenome_seqwish_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.seqwish.gfa"
|
||||||
pangenome_smoothxg_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.smoothxg.gfa"
|
pangenome_smoothxg_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.smoothxg.gfa"
|
||||||
pangenome_gfaffix_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.gfaffix.gfa"
|
pangenome_gfaffix_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.gfaffix.gfa"
|
||||||
'odgi' {
|
'odgi' {
|
||||||
pangenome_og = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.og"
|
pangenome_og = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.og"
|
||||||
pangenome_lay = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.lay"
|
pangenome_lay = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.lay"
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
'illumina' {
|
'illumina' {
|
||||||
|
|
@ -211,131 +212,131 @@ params {
|
||||||
test_paired_end_hla = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam"
|
test_paired_end_hla = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam"
|
||||||
test_paired_end_hla_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam"
|
test_paired_end_hla_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam"
|
||||||
test_paired_end_hla_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam.bai"
|
test_paired_end_hla_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam.bai"
|
||||||
test2_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam"
|
|
||||||
test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai"
|
|
||||||
test2_paired_end_name_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam"
|
|
||||||
test2_paired_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam"
|
|
||||||
test2_paired_end_markduplicates_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam.bai"
|
|
||||||
test2_paired_end_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam"
|
|
||||||
test2_paired_end_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai"
|
|
||||||
test2_paired_end_umi_consensus_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_consensus.bam"
|
|
||||||
test2_paired_end_umi_converted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_converted.bam"
|
|
||||||
test2_paired_end_umi_grouped_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_grouped.bam"
|
|
||||||
test2_paired_end_umi_histogram_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_histogram.txt"
|
|
||||||
test2_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam"
|
|
||||||
test2_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam"
|
|
||||||
|
|
||||||
|
test2_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam"
|
||||||
|
test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai"
|
||||||
|
test2_paired_end_name_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam"
|
||||||
|
test2_paired_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam"
|
||||||
|
test2_paired_end_markduplicates_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam.bai"
|
||||||
|
test2_paired_end_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam"
|
||||||
|
test2_paired_end_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai"
|
||||||
|
test2_paired_end_umi_consensus_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_consensus.bam"
|
||||||
|
test2_paired_end_umi_converted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_converted.bam"
|
||||||
|
test2_paired_end_umi_grouped_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_grouped.bam"
|
||||||
|
test2_paired_end_umi_histogram_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_histogram.txt"
|
||||||
|
test2_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam"
|
||||||
|
test2_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam"
|
||||||
|
|
||||||
mitochon_standin_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam"
|
mitochon_standin_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam"
|
||||||
mitochon_standin_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai"
|
mitochon_standin_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai"
|
||||||
|
|
||||||
test_paired_end_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram"
|
test_paired_end_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram"
|
||||||
test_paired_end_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai"
|
test_paired_end_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai"
|
||||||
test_paired_end_markduplicates_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram"
|
test_paired_end_markduplicates_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram"
|
||||||
test_paired_end_markduplicates_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram.crai"
|
test_paired_end_markduplicates_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram.crai"
|
||||||
test_paired_end_recalibrated_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram"
|
test_paired_end_recalibrated_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram"
|
||||||
test_paired_end_recalibrated_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai"
|
test_paired_end_recalibrated_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai"
|
||||||
|
|
||||||
test2_paired_end_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram"
|
test2_paired_end_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram"
|
||||||
test2_paired_end_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram.crai"
|
test2_paired_end_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram.crai"
|
||||||
test2_paired_end_markduplicates_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram"
|
test2_paired_end_markduplicates_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram"
|
||||||
test2_paired_end_markduplicates_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram.crai"
|
test2_paired_end_markduplicates_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram.crai"
|
||||||
test2_paired_end_recalibrated_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram"
|
test2_paired_end_recalibrated_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram"
|
||||||
test2_paired_end_recalibrated_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai"
|
test2_paired_end_recalibrated_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai"
|
||||||
|
|
||||||
test_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz"
|
test_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz"
|
||||||
test_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz"
|
test_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz"
|
||||||
