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Merge branch 'master' into correcting_stubs

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Lucpen 2022-05-09 08:54:22 +02:00 committed by GitHub
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84
modules/busco/main.nf Normal file
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@ -0,0 +1,84 @@
process BUSCO {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::busco=5.3.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/busco:5.3.2--pyhdfd78af_0':
'quay.io/biocontainers/busco:5.3.2--pyhdfd78af_0' }"
input:
tuple val(meta), path('tmp_input/*')
each lineage // Required: lineage to check against, "auto" enables --auto-lineage instead
path busco_lineages_path // Recommended: path to busco lineages - downloads if not set
path config_file // Optional: busco configuration file
output:
tuple val(meta), path("*-busco.batch_summary.txt"), emit: batch_summary
tuple val(meta), path("short_summary.*.txt") , emit: short_summaries_txt, optional: true
tuple val(meta), path("short_summary.*.json") , emit: short_summaries_json, optional: true
tuple val(meta), path("*-busco") , emit: busco_dir
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}-${lineage}"
def busco_config = config_file ? "--config $config_file" : ''
def busco_lineage = lineage.equals('auto') ? '--auto-lineage' : "--lineage_dataset ${lineage}"
def busco_lineage_dir = busco_lineages_path ? "--offline --download_path ${busco_lineages_path}" : ''
"""
# Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
# Check for container variable initialisation script and source it.
if [ -f "/usr/local/env-activate.sh" ]; then
set +u # Otherwise, errors out because of various unbound variables
. "/usr/local/env-activate.sh"
set -u
fi
# If the augustus config directory is not writable, then copy to writeable area
if [ ! -w "\${AUGUSTUS_CONFIG_PATH}" ]; then
# Create writable tmp directory for augustus
AUG_CONF_DIR=\$( mktemp -d -p \$PWD )
cp -r \$AUGUSTUS_CONFIG_PATH/* \$AUG_CONF_DIR
export AUGUSTUS_CONFIG_PATH=\$AUG_CONF_DIR
echo "New AUGUSTUS_CONFIG_PATH=\${AUGUSTUS_CONFIG_PATH}"
fi
# Ensure the input is uncompressed
INPUT_SEQS=input_seqs
mkdir "\$INPUT_SEQS"
cd "\$INPUT_SEQS"
for FASTA in ../tmp_input/*; do
if [ "\${FASTA##*.}" == 'gz' ]; then
gzip -cdf "\$FASTA" > \$( basename "\$FASTA" .gz )
else
ln -s "\$FASTA" .
fi
done
cd ..
busco \\
--cpu $task.cpus \\
--in "\$INPUT_SEQS" \\
--out ${prefix}-busco \\
$busco_lineage \\
$busco_lineage_dir \\
$busco_config \\
$args
# clean up
rm -rf "\$INPUT_SEQS"
# Move files to avoid staging/publishing issues
mv ${prefix}-busco/batch_summary.txt ${prefix}-busco.batch_summary.txt
mv ${prefix}-busco/*/short_summary.*.{json,txt} . || echo "Short summaries were not available: No genes were found."
cat <<-END_VERSIONS > versions.yml
"${task.process}":
busco: \$( busco --version 2>&1 | sed 's/^BUSCO //' )
END_VERSIONS
"""
}

69
modules/busco/meta.yml Normal file
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@ -0,0 +1,69 @@
name: busco
description: Benchmarking Universal Single Copy Orthologs
keywords:
- quality control
- genome
- transcriptome
- proteome
tools:
- busco:
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.
homepage: https://busco.ezlab.org/
documentation: https://busco.ezlab.org/busco_userguide.html
tool_dev_url: https://gitlab.com/ezlab/busco
doi: "10.1007/978-1-4939-9173-0_14"
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: Nucleic or amino acid sequence file in FASTA format.
pattern: "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}"
- lineage:
type: value
description: The BUSCO lineage to use, or "auto" to automatically select lineage
- busco_lineages_path:
type: directory
description: Path to local BUSCO lineages directory.
- config_file:
type: file
description: Path to BUSCO config file.
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- batch_summary:
type: file
description: Summary of all sequence files analyzed
pattern: "*-busco.batch_summary.txt"
- short_summaries_txt:
type: file
description: Short Busco summary in plain text format
pattern: "short_summary.*.txt"
- short_summaries_json:
type: file
description: Short Busco summary in JSON format
pattern: "short_summary.*.json"
- busco_dir:
type: directory
description: BUSCO lineage specific output
pattern: "*-busco"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@priyanka-surana"
- "@charles-plessy"
- "@mahesh-panchal"
- "@muffato"
- "@jvhagey"

