mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
Merge branch 'master' into meryl_count
This commit is contained in:
Mahesh Binzer-Panchal
GitHub
commit
32b0fdc9d9
27 changed files with 278 additions and 336 deletions
|
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@ -1,4 +1,4 @@
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process SNAPALIGNER_PAIRED {
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process SNAPALIGNER_ALIGN {
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tag '$meta.id'
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label 'process_high'
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@ -21,15 +21,16 @@ process SNAPALIGNER_PAIRED {
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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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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mv $index index/
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snap-aligner paired \\
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snap-aligner ${subcmd} \\
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index \\
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${reads.join(" ")} \\
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-o -bam ${prefix}.bam \\
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-o ${prefix}.bam \\
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-t ${task.cpus} \\
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$args
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|
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@ -1,5 +1,5 @@
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name: "snapaligner_paired"
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description: Performs paired end fastq alignment to a fasta reference using SNAP
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name: "snapaligner_align"
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description: Performs fastq alignment to a fasta reference using SNAP
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keywords:
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- alignment
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- map
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@ -22,7 +22,7 @@ input:
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e.g. [ id:'test', single_end:false ]
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- reads:
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type: file
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description: List of input fastq files of size 2 for fastq or 1 for bam
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description: List of input fastq files of size 2 for paired fastq or 1 for bam or single fastq
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pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}"
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- index:
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type: file
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|
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@ -1,41 +0,0 @@
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process SNAPALIGNER_SINGLE {
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tag '$meta.id'
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label 'process_high'
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conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.1--hd03093a_1':
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'quay.io/biocontainers/snap-aligner:2.0.1--hd03093a_1' }"
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input:
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tuple val(meta), path(reads)
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path index
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output:
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tuple val(meta), path("*.bam"), emit: bam
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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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|
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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}"
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||||
|
||||
"""
|
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mkdir -p index
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mv $index index/
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snap-aligner single \\
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index \\
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${reads.join(" ")} \\
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-o -bam ${prefix}.bam \\
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-t ${task.cpus} \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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snapaligner: \$(snap-aligner 2>&1| head -n 1 | sed 's/^.*version //;s/.\$//')
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END_VERSIONS
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"""
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}
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@ -1,48 +0,0 @@
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name: "snapaligner_single"
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description: Performs single end fastq alignment to a fasta reference using SNAP
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keywords:
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- alignment
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- map
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- fastq
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- bam
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- sam
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tools:
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- "snapaligner":
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description: "Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data"
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homepage: "http://snap.cs.berkeley.edu"
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documentation: "https://1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug"
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tool_dev_url: "https://github.com/amplab/snap"
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doi: "10.1101/2021.11.23.469039"
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licence: "['Apache v2']"
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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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- reads:
|
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type: file
|
||||
description: List of single end input files
|
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pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}"
|
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- index:
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type: file
|
||||
description: List of SNAP genome index files
|
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pattern: "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}"
|
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|
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output:
|
||||
- meta:
|
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type: map
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||||
description: |
|
||||
Groovy Map containing sample information
|
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e.g. [ id:'test', single_end:false ]
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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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- bam:
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type: file
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description: Aligned BAM file
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pattern: "*.{bam}"
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|
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authors:
|
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- "@matthdsm"
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|
|
@ -1,43 +1,26 @@
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process SRATOOLS_PREFETCH {
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tag "$id"
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label 'process_low'
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||||
label 'error_retry'
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||||
|
||||
conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
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||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5262h314213e_0' :
|
||||
'quay.io/biocontainers/sra-tools:2.11.0--pl5262h314213e_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' :
|
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'quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
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|
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input:
|
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tuple val(meta), val(id)
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|
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output:
|
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tuple val(meta), path("$id"), emit: sra
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tuple val(meta), path(id), emit: sra
|
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path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
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def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
|
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"""
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eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
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if [[ ! -f "\${NCBI_SETTINGS}" ]]; then
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mkdir -p "\$(dirname "\${NCBI_SETTINGS}")"
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printf '${config}' > "\${NCBI_SETTINGS}"
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fi
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shell:
|
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args = task.ext.args ?: ''
|
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args2 = task.ext.args2 ?: '5 1 100' // <num retries> <base delay in seconds> <max delay in seconds>
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config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
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prefetch \\
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||||
$args \\
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--progress \\
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||||
$id
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||||
|
||||
vdb-validate $id
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||||
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cat <<-END_VERSIONS > versions.yml
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||||
"${task.process}":
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sratools: \$(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
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||||
END_VERSIONS
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||||
"""
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||||
template 'retry_with_backoff.sh'