test_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz"
|
test_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz"
|
||||||
test_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz"
|
test_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz"
|
||||||
test2_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz"
|
test2_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz"
|
||||||
test2_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz"
|
test2_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz"
|
||||||
test2_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz"
|
test2_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz"
|
||||||
test2_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz"
|
test2_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz"
|
||||||
test_rnaseq_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz"
|
test_rnaseq_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz"
|
||||||
test_rnaseq_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz"
|
test_rnaseq_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz"
|
||||||
|
|
||||||
test_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table"
|
test_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table"
|
||||||
test2_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table"
|
test2_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table"
|
||||||
test_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.pileups.table"
|
test_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.pileups.table"
|
||||||
test2_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.pileups.table"
|
test2_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.pileups.table"
|
||||||
|
|
||||||
test_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
|
test_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
|
||||||
test_pon_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz"
|
test_pon_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz"
|
||||||
|
|
||||||
test2_haplotc_ann_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz"
|
test2_haplotc_ann_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz"
|
||||||
test2_haplotc_ann_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi"
|
test2_haplotc_ann_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi"
|
||||||
|
|
||||||
test2_recal = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal"
|
test2_recal = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal"
|
||||||
test2_recal_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx"
|
test2_recal_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx"
|
||||||
test2_tranches = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches"
|
test2_tranches = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches"
|
||||||
test2_allele_specific_recal = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal"
|
test2_allele_specific_recal = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal"
|
||||||
test2_allele_specific_recal_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal.idx"
|
test2_allele_specific_recal_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal.idx"
|
||||||
test2_allele_specific_tranches = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.tranches"
|
test2_allele_specific_tranches = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.tranches"
|
||||||
|
|
||||||
test_test2_paired_mutect2_calls_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz"
|
test_test2_paired_mutect2_calls_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz"
|
||||||
test_test2_paired_mutect2_calls_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi"
|
test_test2_paired_mutect2_calls_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi"
|
||||||
test_test2_paired_mutect2_calls_vcf_gz_stats = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats"
|
test_test2_paired_mutect2_calls_vcf_gz_stats = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats"
|
||||||
test_test2_paired_mutect2_calls_f1r2_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz"
|
test_test2_paired_mutect2_calls_f1r2_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz"
|
||||||
test_test2_paired_mutect2_calls_artifact_prior_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired_mutect2_calls.artifact-prior.tar.gz"
|
test_test2_paired_mutect2_calls_artifact_prior_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired_mutect2_calls.artifact-prior.tar.gz"
|
||||||
test_test2_paired_segmentation_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.segmentation.table"
|
test_test2_paired_segmentation_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.segmentation.table"
|
||||||
test_test2_paired_contamination_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.contamination.table"
|
test_test2_paired_contamination_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.contamination.table"
|
||||||
|
|
||||||
test_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf"
|
test_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf"
|
||||||
test_genome_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz"
|
test_genome_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz"
|
||||||
test_genome_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi"
|
test_genome_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi"
|
||||||
test_genome_vcf_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx"
|
test_genome_vcf_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx"
|
||||||
|
|
||||||
test2_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf"
|
test2_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf"
|
||||||
test2_genome_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz"
|
test2_genome_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz"
|
||||||
test2_genome_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi"
|
test2_genome_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi"
|
||||||
test2_genome_vcf_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.idx"
|
test2_genome_vcf_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.idx"
|
||||||
|
|
||||||
test_genome21_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz"
|
test_genome21_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz"
|
||||||
test_genome21_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi"
|
test_genome21_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi"
|
||||||
|
|
||||||
test_mpileup = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz"
|
test_mpileup = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz"
|
||||||
test2_mpileup = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz"
