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Merge branch 'master' into meryl_count

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Mahesh Binzer-Panchal 2022-05-09 10:05:28 +02:00 committed by GitHub
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27 changed files with 278 additions and 336 deletions
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7
modules/snapaligner/paired/main.nf → modules/snapaligner/align/main.nf
View file

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

6
modules/snapaligner/paired/meta.yml → modules/snapaligner/align/meta.yml
View file

@ -1,5 +1,5 @@
name: "snapaligner_paired" name: "snapaligner_align"
description: Performs paired end fastq alignment to a fasta reference using SNAP description: Performs fastq alignment to a fasta reference using SNAP
keywords: keywords:
- alignment - alignment
- map - map
@ -22,7 +22,7 @@ input:
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- reads: - reads:
type: file type: file
description: List of input fastq files of size 2 for fastq or 1 for bam description: List of input fastq files of size 2 for paired fastq or 1 for bam or single fastq
pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}" pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}"
- index: - index:
type: file type: file

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
View file

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

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

10
tests/config/pytest_modules.yml
View file

@ -1771,13 +1771,9 @@ snapaligner/index:
- modules/snapaligner/index/** - modules/snapaligner/index/**
- tests/modules/snapaligner/index/** - tests/modules/snapaligner/index/**
snapaligner/paired: snapaligner/align:
- modules/snapaligner/paired/** - modules/snapaligner/align/**
- tests/modules/snapaligner/paired/** - tests/modules/snapaligner/align/**
snapaligner/single:
- modules/snapaligner/single/**
- tests/modules/snapaligner/single/**
snpdists: snpdists:
- modules/snpdists/** - modules/snpdists/**