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}
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||||
|
|
|
|||
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
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||||
|
||||
set -u
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||||
|
||||
retry_with_backoff() {
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||||
local max_attempts=${1}
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||||
local delay=${2}
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||||
local max_time=${3}
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local attempt=1
|
||||
local output=
|
||||
local status=
|
||||
|
||||
# Remove the first three arguments to this function in order to access
|
||||
# the 'real' command with `${@}`.
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||||
shift 3
|
||||
|
||||
while [ ${attempt} -le ${max_attempts} ]; do
|
||||
output=$("${@}")
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||||
status=${?}
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||||
|
||||
if [ ${status} -eq 0 ]; then
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||||
break
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||||
fi
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||||
|
||||
if [ ${attempt} -lt ${max_attempts} ]; then
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echo "Failed attempt ${attempt} of ${max_attempts}. Retrying in ${delay} s." >&2
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||||
sleep ${delay}
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||||
elif [ ${attempt} -eq ${max_attempts} ]; then
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||||
echo "Failed after ${attempt} attempts." >&2
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return ${status}
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||||
fi
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||||
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||||
attempt=$(( ${attempt} + 1 ))
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||||
delay=$(( ${delay} * 2 ))
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||||
if [ ${delay} -ge ${max_time} ]; then
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||||
delay=${max_time}
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||||
fi
|
||||
done
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||||
|
||||
echo "${output}"
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||||
}
|
||||
|
||||
eval "$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
|
||||
if [[ ! -f "${NCBI_SETTINGS}" ]]; then
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||||
mkdir -p "$(dirname "${NCBI_SETTINGS}")"
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||||
printf '!{config}' > "${NCBI_SETTINGS}"
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||||
fi
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||||
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||||
retry_with_backoff !{args2} \
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prefetch \
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!{args} \
|
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!{id}
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||||
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vdb-validate !{id}
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||||
|
||||
cat <<-END_VERSIONS > versions.yml
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||||
"!{task.process}":
|
||||
sratools: $(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
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||||
END_VERSIONS
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|
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@ -1771,13 +1771,9 @@ snapaligner/index:
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|||
- modules/snapaligner/index/**
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- tests/modules/snapaligner/index/**
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||||
|
||||
snapaligner/paired:
|
||||
- modules/snapaligner/paired/**
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||||
- tests/modules/snapaligner/paired/**
|
||||
|
||||
snapaligner/single:
|
||||
- modules/snapaligner/single/**
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||||
- tests/modules/snapaligner/single/**
|
||||
snapaligner/align:
|
||||
- modules/snapaligner/align/**
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||||
- tests/modules/snapaligner/align/**
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||||
|
||||
snpdists:
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||||
- modules/snpdists/**
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||||
|
|
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|||
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@ -125,6 +125,7 @@ params {
|
|||
genome_gff3 = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gff3"
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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"
|
||||
|
|
@ -181,16 +182,16 @@ params {
|
|||
vcfanno_toml = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml"
|
||||
}
|
||||
'pangenome' {
|
||||
pangenome_fa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa"
|
||||
pangenome_fa_gz = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa.gz"
|
||||
pangenome_paf = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf"
|
||||
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_smoothxg_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.smoothxg.gfa"
|
||||
pangenome_gfaffix_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.gfaffix.gfa"
|
||||