|
test2_mpileup = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz"
|
||||||
|
|
||||||
test_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak"
|
test_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak"
|
||||||
test2_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak"
|
test2_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak"
|
||||||
|
|
||||||
test_narrowpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak"
|
test_narrowpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak"
|
||||||
test2_narrowpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak"
|
test2_narrowpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak"
|
||||||
|
|
||||||
test_10x_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R1_001.fastq.gz"
|
test_10x_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R1_001.fastq.gz"
|
||||||
test_10x_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R2_001.fastq.gz"
|
test_10x_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R2_001.fastq.gz"
|
||||||
|
|
||||||
test_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test.yak"
|
test_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test.yak"
|
||||||
test2_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test2.yak"
|
test2_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test2.yak"
|
||||||
|
|
||||||
cutandrun_bedgraph_test_1 = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph"
|
cutandrun_bedgraph_test_1 = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph"
|
||||||
cutandrun_bedgraph_test_2 = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_igg_test_1.bedGraph"
|
cutandrun_bedgraph_test_2 = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_igg_test_1.bedGraph"
|
||||||
|
|
||||||
test_rnaseq_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf"
|
test_rnaseq_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf"
|
||||||
test_sv_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz"
|
test_sv_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz"
|
||||||
|
|
||||||
test_pytor = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor"
|
test_pytor = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor"
|
||||||
}
|
}
|
||||||
'pacbio' {
|
'pacbio' {
|
||||||
primers = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"
|
primers = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"
|
||||||
alz = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam"
|
alz = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam"
|
||||||
alzpbi = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam.pbi"
|
alzpbi = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam.pbi"
|
||||||
ccs = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.bam"
|
ccs = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.bam"
|
||||||
ccs_fa = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta"
|
ccs_fa = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta"
|
||||||
ccs_fa_gz = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta.gz"
|
ccs_fa_gz = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta.gz"
|
||||||
ccs_fq = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq"
|
ccs_fq = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq"
|
||||||
ccs_fq_gz = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz"
|
ccs_fq_gz = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz"
|
||||||
ccs_xml = "${test_data_dir}/genomics/homo_sapiens/pacbio/xml/alz.ccs.consensusreadset.xml"
|
ccs_xml = "${test_data_dir}/genomics/homo_sapiens/pacbio/xml/alz.ccs.consensusreadset.xml"
|
||||||
hifi = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz"
|
hifi = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz"
|
||||||
lima = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam"
|
lima = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam"
|
||||||
refine = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam"
|
refine = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam"
|
||||||
cluster = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.bam"
|
cluster = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.bam"
|
||||||
singletons = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.bam"
|
singletons = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.bam"
|
||||||
aligned = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam"
|
aligned = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam"
|
||||||
alignedbai = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam.bai"
|
alignedbai = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam.bai"
|
||||||
genemodel1 = "${test_data_dir}/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed"
|
genemodel1 = "${test_data_dir}/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed"
|
||||||
genemodel2 = "${test_data_dir}/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed"
|
genemodel2 = "${test_data_dir}/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed"
|
||||||
filelist = "${test_data_dir}/genomics/homo_sapiens/pacbio/txt/filelist.txt"
|
filelist = "${test_data_dir}/genomics/homo_sapiens/pacbio/txt/filelist.txt"
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
'bacteroides_fragilis' {
|
'bacteroides_fragilis' {
|
||||||
|
|
@ -393,31 +394,31 @@ params {
|
||||||
}
|
}
|
||||||
'generic' {
|
'generic' {
|
||||||
'csv' {
|
'csv' {
|
||||||
test_csv = "${test_data_dir}/generic/csv/test.csv"
|
test_csv = "${test_data_dir}/generic/csv/test.csv"
|
||||||
}
|
}
|
||||||
'notebooks' {
|
'notebooks' {
|
||||||
rmarkdown = "${test_data_dir}/generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd"
|
rmarkdown = "${test_data_dir}/generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd"
|
||||||
ipython_md = "${test_data_dir}/generic/notebooks/jupyter/ipython_notebook.md"
|
ipython_md = "${test_data_dir}/generic/notebooks/jupyter/ipython_notebook.md"
|
||||||
ipython_ipynb = "${test_data_dir}/generic/notebooks/jupyter/ipython_notebook.ipynb"
|
ipython_ipynb = "${test_data_dir}/generic/notebooks/jupyter/ipython_notebook.ipynb"
|
||||||
}
|
}
|
||||||
'tsv' {
|
'tsv' {
|
||||||
test_tsv = "${test_data_dir}/generic/tsv/test.tsv"
|
test_tsv = "${test_data_dir}/generic/tsv/test.tsv"
|
||||||
}
|
}
|
||||||
'txt' {
|
'txt' {
|
||||||
hello = "${test_data_dir}/generic/txt/hello.txt"
|
hello = "${test_data_dir}/generic/txt/hello.txt"
|
||||||
}
|
}
|
||||||
'cnn' {
|
'cnn' {
|
||||||
reference = "${test_data_dir}/generic/cnn/reference.cnn"
|
reference = "${test_data_dir}/generic/cnn/reference.cnn"
|
||||||
}
|
}
|
||||||
'cooler'{
|
'cooler'{
|
||||||