253
tests/config/test_data.config
View file

@ -125,6 +125,7 @@ params {
genome_gff3 = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gff3" genome_gff3 = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gff3"
genome_gtf = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gtf" genome_gtf = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gtf"
genome_interval_list = "${test_data_dir}/genomics/homo_sapiens/genome/genome.interval_list" genome_interval_list = "${test_data_dir}/genomics/homo_sapiens/genome/genome.interval_list"
genome_multi_interval_bed = "${test_data_dir}/genomics/homo_sapiens/genome/genome.multi_intervals.bed"
genome_sizes = "${test_data_dir}/genomics/homo_sapiens/genome/genome.sizes" genome_sizes = "${test_data_dir}/genomics/homo_sapiens/genome/genome.sizes"
genome_bed = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed" genome_bed = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed"
genome_header = "${test_data_dir}/genomics/homo_sapiens/genome/genome.header" genome_header = "${test_data_dir}/genomics/homo_sapiens/genome/genome.header"
@ -181,16 +182,16 @@ params {
vcfanno_toml = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml" vcfanno_toml = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml"
} }
'pangenome' { 'pangenome' {
pangenome_fa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa" pangenome_fa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa"
pangenome_fa_gz = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa.gz" pangenome_fa_gz = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa.gz"
pangenome_paf = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf" pangenome_paf = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf"
pangenome_paf_gz = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf.gz" pangenome_paf_gz = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf.gz"
pangenome_seqwish_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.seqwish.gfa" pangenome_seqwish_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.seqwish.gfa"
pangenome_smoothxg_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.smoothxg.gfa" pangenome_smoothxg_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.smoothxg.gfa"
pangenome_gfaffix_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.gfaffix.gfa" pangenome_gfaffix_gfa = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.gfaffix.gfa"
'odgi' { 'odgi' {
pangenome_og = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.og" pangenome_og = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.og"
pangenome_lay = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.lay" pangenome_lay = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.lay"
} }
} }
'illumina' { 'illumina' {
@ -211,131 +212,131 @@ params {
test_paired_end_hla = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam" test_paired_end_hla = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam"
test_paired_end_hla_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam" test_paired_end_hla_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam"
test_paired_end_hla_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam.bai" test_paired_end_hla_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam.bai"
test2_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam"
test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai"
test2_paired_end_name_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam"
test2_paired_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam"
test2_paired_end_markduplicates_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam.bai"
test2_paired_end_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam"
test2_paired_end_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai"
test2_paired_end_umi_consensus_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_consensus.bam"
test2_paired_end_umi_converted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_converted.bam"
test2_paired_end_umi_grouped_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_grouped.bam"
test2_paired_end_umi_histogram_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_histogram.txt"
test2_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam"
test2_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam"
test2_paired_end_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam"
test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai"
test2_paired_end_name_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam"
test2_paired_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam"
test2_paired_end_markduplicates_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam.bai"
test2_paired_end_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam"
test2_paired_end_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai"
test2_paired_end_umi_consensus_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_consensus.bam"
test2_paired_end_umi_converted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_converted.bam"
test2_paired_end_umi_grouped_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_grouped.bam"
test2_paired_end_umi_histogram_txt = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_histogram.txt"
test2_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam"
test2_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam"
mitochon_standin_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam" mitochon_standin_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam"
mitochon_standin_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai" mitochon_standin_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai"
test_paired_end_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram" test_paired_end_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram"
test_paired_end_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai" test_paired_end_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai"
test_paired_end_markduplicates_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram" test_paired_end_markduplicates_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram"
test_paired_end_markduplicates_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram.crai" test_paired_end_markduplicates_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram.crai"
test_paired_end_recalibrated_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram" test_paired_end_recalibrated_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram"
test_paired_end_recalibrated_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai" test_paired_end_recalibrated_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai"
test2_paired_end_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram" test2_paired_end_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram"
test2_paired_end_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram.crai" test2_paired_end_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram.crai"
test2_paired_end_markduplicates_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram" test2_paired_end_markduplicates_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram"
test2_paired_end_markduplicates_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram.crai" test2_paired_end_markduplicates_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram.crai"
test2_paired_end_recalibrated_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram" test2_paired_end_recalibrated_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram"
test2_paired_end_recalibrated_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai" test2_paired_end_recalibrated_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai"
test_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz" test_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz"
test_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz" test_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz"
test_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz" test_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz"
test_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz" test_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz"
test2_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz" test2_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz"
test2_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz" test2_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz"
test2_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz" test2_umi_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz"
test2_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz" test2_umi_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz"
test_rnaseq_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz" test_rnaseq_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz"
test_rnaseq_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz" test_rnaseq_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz"
test_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table" test_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table"
test2_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table" test2_baserecalibrator_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table"
test_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.pileups.table" test_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.pileups.table"
test2_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.pileups.table" test2_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.pileups.table"
test_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz" test_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
test_pon_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz" test_pon_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz"
test2_haplotc_ann_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz" test2_haplotc_ann_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz"
test2_haplotc_ann_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi" test2_haplotc_ann_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi"
test2_recal = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal" test2_recal = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal"
test2_recal_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx" test2_recal_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx"
test2_tranches = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches" test2_tranches = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches"
test2_allele_specific_recal = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal" test2_allele_specific_recal = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal"