pangenome_fa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa"
|
||||
pangenome_fa_gz = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa.gz"
|
||||
pangenome_paf = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf"
|
||||
pangenome_paf_gz = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf.gz"
|
||||
pangenome_seqwish_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.seqwish.gfa"
|
||||
pangenome_smoothxg_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.smoothxg.gfa"
|
||||
pangenome_gfaffix_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.gfaffix.gfa"
|
||||
'odgi' {
|
||||
pangenome_og = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.og"
|
||||
pangenome_lay = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.lay"
|
||||
pangenome_og = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.og"
|
||||
pangenome_lay = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.lay"
|
||||
}
|
||||
}
|
||||
'illumina' {
|
||||
|
|
@ -211,131 +212,131 @@ params {
|
|||
test_paired_end_hla = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam"
|
||||
test_paired_end_hla_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 = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam"
|
||||
test2_paired_end_markduplicates_sorted_bam = "${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 = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam"
|
||||
mitochon_standin_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai"
|
||||
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"
|
||||
|
||||
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_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_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_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_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_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"
|
||||
|
||||
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_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_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_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_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_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"
|
||||
|
||||
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_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"
|
||||
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_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"
|
||||
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_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_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"
|
||||
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_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"
|
||||
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_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"
|
||||
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"
|
||||
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"
|
||||
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"
|
||||
|
||||
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_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"
|
||||
|
||||
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 = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz"
|
||||
test2_haplotc_ann_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi"
|
||||
|
||||
test2_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_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_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_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_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_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"
|
||||
|
||||
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_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_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_contamination_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.contamination.table"
|
||||
test_test2_paired_mutect2_calls_vcf_gz = "${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 = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi"
|
||||
test_test2_paired_mutect2_calls_vcf_gz_stats = "${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 = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz"
|
||||
test_test2_paired_mutect2_calls_artifact_prior_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired_mutect2_calls.artifact-prior.tar.gz"
|
||||
test_test2_paired_segmentation_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.segmentation.table"
|
||||
test_test2_paired_contamination_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.contamination.table"
|
||||
|
||||
test_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf"
|
||||
test_genome_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz"
|
||||
test_genome_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi"
|
||||
test_genome_vcf_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx"
|
||||
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_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"
|
||||
|
||||
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_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 = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf"
|
||||
test2_genome_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz"
|
||||
test2_genome_vcf_gz_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"
|
||||
|
||||
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 = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz"
|
||||
test_genome21_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi"
|
||||
|
||||
test_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"
|
||||
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"