test_pairix_pair_gz = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz"
|
test_pairix_pair_gz = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz"
|
||||||
test_pairix_pair_gz_px2 = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2"
|
test_pairix_pair_gz_px2 = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2"
|
||||||
test_pairs_pair = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.sample1.pairs"
|
test_pairs_pair = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.sample1.pairs"
|
||||||
test_tabix_pair_gz = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz"
|
test_tabix_pair_gz = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz"
|
||||||
test_tabix_pair_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz.tbi"
|
test_tabix_pair_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz.tbi"
|
||||||
hg19_chrom_sizes = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.chrom.sizes"
|
hg19_chrom_sizes = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.chrom.sizes"
|
||||||
test_merge_cool = "${test_data_dir}/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cool"
|
test_merge_cool = "${test_data_dir}/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cool"
|
||||||
test_merge_cool_cp2 = "${test_data_dir}/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cp2.cool"
|
test_merge_cool_cp2 = "${test_data_dir}/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cp2.cool"
|
||||||
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
|
||||||
404
tests/modules/busco/main.nf
Normal file
404
tests/modules/busco/main.nf
Normal file
|
|
@ -0,0 +1,404 @@
|
||||||
|
#!/usr/bin/env nextflow
|
||||||
|
|
||||||
|
nextflow.enable.dsl = 2
|
||||||
|
|
||||||
|
include { BUSCO } from '../../../modules/busco/main.nf'
|
||||||
|
|
||||||
|
workflow test_busco_genome_single_fasta {
|
||||||
|
|
||||||
|
input = [
|
||||||
|
[ id:'test' ], // meta map
|
||||||
|
file( params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
|
||||||
|
]
|
||||||
|
|
||||||
|
BUSCO (
|
||||||
|
input,
|
||||||
|
['bacteria_odb10', 'bacteroidetes_odb10'], // Launch with 'auto' to use --auto-lineage, and specified lineages // 'auto' removed from test due to memory issues
|
||||||
|
[], // Download busco lineage
|
||||||
|
[], // No config
|
||||||
|
)
|
||||||
|
|
||||||
|
/* Output tree:
|
||||||
|
/tmp/tmpyz_hi62i/busco/
|
||||||
|
├── short_summary.specific.bacteria_odb10.genome.fna.json -> /tmp/tmpza_0dth3/33/7d8c9b2c8931d9ad6a67aa843895e7/short_summary.specific.bacteria_odb10.genome.fna.json
|
||||||
|
├── short_summary.specific.bacteria_odb10.genome.fna.txt -> /tmp/tmpza_0dth3/33/7d8c9b2c8931d9ad6a67aa843895e7/short_summary.specific.bacteria_odb10.genome.fna.txt
|
||||||
|
├── short_summary.specific.bacteroidetes_odb10.genome.fna.json -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/short_summary.specific.bacteroidetes_odb10.genome.fna.json
|
||||||
|
├── short_summary.specific.bacteroidetes_odb10.genome.fna.txt -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/short_summary.specific.bacteroidetes_odb10.genome.fna.txt
|
||||||
|
├── test-bacteria_odb10-busco -> /tmp/tmpza_0dth3/33/7d8c9b2c8931d9ad6a67aa843895e7/test-bacteria_odb10-busco/
|
||||||
|
│ ├── genome.fna/
|
||||||
|
│ │ ├── logs/
|
||||||
|
│ │ │ ├── hmmsearch_err.log
|
||||||
|
│ │ │ ├── hmmsearch_out.log
|
||||||
|
│ │ │ ├── prodigal_err.log
|
||||||
|
│ │ │ └── prodigal_out.log
|
||||||
|
│ │ ├── prodigal_output/
|
||||||
|
│ │ │ └── predicted_genes/
|
||||||
|
│ │ └── run_bacteria_odb10/
|
||||||
|
│ │ ├── busco_sequences/
|
||||||
|
│ │ ├── full_table.tsv
|
||||||
|
│ │ ├── hmmer_output/
|
||||||
|
│ │ ├── missing_busco_list.tsv
|
||||||
|
│ │ ├── short_summary.json
|
||||||
|
│ │ └── short_summary.txt
|
||||||
|
│ └── logs/
|
||||||
|
│ └── busco.log
|
||||||
|
├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmpza_0dth3/33/7d8c9b2c8931d9ad6a67aa843895e7/test-bacteria_odb10-busco.batch_summary.txt
|
||||||
|
├── test-bacteroidetes_odb10-busco -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/test-bacteroidetes_odb10-busco/
|
||||||
|
│ ├── genome.fna/
|
||||||
|
│ │ ├── logs/
|
||||||
|
│ │ │ ├── hmmsearch_err.log
|
||||||
|
│ │ │ ├── hmmsearch_out.log
|
||||||
|
│ │ │ ├── prodigal_err.log
|
||||||
|
│ │ │ └── prodigal_out.log
|
||||||
|
│ │ ├── prodigal_output/
|
||||||
|
│ │ │ └── predicted_genes/
|
||||||
|
│ │ └── run_bacteroidetes_odb10/
|
||||||
|
│ │ ├── busco_sequences/
|
||||||
|
│ │ ├── full_table.tsv
|
||||||
|
│ │ ├── hmmer_output/
|
||||||
|
│ │ ├── missing_busco_list.tsv
|
||||||
|
│ │ ├── short_summary.json
|
||||||
|
│ │ └── short_summary.txt
|
||||||
|
│ └── logs/
|
||||||
|
│ └── busco.log
|
||||||
|
├── test-bacteroidetes_odb10-busco.batch_summary.txt -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/test-bacteroidetes_odb10-busco.batch_summary.txt
|
||||||
|
└── versions.yml -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/versions.yml
|
||||||
|
|
||||||
|
Former Output tree -w 'auto':
|
||||||
|
/tmp/tmp846crjv2/busco/
|
||||||
|
├── short_summary.generic.bacteria_odb10.genome.fna.json -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.generic.bacteria_odb10.genome.fna.json
|
||||||
|
├── short_summary.generic.bacteria_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.generic.bacteria_odb10.genome.fna.txt
|
||||||
|
├── short_summary.specific.bacteria_odb10.genome.fna.json -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/short_summary.specific.bacteria_odb10.genome.fna.json
|
||||||
|
├── short_summary.specific.bacteria_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/short_summary.specific.bacteria_odb10.genome.fna.txt
|
||||||
|
├── short_summary.specific.bacteroidales_odb10.genome.fna.json -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.specific.bacteroidales_odb10.genome.fna.json
|
||||||
|
├── short_summary.specific.bacteroidales_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.specific.bacteroidales_odb10.genome.fna.txt
|
||||||
|
├── short_summary.specific.bacteroidetes_odb10.genome.fna.json -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/short_summary.specific.bacteroidetes_odb10.genome.fna.json
|
||||||
|
├── short_summary.specific.bacteroidetes_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/short_summary.specific.bacteroidetes_odb10.genome.fna.txt
|
||||||
|
├── test-auto-busco -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco/
|
||||||
|
│ ├── genome.fna/
|
||||||
|
│ │ ├── auto_lineage/
|
||||||
|
│ │ │ ├── run_archaea_odb10/
|
||||||
|
│ │ │ ├── run_bacteria_odb10/
|
||||||
|