test2_allele_specific_recal_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal.idx" test2_allele_specific_recal_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal.idx"
test2_allele_specific_tranches = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.tranches" test2_allele_specific_tranches = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.tranches"
test_test2_paired_mutect2_calls_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz" test_test2_paired_mutect2_calls_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz"
test_test2_paired_mutect2_calls_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi" test_test2_paired_mutect2_calls_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi"
test_test2_paired_mutect2_calls_vcf_gz_stats = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats" test_test2_paired_mutect2_calls_vcf_gz_stats = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats"
test_test2_paired_mutect2_calls_f1r2_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz" test_test2_paired_mutect2_calls_f1r2_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz"
test_test2_paired_mutect2_calls_artifact_prior_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired_mutect2_calls.artifact-prior.tar.gz" test_test2_paired_mutect2_calls_artifact_prior_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired_mutect2_calls.artifact-prior.tar.gz"
test_test2_paired_segmentation_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.segmentation.table" test_test2_paired_segmentation_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.segmentation.table"
test_test2_paired_contamination_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.contamination.table" test_test2_paired_contamination_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.contamination.table"
test_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf" test_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf"
test_genome_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz" test_genome_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz"
test_genome_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi" test_genome_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi"
test_genome_vcf_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx" test_genome_vcf_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx"
test2_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf" test2_genome_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf"
test2_genome_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz" test2_genome_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz"
test2_genome_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi" test2_genome_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi"
test2_genome_vcf_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.idx" test2_genome_vcf_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.idx"
test_genome21_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz" test_genome21_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz"
test_genome21_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi" test_genome21_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi"
test_mpileup = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz" test_mpileup = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz"
test2_mpileup = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz" test2_mpileup = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz"
test_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak" test_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak"
test2_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak" test2_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak"
test_narrowpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak" test_narrowpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak"
test2_narrowpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak" test2_narrowpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak"
test_10x_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R1_001.fastq.gz" test_10x_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R1_001.fastq.gz"
test_10x_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R2_001.fastq.gz" test_10x_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R2_001.fastq.gz"
test_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test.yak" test_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test.yak"
test2_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test2.yak" test2_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test2.yak"
cutandrun_bedgraph_test_1 = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph" cutandrun_bedgraph_test_1 = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph"
cutandrun_bedgraph_test_2 = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_igg_test_1.bedGraph" cutandrun_bedgraph_test_2 = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_igg_test_1.bedGraph"
test_rnaseq_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf" test_rnaseq_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf"
test_sv_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz" test_sv_vcf = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz"
test_pytor = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor" test_pytor = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor"
} }
'pacbio' { 'pacbio' {
primers = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta" primers = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"
alz = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam" alz = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam"
alzpbi = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam.pbi" alzpbi = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam.pbi"
ccs = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.bam" ccs = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.bam"
ccs_fa = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta" ccs_fa = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta"
ccs_fa_gz = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta.gz" ccs_fa_gz = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta.gz"
ccs_fq = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq" ccs_fq = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq"
ccs_fq_gz = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz" ccs_fq_gz = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz"
ccs_xml = "${test_data_dir}/genomics/homo_sapiens/pacbio/xml/alz.ccs.consensusreadset.xml" ccs_xml = "${test_data_dir}/genomics/homo_sapiens/pacbio/xml/alz.ccs.consensusreadset.xml"
hifi = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz" hifi = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz"
lima = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam" lima = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam"
refine = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam" refine = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam"
cluster = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.bam" cluster = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.bam"
singletons = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.bam" singletons = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.bam"
aligned = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam" aligned = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam"
alignedbai = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam.bai" alignedbai = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam.bai"
genemodel1 = "${test_data_dir}/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed" genemodel1 = "${test_data_dir}/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed"
genemodel2 = "${test_data_dir}/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed" genemodel2 = "${test_data_dir}/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed"
filelist = "${test_data_dir}/genomics/homo_sapiens/pacbio/txt/filelist.txt" filelist = "${test_data_dir}/genomics/homo_sapiens/pacbio/txt/filelist.txt"
} }
} }
'bacteroides_fragilis' { 'bacteroides_fragilis' {
@ -393,31 +394,31 @@ params {
} }
'generic' { 'generic' {
'csv' { 'csv' {
test_csv = "${test_data_dir}/generic/csv/test.csv" test_csv = "${test_data_dir}/generic/csv/test.csv"
} }
'notebooks' { 'notebooks' {
rmarkdown = "${test_data_dir}/generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd" rmarkdown = "${test_data_dir}/generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd"
ipython_md = "${test_data_dir}/generic/notebooks/jupyter/ipython_notebook.md" ipython_md = "${test_data_dir}/generic/notebooks/jupyter/ipython_notebook.md"
ipython_ipynb = "${test_data_dir}/generic/notebooks/jupyter/ipython_notebook.ipynb" ipython_ipynb = "${test_data_dir}/generic/notebooks/jupyter/ipython_notebook.ipynb"
} }
'tsv' { 'tsv' {
test_tsv = "${test_data_dir}/generic/tsv/test.tsv" test_tsv = "${test_data_dir}/generic/tsv/test.tsv"
} }
'txt' { 'txt' {
hello = "${test_data_dir}/generic/txt/hello.txt" hello = "${test_data_dir}/generic/txt/hello.txt"
} }
'cnn' { 'cnn' {
reference = "${test_data_dir}/generic/cnn/reference.cnn" reference = "${test_data_dir}/generic/cnn/reference.cnn"
} }
'cooler'{ 'cooler'{
test_pairix_pair_gz = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz" test_pairix_pair_gz = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz"
test_pairix_pair_gz_px2 = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2" test_pairix_pair_gz_px2 = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2"
test_pairs_pair = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.sample1.pairs" test_pairs_pair = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.sample1.pairs"
test_tabix_pair_gz = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz" test_tabix_pair_gz = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz"
test_tabix_pair_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz.tbi" test_tabix_pair_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz.tbi"
hg19_chrom_sizes = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.chrom.sizes" hg19_chrom_sizes = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.chrom.sizes"
test_merge_cool = "${test_data_dir}/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cool" test_merge_cool = "${test_data_dir}/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cool"
test_merge_cool_cp2 = "${test_data_dir}/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cp2.cool" test_merge_cool_cp2 = "${test_data_dir}/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cp2.cool"
} }
} }