|
||||
|
||||
test_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak"
|
||||
test2_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test2.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"
|
||||
|
||||
test_narrowpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak"
|
||||
test2_narrowpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test2.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"
|
||||
|
||||
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_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_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test.yak"
|
||||
test2_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test2.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"
|
||||
|
||||
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_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"
|
||||
|
||||
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_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_pytor = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor"
|
||||
test_pytor = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor"
|
||||
}
|
||||
'pacbio' {
|
||||
primers = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"
|
||||
alz = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam"
|
||||
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_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_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_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"
|
||||
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"
|
||||
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"
|
||||
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"
|
||||
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"
|
||||
filelist = "${test_data_dir}/genomics/homo_sapiens/pacbio/txt/filelist.txt"
|
||||
primers = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"
|
||||
alz = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam"
|
||||
alzpbi = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam.pbi"
|
||||
ccs = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.bam"
|
||||
ccs_fa = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta"
|
||||
ccs_fa_gz = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta.gz"
|
||||
ccs_fq = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq"
|
||||
ccs_fq_gz = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz"
|
||||
ccs_xml = "${test_data_dir}/genomics/homo_sapiens/pacbio/xml/alz.ccs.consensusreadset.xml"
|
||||
hifi = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz"
|
||||
lima = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam"
|
||||
refine = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam"
|
||||
cluster = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.bam"
|
||||
singletons = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.bam"
|
||||
aligned = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam"
|
||||
alignedbai = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam.bai"
|
||||
genemodel1 = "${test_data_dir}/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed"
|
||||
genemodel2 = "${test_data_dir}/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed"
|
||||
filelist = "${test_data_dir}/genomics/homo_sapiens/pacbio/txt/filelist.txt"
|
||||
}
|
||||
}
|
||||
'bacteroides_fragilis' {
|
||||
|
|
@ -393,31 +394,31 @@ params {
|
|||
}
|
||||
'generic' {
|
||||
'csv' {
|
||||
test_csv = "${test_data_dir}/generic/csv/test.csv"
|
||||
test_csv = "${test_data_dir}/generic/csv/test.csv"
|
||||
}
|
||||
'notebooks' {
|
||||
rmarkdown = "${test_data_dir}/generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd"
|
||||
ipython_md = "${test_data_dir}/generic/notebooks/jupyter/ipython_notebook.md"
|
||||
ipython_ipynb = "${test_data_dir}/generic/notebooks/jupyter/ipython_notebook.ipynb"
|
||||
rmarkdown = "${test_data_dir}/generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd"
|
||||
ipython_md = "${test_data_dir}/generic/notebooks/jupyter/ipython_notebook.md"
|
||||
ipython_ipynb = "${test_data_dir}/generic/notebooks/jupyter/ipython_notebook.ipynb"
|
||||
}
|
||||
'tsv' {
|
||||
test_tsv = "${test_data_dir}/generic/tsv/test.tsv"
|
||||
test_tsv = "${test_data_dir}/generic/tsv/test.tsv"
|
||||
}
|
||||
'txt' {
|
||||
hello = "${test_data_dir}/generic/txt/hello.txt"
|
||||
hello = "${test_data_dir}/generic/txt/hello.txt"
|
||||
}
|
||||
'cnn' {
|
||||
reference = "${test_data_dir}/generic/cnn/reference.cnn"
|
||||
reference = "${test_data_dir}/generic/cnn/reference.cnn"
|
||||
}
|
||||
'cooler'{
|
||||
test_pairix_pair_gz = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz"
|
||||
test_pairix_pair_gz_px2 = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2"
|
||||
test_pairs_pair = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.sample1.pairs"
|
||||
test_tabix_pair_gz = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz"
|
||||
test_tabix_pair_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz.tbi"
|
||||
hg19_chrom_sizes = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.chrom.sizes"
|
||||
test_merge_cool = "${test_data_dir}/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cool"
|
||||
test_merge_cool_cp2 = "${test_data_dir}/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cp2.cool"
|
||||
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_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_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"
|
||||
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"
|
||||
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -17,11 +17,11 @@ workflow test_gatk4_mergebamalignment {
|
|||
|
||||
workflow test_gatk4_mergebamalignment_stubs {
|
||||