│ │ │ └── run_eukaryota_odb10/
|
||||||
|
│ │ ├── logs/
|
||||||
|
│ │ │ ├── hmmsearch_err.log
|
||||||
|
│ │ │ ├── hmmsearch_out.log
|
||||||
|
│ │ │ ├── metaeuk_err.log
|
||||||
|
│ │ │ ├── metaeuk_out.log
|
||||||
|
│ │ │ ├── prodigal_err.log
|
||||||
|
│ │ │ ├── prodigal_out.log
|
||||||
|
│ │ │ ├── sepp_err.log
|
||||||
|
│ │ │ └── sepp_out.log
|
||||||
|
│ │ ├── prodigal_output/
|
||||||
|
│ │ │ └── predicted_genes/
|
||||||
|
│ │ ├── run_bacteria_odb10 -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco/genome.fna/auto_lineage/run_bacteria_odb10/ [recursive, not followed]
|
||||||
|
│ │ └── run_bacteroidales_odb10/
|
||||||
|
│ │ ├── busco_sequences/
|
||||||
|
│ │ ├── full_table.tsv
|
||||||
|
│ │ ├── hmmer_output/
|
||||||
|
│ │ ├── missing_busco_list.tsv
|
||||||
|
│ │ ├── short_summary.json
|
||||||
|
│ │ └── short_summary.txt
|
||||||
|
│ └── logs/
|
||||||
|
│ └── busco.log
|
||||||
|
├── test-auto-busco.batch_summary.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco.batch_summary.txt
|
||||||
|
├── test-bacteria_odb10-busco -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/test-bacteria_odb10-busco/
|
||||||
|
│ ├── genome.fna/
|
||||||
|
│ │ ├── logs/
|
||||||
|
│ │ │ ├── hmmsearch_err.log
|
||||||
|
│ │ │ ├── hmmsearch_out.log
|
||||||
|
│ │ │ ├── prodigal_err.log
|
||||||
|
│ │ │ └── prodigal_out.log
|
||||||
|
│ │ ├── prodigal_output/
|
||||||
|
│ │ │ └── predicted_genes/
|
||||||
|
│ │ └── run_bacteria_odb10/
|
||||||
|
│ │ ├── busco_sequences/
|
||||||
|
│ │ ├── full_table.tsv
|
||||||
|
│ │ ├── hmmer_output/
|
||||||
|
│ │ ├── missing_busco_list.tsv
|
||||||
|
│ │ ├── short_summary.json
|
||||||
|
│ │ └── short_summary.txt
|
||||||
|
│ └── logs/
|
||||||
|
│ └── busco.log
|
||||||
|
├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/test-bacteria_odb10-busco.batch_summary.txt
|
||||||
|
├── test-bacteroidetes_odb10-busco -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/test-bacteroidetes_odb10-busco/
|
||||||
|
│ ├── genome.fna/
|
||||||
|
│ │ ├── logs/
|
||||||
|
│ │ │ ├── hmmsearch_err.log
|
||||||
|
│ │ │ ├── hmmsearch_out.log
|
||||||
|
│ │ │ ├── prodigal_err.log
|
||||||
|
│ │ │ └── prodigal_out.log
|
||||||
|
│ │ ├── prodigal_output/
|
||||||
|
│ │ │ └── predicted_genes/
|
||||||
|
│ │ └── run_bacteroidetes_odb10/
|
||||||
|
│ │ ├── busco_sequences/
|
||||||
|
│ │ ├── full_table.tsv
|
||||||
|
│ │ ├── hmmer_output/
|
||||||
|
│ │ ├── missing_busco_list.tsv
|
||||||
|
│ │ ├── short_summary.json
|
||||||
|
│ │ └── short_summary.txt
|
||||||
|
│ └── logs/
|
||||||
|
│ └── busco.log
|
||||||
|
├── test-bacteroidetes_odb10-busco.batch_summary.txt -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/test-bacteroidetes_odb10-busco.batch_summary.txt
|
||||||
|
└── versions.yml -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/versions.yml
|
||||||
|
*/
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
workflow test_busco_genome_multi_fasta {
|
||||||
|
|
||||||
|
input = [
|
||||||
|
[ id:'test' ], // meta map
|
||||||
|
[
|
||||||
|
file( params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true),
|
||||||
|
file( params.test_data['candidatus_portiera_aleyrodidarum']['genome']['genome_fasta'], checkIfExists: true)
|
||||||
|
]
|
||||||
|
]
|
||||||
|
|
||||||
|
BUSCO (
|
||||||
|
input,
|
||||||
|
'bacteria_odb10',
|
||||||
|
[], // Download busco lineage
|
||||||
|
[], // No config
|
||||||
|
)
|
||||||
|
|
||||||
|
/* Output tree:
|
||||||
|
/tmp/tmpk19byek7/busco/
|
||||||
|
├── short_summary.specific.bacteria_odb10.genome.fasta.json -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/short_summary.specific.bacteria_odb10.genome.fasta.json
|
||||||
|
├── short_summary.specific.bacteria_odb10.genome.fasta.txt -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/short_summary.specific.bacteria_odb10.genome.fasta.txt
|
||||||
|
├── short_summary.specific.bacteria_odb10.genome.fna.json -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/short_summary.specific.bacteria_odb10.genome.fna.json
|
||||||
|
├── short_summary.specific.bacteria_odb10.genome.fna.txt -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/short_summary.specific.bacteria_odb10.genome.fna.txt
|
||||||
|
├── test-bacteria_odb10-busco -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/test-bacteria_odb10-busco/
|
||||||
|
│ ├── genome.fasta/
|
||||||
|
│ │ ├── logs/
|
||||||
|
│ │ │ ├── hmmsearch_err.log
|
||||||
|
│ │ │ ├── hmmsearch_out.log
|
||||||
|
│ │ │ ├── prodigal_err.log
|
||||||
|
│ │ │ └── prodigal_out.log
|
||||||
|
│ │ ├── prodigal_output/
|
||||||
|
│ │ │ └── predicted_genes/
|
||||||
|
│ │ └── run_bacteria_odb10/
|
||||||
|
│ │ ├── busco_sequences/
|
||||||
|
│ │ ├── full_table.tsv
|
||||||
|
│ │ ├── hmmer_output/
|
||||||
|
│ │ ├── missing_busco_list.tsv
|
||||||
|
│ │ ├── short_summary.json
|
||||||
|
│ │ └── short_summary.txt
|
||||||
|
│ ├── genome.fna/
|
||||||
|
│ │ ├── logs/
|
||||||
|
│ │ │ ├── hmmsearch_err.log
|
||||||
|
│ │ │ ├── hmmsearch_out.log
|
||||||
|
│ │ │ ├── prodigal_err.log
|
||||||
|
│ │ │ └── prodigal_out.log
|
||||||
|
│ │ ├── prodigal_output/
|
||||||
|
│ │ │ └── predicted_genes/
|
||||||
|
│ │ └── run_bacteria_odb10/
|
||||||
|
│ │ ├── busco_sequences/
|
||||||
|
│ │ ├── full_table.tsv
|
||||||
|
│ │ ├── hmmer_output/
|
||||||
|
│ │ ├── missing_busco_list.tsv
|
||||||
|
│ │ ├── short_summary.json
|
||||||
|
│ │ └── short_summary.txt
|
||||||
|
│ └── logs/
|
||||||
|
│ └── busco.log
|
||||||
|
├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/test-bacteria_odb10-busco.batch_summary.txt
|
||||||
|
└── versions.yml -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/versions.yml
|
||||||
|
*/
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
workflow test_busco_eukaryote_metaeuk {
|
||||||
|
|
||||||
|
input = [
|
||||||
|
[ id:'test' ], // meta map
|
||||||
|
file( params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||||
|
]
|
||||||
|
|
||||||
|
BUSCO (
|
||||||
|
input,
|
||||||
|
'eukaryota_odb10',
|
||||||
|
[], // Download busco lineage
|
||||||
|
[], // No config
|
||||||
|
)
|
||||||
|
|
||||||
|
/* Output tree:
|
||||||
|
/tmp/tmpeq4dsir5/busco/
|
||||||
|
├── short_summary.specific.eukaryota_odb10.genome.fasta.json -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/short_summary.specific.eukaryota_odb10.genome.fasta.json
|
||||||
|
├── short_summary.specific.eukaryota_odb10.genome.fasta.txt -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/short_summary.specific.eukaryota_odb10.genome.fasta.txt
|
||||||
|
├── test-eukaryota_odb10-busco -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/test-eukaryota_odb10-busco/