7
modules/snapaligner/paired/main.nf → modules/snapaligner/align/main.nf
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@ -1,4 +1,4 @@
process SNAPALIGNER_PAIRED {
process SNAPALIGNER_ALIGN {
tag '$meta.id'
label 'process_high'
@ -21,15 +21,16 @@ process SNAPALIGNER_PAIRED {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def subcmd = meta.single_end ? "single" : "paired"
"""
mkdir -p index
mv $index index/
snap-aligner paired \\
snap-aligner ${subcmd} \\
index \\
${reads.join(" ")} \\
-o -bam ${prefix}.bam \\
-o ${prefix}.bam \\
-t ${task.cpus} \\
$args

6
modules/snapaligner/paired/meta.yml → modules/snapaligner/align/meta.yml
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@ -1,5 +1,5 @@
name: "snapaligner_paired"
description: Performs paired end fastq alignment to a fasta reference using SNAP
name: "snapaligner_align"
description: Performs fastq alignment to a fasta reference using SNAP
keywords:
- alignment
- map
@ -22,7 +22,7 @@ input:
e.g. [ id:'test', single_end:false ]
- reads:
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}"
- index:
type: file

41
modules/snapaligner/single/main.nf
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@ -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
"""
}

48
modules/snapaligner/single/meta.yml
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@ -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"

33
modules/sratools/prefetch/main.nf
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@ -1,43 +1,26 @@
process SRATOOLS_PREFETCH {
tag "$id"
label 'process_low'
label 'error_retry'
conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5262h314213e_0' :
'quay.io/biocontainers/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--pl5321ha49a11a_3' }"
input:
tuple val(meta), val(id)
output:
tuple val(meta), path("$id"), emit: sra
tuple val(meta), path(id), emit: sra
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def config = "/LIBS/GUID = \"${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 '${config}' > "\${NCBI_SETTINGS}"
fi
shell:
args = task.ext.args ?: ''
args2 = task.ext.args2 ?: '5 1 100' // <num retries> <base delay in seconds> <max delay in seconds>
config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
prefetch \\
$args \\
--progress \\
$id
vdb-validate $id
cat <<-END_VERSIONS > versions.yml
"${task.process}":
sratools: \$(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
END_VERSIONS
"""
template 'retry_with_backoff.sh'
}

59
modules/sratools/prefetch/templates/retry_with_backoff.sh Executable file
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@ -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

14
tests/config/pytest_modules.yml
View file

@ -337,6 +337,10 @@ bracken/bracken:
- modules/bracken/bracken/**
- tests/modules/bracken/bracken/**
busco:
- modules/busco/**
- tests/modules/busco/**
bwa/aln:
- modules/bwa/aln/**
- tests/modules/bwa/aln/**
@ -1763,13 +1767,9 @@ snapaligner/index:
- modules/snapaligner/index/**
- tests/modules/snapaligner/index/**
snapaligner/paired:
- modules/snapaligner/paired/**
- tests/modules/snapaligner/paired/**
snapaligner/single:
- modules/snapaligner/single/**
- tests/modules/snapaligner/single/**
snapaligner/align:
- modules/snapaligner/align/**
- tests/modules/snapaligner/align/**
snpdists:
- modules/snpdists/**

3
tests/config/test_data.config
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@ -125,6 +125,7 @@ params {
genome_gff3 = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gff3"
genome_gtf = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gtf"
genome_interval_list = "${test_data_dir}/genomics/homo_sapiens/genome/genome.interval_list"
genome_multi_interval_bed = "${test_data_dir}/genomics/homo_sapiens/genome/genome.multi_intervals.bed"
genome_sizes = "${test_data_dir}/genomics/homo_sapiens/genome/genome.sizes"
genome_bed = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed"
genome_header = "${test_data_dir}/genomics/homo_sapiens/genome/genome.header"
@ -211,6 +212,7 @@ params {
test_paired_end_hla = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam"
test_paired_end_hla_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam"
test_paired_end_hla_sorted_bam_bai = "${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 = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam"
@ -225,7 +227,6 @@ params {
test2_paired_end_umi_unsorted_bam = "${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_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai"

404
tests/modules/busco/main.nf Normal file
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@ -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
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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
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- 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
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#!/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 )
}

0
tests/modules/snapaligner/paired/nextflow.config → tests/modules/snapaligner/align/nextflow.config
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19
tests/modules/snapaligner/align/test.yml Normal file
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- 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

17
tests/modules/snapaligner/paired/main.nf
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@ -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 )
}

9
tests/modules/snapaligner/paired/test.yml
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@ -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

17
tests/modules/snapaligner/single/main.nf
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@ -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 )
}

5
tests/modules/snapaligner/single/nextflow.config
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@ -1,5 +0,0 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

9
tests/modules/snapaligner/single/test.yml
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@ -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
tests/subworkflows/nf-core/annotation/snpeff/main.nf
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@ -2,7 +2,7 @@
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 {
input = [