8
tests/modules/gatk4/mergebamalignment/main.nf
View file

@ -17,11 +17,11 @@ workflow test_gatk4_mergebamalignment {
workflow test_gatk4_mergebamalignment_stubs { workflow test_gatk4_mergebamalignment_stubs {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
"test_foo.bam", file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
"test_bar.bam" file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
] ]
fasta = "genome.fasta" fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
dict = "genome.fasta.dict" dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
GATK4_MERGEBAMALIGNMENT ( input, fasta, dict ) GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
} }

2
tests/modules/gatk4/mergebamalignment/test.yml
View file

@ -9,7 +9,7 @@
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
- name: gatk4 mergebamalignment test_gatk4_mergebamalignment_stubs - 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: tags:
- gatk4 - gatk4
- gatk4/mergebamalignment - gatk4/mergebamalignment

24
tests/modules/gatk4/mutect2/main.nf
View file

@ -120,23 +120,23 @@ workflow test_gatk4_mutect2_mitochondria {
} }
workflow test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs { workflow test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs {
input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
[ "foo_paired.bam", [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
"foo_paired2.bam" file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
], ],
[ "foo_paired.bam.bai", [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
"foo_paired2.bam.bai" file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)
], ],
[] []
] ]
fasta = "genome.fasta" fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
fai = "genome.fasta.fai" fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
dict = "genome.fasta.dict" dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
germline_resource = "genome_gnomAD.r2.1.1.vcf.gz" germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
germline_resource_tbi = "genome_gnomAD.r2.1.1.vcf.gz.tbi" germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
panel_of_normals = "genome_mills_and_1000G.indels.hg38.vcf.gz" panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
panel_of_normals_tbi = "genome_mills_and_1000G.indels.hg38.vcf.gz.tbi" 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 ) GATK4_MUTECT2_F1R2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
} }

2
tests/modules/gatk4/mutect2/test.yml
View file

@ -71,7 +71,7 @@
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
- name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs - 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: tags:
- gatk4 - gatk4
- gatk4/mutect2 - gatk4/mutect2

2
tests/modules/gatk4/revertsam/main.nf
View file

@ -14,7 +14,7 @@ workflow test_gatk4_revertsam {
workflow test_gatk4_revertsam_stubs { workflow test_gatk4_revertsam_stubs {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
"foo_paired_end.bam" file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
] ]
GATK4_REVERTSAM ( input ) GATK4_REVERTSAM ( input )

2
tests/modules/gatk4/revertsam/test.yml
View file

@ -9,7 +9,7 @@
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
- name: gatk4 revertsam test_gatk4_revertsam_stubs - 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: tags:
- gatk4 - gatk4
- gatk4/revertsam - gatk4/revertsam

4
tests/modules/gatk4/samtofastq/main.nf
View file

@ -21,8 +21,8 @@ workflow test_gatk4_samtofastq_paired_end {
} }
workflow test_gatk4_samtofastq_paired_end_stubs { workflow test_gatk4_samtofastq_paired_end_stubs {
input = [ [ id:'test', single_end: false ], // meta map input = [ [ id:'test', single_end: true ], // meta map
[ "foo_paired_end.bam" ] [ file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
] ]
GATK4_SAMTOFASTQ ( input ) GATK4_SAMTOFASTQ ( input )

2
tests/modules/gatk4/samtofastq/test.yml
View file

@ -21,7 +21,7 @@
- path: output/gatk4/versions.yml - path: output/gatk4/versions.yml
- name: gatk4 samtofastq test_gatk4_samtofastq_paired_end_stubs - 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: tags:
- gatk4 - gatk4
- gatk4/samtofastq - gatk4/samtofastq

2
tests/modules/samtools/view/main.nf
View file

@ -25,7 +25,7 @@ workflow test_samtools_view_cram {
workflow test_samtools_view_stubs { workflow test_samtools_view_stubs {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
"foo_paired_end.bam", file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
[] []
] ]

2
tests/modules/samtools/view/test.yml
View file

@ -16,7 +16,7 @@
- path: output/samtools/test.cram - path: output/samtools/test.cram
- name: samtools view test_samtools_view_stubs - 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: tags:
- samtools/view - samtools/view
- samtools - samtools

29
tests/modules/snapaligner/align/main.nf Normal file
View 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 )
}

0
tests/modules/snapaligner/paired/nextflow.config → tests/modules/snapaligner/align/nextflow.config
View file

19
tests/modules/snapaligner/align/test.yml Normal file
View 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

17
tests/modules/snapaligner/paired/main.nf
View file

@ -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
View file

@ -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
View file

@ -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
View file

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

9
tests/modules/snapaligner/single/test.yml
View file

@ -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
View file

@ -2,7 +2,7 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { ANNOTATION_SNPEFF } from '../../../../../subworkflows/nf-core/annotation_snpeff/main' include { ANNOTATION_SNPEFF } from '../../../../../subworkflows/nf-core/annotation/snpeff/main'
workflow annotation_snpeff { workflow annotation_snpeff {
input = [ input = [