|
||||||
|
│ ├── genome.fasta/
|
||||||
|
│ │ ├── logs/
|
||||||
|
│ │ │ ├── hmmsearch_err.log
|
||||||
|
│ │ │ ├── hmmsearch_out.log
|
||||||
|
│ │ │ ├── metaeuk_err.log
|
||||||
|
│ │ │ └── metaeuk_out.log
|
||||||
|
│ │ └── run_eukaryota_odb10/
|
||||||
|
│ │ ├── busco_sequences/
|
||||||
|
│ │ ├── full_table.tsv
|
||||||
|
│ │ ├── hmmer_output/
|
||||||
|
│ │ ├── metaeuk_output/
|
||||||
|
│ │ ├── missing_busco_list.tsv
|
||||||
|
│ │ ├── short_summary.json
|
||||||
|
│ │ └── short_summary.txt
|
||||||
|
│ └── logs/
|
||||||
|
│ └── busco.log
|
||||||
|
├── test-eukaryota_odb10-busco.batch_summary.txt -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/test-eukaryota_odb10-busco.batch_summary.txt
|
||||||
|
└── versions.yml -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/versions.yml
|
||||||
|
*/
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
workflow test_busco_eukaryote_augustus {
|
||||||
|
|
||||||
|
input = [
|
||||||
|
[ id:'test' ], // meta map
|
||||||
|
file( params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||||
|
]
|
||||||
|
|
||||||
|
BUSCO (
|
||||||
|
input,
|
||||||
|
'eukaryota_odb10',
|
||||||
|
[], // Download busco lineage
|
||||||
|
[], // No config
|
||||||
|
)
|
||||||
|
|
||||||
|
/* Output tree:
|
||||||
|
/tmp/tmp2xqaygjj/busco/
|
||||||
|
├── test-eukaryota_odb10-busco -> /tmp/tmpjqs61x9o/3f/67cc14e873c0ceb45e2a27594d624c/test-eukaryota_odb10-busco/
|
||||||
|
│ ├── genome.fasta/
|
||||||
|
│ │ ├── blast_db/
|
||||||
|
│ │ │ ├── genome.fasta.ndb
|
||||||
|
│ │ │ ├── genome.fasta.nhr
|
||||||
|
│ │ │ ├── genome.fasta.nin
|
||||||
|
│ │ │ ├── genome.fasta.not
|
||||||
|
│ │ │ ├── genome.fasta.nsq
|
||||||
|
│ │ │ ├── genome.fasta.ntf
|
||||||
|
│ │ │ └── genome.fasta.nto
|
||||||
|
│ │ ├── logs/
|
||||||
|
│ │ │ ├── makeblastdb_err.log
|
||||||
|
│ │ │ ├── makeblastdb_out.log
|
||||||
|
│ │ │ ├── tblastn_err.log
|
||||||
|
│ │ │ └── tblastn_out.log
|
||||||
|
│ │ └── run_eukaryota_odb10/
|
||||||
|
│ │ ├── augustus_output/
|
||||||
|
│ │ ├── blast_output/
|
||||||
|
│ │ ├── busco_sequences/
|
||||||
|
│ │ └── hmmer_output/
|
||||||
|
│ └── logs/
|
||||||
|
│ └── busco.log
|
||||||
|
├── test-eukaryota_odb10-busco.batch_summary.txt -> /tmp/tmpjqs61x9o/3f/67cc14e873c0ceb45e2a27594d624c/test-eukaryota_odb10-busco.batch_summary.txt
|
||||||
|
└── versions.yml -> /tmp/tmpjqs61x9o/3f/67cc14e873c0ceb45e2a27594d624c/versions.yml
|
||||||
|
*/
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
workflow test_busco_protein {
|
||||||
|
|
||||||
|
input = [
|
||||||
|
[ id:'test' ], // meta map
|
||||||
|
file( params.test_data['candidatus_portiera_aleyrodidarum']['genome']['proteome_fasta'], checkIfExists: true)
|
||||||
|
]
|
||||||
|
|
||||||
|
BUSCO (
|
||||||
|
input,
|
||||||
|
'bacteria_odb10',
|
||||||
|
[], // Download busco lineage
|
||||||
|
[], // No config
|
||||||
|
)
|
||||||
|
|
||||||
|
/* Output tree:
|
||||||
|
/tmp/tmpzwd5dn56/busco/
|
||||||
|
├── short_summary.specific.bacteria_odb10.proteome.fasta.json -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/short_summary.specific.bacteria_odb10.proteome.fasta.json
|
||||||
|
├── short_summary.specific.bacteria_odb10.proteome.fasta.txt -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/short_summary.specific.bacteria_odb10.proteome.fasta.txt
|
||||||
|
├── test-bacteria_odb10-busco -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/test-bacteria_odb10-busco/
|
||||||
|
│ ├── logs/
|
||||||
|
│ │ └── busco.log
|
||||||
|
│ └── proteome.fasta/
|
||||||
|
│ ├── logs/
|
||||||
|
│ │ ├── hmmsearch_err.log
|
||||||
|
│ │ └── hmmsearch_out.log
|
||||||
|
│ └── run_bacteria_odb10/
|
||||||
|
│ ├── busco_sequences/
|
||||||
|
│ ├── full_table.tsv
|
||||||
|
│ ├── hmmer_output/
|
||||||
|
│ ├── missing_busco_list.tsv
|
||||||
|
│ ├── short_summary.json
|
||||||
|
│ └── short_summary.txt
|
||||||
|
├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/test-bacteria_odb10-busco.batch_summary.txt
|
||||||
|
└── versions.yml -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/versions.yml
|
||||||
|
*/
|
||||||
|
}
|
||||||
|
workflow test_busco_transcriptome {
|
||||||
|
|
||||||
|
input = [
|
||||||
|
[ id:'test' ], // meta map
|
||||||
|
file( params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
|
||||||
|
]
|
||||||
|
|
||||||
|
BUSCO (
|
||||||
|
input,
|
||||||
|
'bacteria_odb10',
|
||||||
|
[], // Download busco lineage
|
||||||
|
[], // No config
|
||||||
|
)
|
||||||
|
|
||||||
|
/* Output tree:
|
||||||
|
/tmp/tmpitjyvo9g/busco/
|
||||||
|
├── short_summary.specific.bacteria_odb10.test1.contigs.fa.json -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/short_summary.specific.bacteria_odb10.test1.contigs.fa.json
|
||||||
|
├── short_summary.specific.bacteria_odb10.test1.contigs.fa.txt -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/short_summary.specific.bacteria_odb10.test1.contigs.fa.txt
|
||||||
|
├── test-bacteria_odb10-busco -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/test-bacteria_odb10-busco/
|
||||||
|
│ ├── logs/
|
||||||
|
│ │ └── busco.log
|
||||||
|
│ └── test1.contigs.fa/
|
||||||
|
│ ├── blast_db/
|
||||||
|
│ │ ├── test1.contigs.fa.ndb
|
||||||
|
│ │ ├── test1.contigs.fa.nhr
|
||||||
|
│ │ ├── test1.contigs.fa.nin
|
||||||
|
│ │ ├── test1.contigs.fa.not
|
||||||
|
│ │ ├── test1.contigs.fa.nsq
|
||||||
|
│ │ ├── test1.contigs.fa.ntf
|
||||||
|
│ │ └── test1.contigs.fa.nto
|
||||||
|
│ ├── logs/
|
||||||
|
│ │ ├── hmmsearch_err.log
|
||||||
|
│ │ ├── hmmsearch_out.log
|
||||||
|
│ │ ├── makeblastdb_err.log
|
||||||
|
│ │ ├── makeblastdb_out.log
|
||||||
|
│ │ ├── tblastn_err.log
|
||||||
|
│ │ └── tblastn_out.log
|
||||||
|
│ ├── run_bacteria_odb10/
|
||||||
|
│ │ ├── blast_output/
|
||||||
|
│ │ ├── busco_sequences/
|
||||||
|
│ │ ├── full_table.tsv
|
||||||
|
│ │ ├── hmmer_output/
|
||||||
|
│ │ ├── missing_busco_list.tsv
|
||||||
|
│ │ ├── short_summary.json
|
||||||
|
│ │ ├── short_summary.txt
|
||||||
|
│ │ └── single_copy_proteins.faa
|
||||||
|
│ └── translated_proteins/
|
||||||
|
│ ├── 1024388at2.faa
|
||||||
|
│ ├── 1054741at2.faa
|
||||||
|
│ ├── 1093223at2.faa
|
||||||
|
│ ├── 1151822at2.faa
|
||||||
|
│ ├── 143460at2.faa
|
||||||
|
│ ├── 1491686at2.faa
|
||||||
|
│ ├── 1504821at2.faa
|
||||||
|
│ ├── 1574817at2.faa
|
||||||
|
│ ├── 1592033at2.faa
|
||||||
|
│ ├── 1623045at2.faa
|
||||||
|
│ ├── 1661836at2.faa
|
||||||
|
│ ├── 1674344at2.faa
|
||||||
|
│ ├── 1698718at2.faa
|
||||||
|
│ ├── 1990650at2.faa
|
||||||
|
│ ├── 223233at2.faa
|
||||||
|
│ ├── 402899at2.faa
|