input = [ [ id:'test' ], // meta map
|
||||
"test_foo.bam",
|
||||
"test_bar.bam"
|
||||
file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
|
||||
file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
|
||||
]
|
||||
fasta = "genome.fasta"
|
||||
dict = "genome.fasta.dict"
|
||||
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||||
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
|
||||
|
||||
GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -9,7 +9,7 @@
|
|||
- path: output/gatk4/versions.yml
|
||||
|
||||
- name: gatk4 mergebamalignment test_gatk4_mergebamalignment_stubs
|
||||
command: nextflow run ./tests/modules/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mergebamalignment/nextflow.config -stub-run
|
||||
command: nextflow run ./tests/modules/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mergebamalignment/nextflow.config -stub-run
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4/mergebamalignment
|
||||
|
|
|
|||
|
|
@ -120,23 +120,23 @@ workflow test_gatk4_mutect2_mitochondria {
|
|||
}
|
||||
|
||||
workflow test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs {
|
||||
input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
|
||||
[ "foo_paired.bam",
|
||||
"foo_paired2.bam"
|
||||
input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
|
||||
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
|
||||
],
|
||||
[ "foo_paired.bam.bai",
|
||||
"foo_paired2.bam.bai"
|
||||
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)
|
||||
],
|
||||
[]
|
||||
]
|
||||
|
||||
fasta = "genome.fasta"
|
||||
fai = "genome.fasta.fai"
|
||||
dict = "genome.fasta.dict"
|
||||
germline_resource = "genome_gnomAD.r2.1.1.vcf.gz"
|
||||
germline_resource_tbi = "genome_gnomAD.r2.1.1.vcf.gz.tbi"
|
||||
panel_of_normals = "genome_mills_and_1000G.indels.hg38.vcf.gz"
|
||||
panel_of_normals_tbi = "genome_mills_and_1000G.indels.hg38.vcf.gz.tbi"
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||||
dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
|
||||
germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
|
||||
germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
|
||||
panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
|
||||
panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
|
||||
|
||||
GATK4_MUTECT2_F1R2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -71,7 +71,7 @@
|
|||
- path: output/gatk4/versions.yml
|
||||
|
||||
- name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs
|
||||
command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair_f1r2 -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config -stub-run
|
||||
command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config -stub-run
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4/mutect2
|
||||
|
|
|
|||
|
|
@ -14,7 +14,7 @@ workflow test_gatk4_revertsam {
|
|||
|
||||
workflow test_gatk4_revertsam_stubs {
|
||||
input = [ [ id:'test' ], // meta map
|
||||
"foo_paired_end.bam"
|
||||
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
||||
]
|
||||
|
||||
GATK4_REVERTSAM ( input )
|
||||
|
|
|
|||
|
|
@ -9,7 +9,7 @@
|
|||
- path: output/gatk4/versions.yml
|
||||
|
||||
- name: gatk4 revertsam test_gatk4_revertsam_stubs
|
||||
command: nextflow run ./tests/modules/gatk4/revertsam -entry test_gatk4_revertsam -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/revertsam/nextflow.config -stub-run
|
||||
command: nextflow run ./tests/modules/gatk4/revertsam -entry test_gatk4_revertsam_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/revertsam/nextflow.config -stub-run
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4/revertsam
|
||||
|
|
|
|||
|
|
@ -21,8 +21,8 @@ workflow test_gatk4_samtofastq_paired_end {
|
|||
}
|
||||
|
||||
workflow test_gatk4_samtofastq_paired_end_stubs {
|
||||
input = [ [ id:'test', single_end: false ], // meta map
|
||||
[ "foo_paired_end.bam" ]
|
||||
input = [ [ id:'test', single_end: true ], // meta map
|
||||
[ file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
|
||||
]
|
||||
|
||||
GATK4_SAMTOFASTQ ( input )
|
||||
|
|
|
|||
|
|
@ -21,7 +21,7 @@
|
|||
- path: output/gatk4/versions.yml
|
||||
|
||||
- name: gatk4 samtofastq test_gatk4_samtofastq_paired_end_stubs
|
||||
command: nextflow run ./tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/samtofastq/nextflow.config -stub-run
|
||||
command: nextflow run ./tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/samtofastq/nextflow.config -stub-run
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4/samtofastq
|
||||
|
|
|
|||
|
|
@ -25,7 +25,7 @@ workflow test_samtools_view_cram {
|
|||
|
||||
workflow test_samtools_view_stubs {
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
"foo_paired_end.bam",
|
||||
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
|
||||
[]
|
||||
]
|
||||
|
||||
|
|
|
|||
|
|
@ -16,7 +16,7 @@
|
|||
- path: output/samtools/test.cram
|
||||
|
||||
- name: samtools view test_samtools_view_stubs
|
||||
command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view -c ./tests/config/nextflow.config -c ./tests/modules/samtools/view/nextflow.config -stub-run
|
||||
command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_stubs -c ./tests/config/nextflow.config -c ./tests/modules/samtools/view/nextflow.config -stub-run
|
||||
tags:
|
||||
- samtools/view
|
||||
- samtools
|
||||
|
|
|
|||
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
|
||||
|
||||
include { ANNOTATION_SNPEFF } from '../../../../../subworkflows/nf-core/annotation_snpeff/main'
|
||||
include { ANNOTATION_SNPEFF } from '../../../../../subworkflows/nf-core/annotation/snpeff/main'
|
||||
|
||||
workflow annotation_snpeff {
|
||||
input = [
|
||||
|
|
|
|||
Loading…
Reference in a new issue