||||||
|
│ ├── 505485at2.faa
|
||||||
|
│ ├── 665824at2.faa
|
||||||
|
│ ├── 776861at2.faa
|
||||||
|
│ ├── 874197at2.faa
|
||||||
|
│ ├── 932854at2.faa
|
||||||
|
│ └── 95696at2.faa
|
||||||
|
├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/test-bacteria_odb10-busco.batch_summary.txt
|
||||||
|
└── versions.yml -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/versions.yml
|
||||||
|
*/
|
||||||
|
|
||||||
|
}
|
||||||
28
tests/modules/busco/nextflow.config
Normal file
28
tests/modules/busco/nextflow.config
Normal file
|
|
@ -0,0 +1,28 @@
|
||||||
|
process {
|
||||||
|
|
||||||
|
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||||
|
|
||||||
|
withName: 'test_busco_genome_single_fasta:BUSCO' {
|
||||||
|
ext.args = '--mode genome'
|
||||||
|
}
|
||||||
|
|
||||||
|
withName: 'test_busco_genome_multi_fasta:BUSCO' {
|
||||||
|
ext.args = '--mode genome'
|
||||||
|
}
|
||||||
|
|
||||||
|
withName: 'test_busco_eukaryote_metaeuk:BUSCO' {
|
||||||
|
ext.args = '--mode genome'
|
||||||
|
}
|
||||||
|
|
||||||
|
withName: 'test_busco_eukaryote_augustus:BUSCO' {
|
||||||
|
ext.args = '--mode genome --augustus'
|
||||||
|
}
|
||||||
|
|
||||||
|
withName: 'test_busco_protein:BUSCO' {
|
||||||
|
ext.args = '--mode proteins'
|
||||||
|
}
|
||||||
|
|
||||||
|
withName: 'test_busco_transcriptome:BUSCO'{
|
||||||
|
ext.args = '--mode transcriptome'
|
||||||
|
}
|
||||||
|
}
|
||||||
159
tests/modules/busco/test.yml
Normal file
159
tests/modules/busco/test.yml
Normal file
|
|
@ -0,0 +1,159 @@
|
||||||
|
- name: busco test_busco_genome_single_fasta
|
||||||
|
command: nextflow run tests/modules/busco -entry test_busco_genome_single_fasta -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- busco
|
||||||
|
files:
|
||||||
|
- path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
|
||||||
|
contains:
|
||||||
|
- "one_line_summary"
|
||||||
|
- "input_file"
|
||||||
|
- "mode"
|
||||||
|
- "dataset"
|
||||||
|
- path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.txt
|
||||||
|
contains:
|
||||||
|
- "BUSCO version"
|
||||||
|
- "The lineage dataset is"
|
||||||
|
- "BUSCO was run in mode"
|
||||||
|
- "Complete BUSCOs"
|
||||||
|
- "Missing BUSCOs"
|
||||||
|
- "Dependencies and versions"
|
||||||
|
- path: output/busco/short_summary.specific.bacteroidetes_odb10.genome.fna.json
|
||||||
|
contains:
|
||||||
|
- "one_line_summary"
|
||||||
|
- "input_file"
|
||||||
|
- "mode"
|
||||||
|
- "dataset"
|
||||||
|
- path: output/busco/short_summary.specific.bacteroidetes_odb10.genome.fna.txt
|
||||||
|
contains:
|
||||||
|
- "BUSCO version"
|
||||||
|
- "The lineage dataset is"
|
||||||
|
- "BUSCO was run in mode"
|
||||||
|
- "Complete BUSCOs"
|
||||||
|
- "Missing BUSCOs"
|
||||||
|
- "Dependencies and versions"
|
||||||
|
- path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
|
||||||
|
md5sum: e50690742e9ae6abdd2bf99334ff9e12
|
||||||
|
- path: output/busco/test-bacteroidetes_odb10-busco.batch_summary.txt
|
||||||
|
md5sum: 4c1b2c4317c88398eddc30877ed740d9
|
||||||
|
- path: output/busco/versions.yml
|
||||||
|
md5sum: 8aa830f71587d859df35c6cfab59f35d
|
||||||
|
|
||||||
|
- name: busco test_busco_genome_multi_fasta
|
||||||
|
command: nextflow run tests/modules/busco -entry test_busco_genome_multi_fasta -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- busco
|
||||||
|
files:
|
||||||
|
- path: output/busco/short_summary.specific.bacteria_odb10.genome.fasta.json
|
||||||
|
contains:
|
||||||
|
- "one_line_summary"
|
||||||
|
- "input_file"
|
||||||
|
- "mode"
|
||||||
|
- "dataset"
|
||||||
|
- path: output/busco/short_summary.specific.bacteria_odb10.genome.fasta.txt
|
||||||
|
contains:
|
||||||
|
- "BUSCO version"
|
||||||
|
- "The lineage dataset is"
|
||||||
|
- "BUSCO was run in mode"
|
||||||
|
- "Complete BUSCOs"
|
||||||
|
- "Missing BUSCOs"
|
||||||
|
- "Dependencies and versions"
|
||||||
|
- path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
|
||||||
|
contains:
|
||||||
|
- "one_line_summary"
|
||||||
|
- "input_file"
|
||||||
|
- "mode"
|
||||||
|
- "dataset"
|
||||||
|
- path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.txt
|
||||||
|
contains:
|
||||||
|
- "BUSCO version"
|
||||||
|
- "The lineage dataset is"
|
||||||
|
- "BUSCO was run in mode"
|
||||||
|
- "Complete BUSCOs"
|
||||||
|
- "Missing BUSCOs"
|
||||||
|
- "Dependencies and versions"
|
||||||
|
- path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
|
||||||
|
md5sum: 5360dfe83bec1f5741ee115e53e6b517
|
||||||
|
- path: output/busco/versions.yml
|
||||||
|
md5sum: 9a959eb0a1f765777dff1ea2f5c139c0
|
||||||
|
|
||||||
|
- name: busco test_busco_eukaryote_metaeuk
|
||||||
|
command: nextflow run tests/modules/busco -entry test_busco_eukaryote_metaeuk -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- busco
|
||||||
|
files:
|
||||||
|
- path: output/busco/short_summary.specific.eukaryota_odb10.genome.fasta.json
|
||||||
|
contains:
|
||||||
|
- "one_line_summary"
|
||||||
|
- "input_file"
|
||||||
|
- "mode"
|
||||||
|
- "dataset"
|
||||||
|
- path: output/busco/short_summary.specific.eukaryota_odb10.genome.fasta.txt
|
||||||
|
contains:
|
||||||
|
- "BUSCO version"
|
||||||
|
- "The lineage dataset is"
|
||||||
|
- "BUSCO was run in mode"
|
||||||
|
- "Complete BUSCOs"
|
||||||
|
- "Missing BUSCOs"
|
||||||
|
- "Dependencies and versions"
|
||||||
|
- path: output/busco/test-eukaryota_odb10-busco.batch_summary.txt
|
||||||
|
md5sum: a70806f99ba5706d7353d3353b3f1d2b
|
||||||
|
- path: output/busco/versions.yml
|
||||||
|
md5sum: 34a808c257e6db1b0456f3b4372bc477
|
||||||
|
|
||||||
|
- name: busco test_busco_eukaryote_augustus
|
||||||
|
command: nextflow run tests/modules/busco -entry test_busco_eukaryote_augustus -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- busco
|
||||||
|
files:
|
||||||
|
- path: output/busco/test-eukaryota_odb10-busco.batch_summary.txt
|
||||||
|
md5sum: 660393dd43cd6a093b952d4b8ad41e40
|
||||||
|
- path: output/busco/versions.yml
|
||||||
|
md5sum: 2caac915461410b16a1524ac064cd0df
|
||||||
|
|
||||||
|
- name: busco test_busco_protein
|
||||||
|
command: nextflow run tests/modules/busco -entry test_busco_protein -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- busco
|
||||||
|
files:
|
||||||
|
- path: output/busco/short_summary.specific.bacteria_odb10.proteome.fasta.json
|
||||||
|
contains:
|
||||||
|
- "one_line_summary"
|
||||||
|
- "input_file"
|
||||||
|
- "mode"
|
||||||
|
- "dataset"
|
||||||
|
- path: output/busco/short_summary.specific.bacteria_odb10.proteome.fasta.txt
|
||||||
|
contains:
|
||||||
|
- "BUSCO version"
|
||||||
|
- "The lineage dataset is"
|
||||||
|
- "BUSCO was run in mode"
|
||||||
|
- "Complete BUSCOs"
|
||||||
|
- "Missing BUSCOs"
|
||||||
|
- "Dependencies and versions"
|
||||||
|
- path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
|
||||||
|
md5sum: fd3b4e30ce74d1fcb95d6286d6e2049f
|
||||||
|
- path: output/busco/versions.yml
|
||||||
|
md5sum: d7392261a57960a7e6aea609dce824f5
|
||||||
|
|
||||||
|
- name: busco test_busco_transcriptome
|
||||||
|
command: nextflow run tests/modules/busco -entry test_busco_transcriptome -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- busco
|
||||||
|
files:
|
||||||
|
- path: output/busco/short_summary.specific.bacteria_odb10.test1.contigs.fa.json
|
||||||
|
contains:
|
||||||
|
- "one_line_summary"
|
||||||
|
- "input_file"
|
||||||
|
- "mode"
|
||||||
|
- "dataset"
|
||||||
|
- path: output/busco/short_summary.specific.bacteria_odb10.test1.contigs.fa.txt
|
||||||
|
contains:
|
||||||
|
- "BUSCO version"
|
||||||
|
- "The lineage dataset is"
|
||||||
|
- "BUSCO was run in mode"
|
||||||
|
- "Complete BUSCOs"
|
||||||
|
- "Missing BUSCOs"
|
||||||
|
- "Dependencies and versions"
|
||||||
|
- path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
|
||||||
|
md5sum: 9a176cafe66ac0adca89dc34ad2be13f
|
||||||
|
- path: output/busco/versions.yml
|
||||||
|
md5sum: 30eacbc7df70f6b1e72e0a7b6d02a7e1
|
||||||
29
tests/modules/snapaligner/align/main.nf
Normal file
29
tests/modules/snapaligner/align/main.nf
Normal file
|
|
@ -0,0 +1,29 @@
|
||||||
|
#!/usr/bin/env nextflow
|
||||||
|
|
||||||
|
nextflow.enable.dsl = 2
|
||||||
|
|
||||||
|
include { SNAPALIGNER_INDEX } from '../../../../modules/snapaligner/index/main.nf'
|
||||||
|
include { SNAPALIGNER_ALIGN as SNAPALIGNER_SINGLE } from '../../../../modules/snapaligner/align/main.nf'
|
||||||
|
include { SNAPALIGNER_ALIGN as SNAPALIGNER_PAIRED } from '../../../../modules/snapaligner/align/main.nf'
|
||||||
|
|
||||||
|
workflow test_snapaligner_single {
|
||||||
|
|
||||||
|
input = [
|
||||||
|
[ id:'test', single_end:true ], // meta map
|
||||||
|
[file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
|
||||||
|
]
|
||||||
|
|
||||||
|
SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
|
||||||
|
SNAPALIGNER_SINGLE ( input, SNAPALIGNER_INDEX.out.index )
|
||||||
|
}
|
||||||
|
|
||||||
|
workflow test_snapaligner_paired {
|
||||||
|
|
||||||
|
input = [
|
||||||
|
[ id:'test', single_end:false ], // meta map
|
||||||
|
[file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)]
|
||||||
|
]
|
||||||
|
|
||||||
|
SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
|
||||||
|
SNAPALIGNER_PAIRED ( input, SNAPALIGNER_INDEX.out.index )
|
||||||
|
}
|
||||||
19
tests/modules/snapaligner/align/test.yml
Normal file
19
tests/modules/snapaligner/align/test.yml
Normal file
|
|
@ -0,0 +1,19 @@
|
||||||
|
- name: snapaligner align test_snapaligner_single
|
||||||
|
command: nextflow run tests/modules/snapaligner/align -entry test_snapaligner_single -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- snapaligner/align
|
||||||
|
- snapaligner
|
||||||
|
files:
|
||||||
|
- path: output/snapaligner/test.bam
|
||||||
|
md5sum: 5d95594e4ef1ee23ce56e6a7cb64f0f2
|
||||||
|
- path: output/snapaligner/versions.yml
|
||||||
|
|
||||||
|
- name: snapaligner align test_snapaligner_paired
|
||||||
|
command: nextflow run tests/modules/snapaligner/align -entry test_snapaligner_paired -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- snapaligner/align
|
||||||
|
- snapaligner
|
||||||
|
files:
|
||||||
|
- path: output/snapaligner/test.bam
|
||||||
|
md5sum: a1405da5876f15dbe8a81516b94c2a15
|
||||||
|
- path: output/snapaligner/versions.yml
|
||||||
|
|
@ -1,17 +0,0 @@
|
||||||
#!/usr/bin/env nextflow
|
|
||||||
|
|
||||||
nextflow.enable.dsl = 2
|
|
||||||
|
|
||||||
include { SNAPALIGNER_INDEX } from '../../../../modules/snapaligner/index/main.nf'
|
|
||||||
include { SNAPALIGNER_PAIRED } from '../../../../modules/snapaligner/paired/main.nf'
|
|
||||||
|
|
||||||
workflow test_snapaligner_paired {
|
|
||||||
|
|
||||||
input = [
|
|
||||||
[ id:'test', single_end:false ], // meta map
|
|
||||||
[file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)]
|
|
||||||
]
|
|
||||||
|
|
||||||
SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
|
|
||||||
SNAPALIGNER_PAIRED ( input, SNAPALIGNER_INDEX.out.index )
|
|
||||||
}
|
|
||||||
|
|
@ -1,9 +0,0 @@
|
||||||
- name: snapaligner paired test_snapaligner_paired
|
|
||||||
command: nextflow run tests/modules/snapaligner/paired -entry test_snapaligner_paired -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- snapaligner
|
|
||||||
- snapaligner/paired
|
|
||||||
files:
|
|
||||||
- path: output/snapaligner/test.bam
|
|
||||||
md5sum: 2ac92e9539fa246dd6db52b5de56fca5
|
|
||||||
- path: output/snapaligner/versions.yml
|
|
||||||
|
|
@ -1,17 +0,0 @@
|
||||||
#!/usr/bin/env nextflow
|
|
||||||
|
|
||||||
nextflow.enable.dsl = 2
|
|
||||||
|
|
||||||
include { SNAPALIGNER_INDEX } from '../../../../modules/snapaligner/index/main.nf'
|
|
||||||
include { SNAPALIGNER_SINGLE } from '../../../../modules/snapaligner/single/main.nf'
|
|
||||||
|
|
||||||
workflow test_snapaligner_single {
|
|
||||||
|
|
||||||
input = [
|
|
||||||
[ id:'test', single_end:false ], // meta map
|
|
||||||
[file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
|
|
||||||
]
|
|
||||||
|
|
||||||
SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
|
|
||||||
SNAPALIGNER_SINGLE ( input, SNAPALIGNER_INDEX.out.index )
|
|
||||||
}
|
|
||||||
|
|
@ -1,5 +0,0 @@
|
||||||
process {
|
|
||||||
|
|
||||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
@ -1,9 +0,0 @@
|
||||||
- name: snapaligner single test_snapaligner_single
|
|
||||||
command: nextflow run tests/modules/snapaligner/single -entry test_snapaligner_single -c tests/config/nextflow.config
|
|
||||||
tags:
|
|
||||||
- snapaligner/single
|
|
||||||
- snapaligner
|
|
||||||
files:
|
|
||||||
- path: output/snapaligner/test.bam
|
|
||||||
md5sum: 696f7ea8e1aa5f9d7dafb9d0134fe25d
|
|
||||||
- path: output/snapaligner/versions.yml
|
|
||||||
|
|
@ -2,7 +2,7 @@
|
||||||
|
|
||||||
nextflow.enable.dsl = 2
|
nextflow.enable.dsl = 2
|
||||||
|
|
||||||
include { ANNOTATION_SNPEFF } from '../../../../../subworkflows/nf-core/annotation_snpeff/main'
|
include { ANNOTATION_SNPEFF } from '../../../../../subworkflows/nf-core/annotation/snpeff/main'
|
||||||
|
|
||||||
workflow annotation_snpeff {
|
workflow annotation_snpeff {
|
||||||
input = [
|
input = [
|
||||||
|
|
|
||||||
Loading…
Reference in a new issue