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Adding meta to multivcfanalyzer, updating test to nf-test #5773

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merged 11 commits into from
Jun 21, 2024
Merged

Adding meta to multivcfanalyzer, updating test to nf-test #5773

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8781136
Adding meta to multivcfanalyzer, updating test to nf-test
aidaanva Jun 7, 2024
252f93c
Merge branch 'master' into multivcfanalyzer_fix_meta
aidaanva Jun 7, 2024
c8f0851
Apply suggestions from code review
aidaanva Jun 7, 2024
046abd7
fix meta.yml
aidaanva Jun 7, 2024
981713d
Merge branch 'multivcfanalyzer_fix_meta' of github.com:aidaanva/modul…
aidaanva Jun 7, 2024
8182320
Merge branch 'master' into multivcfanalyzer_fix_meta
aidaanva Jun 7, 2024
5ae52b5
Add sort to vcfs
SPPearce Jun 18, 2024
99cefa4
Merge branch 'master' into multivcfanalyzer_fix_meta
SPPearce Jun 18, 2024
d4c7c72
Add tab to tags
SPPearce Jun 18, 2024
0b5df66
add checks for files due to failing md5 sums across docker,conda,sing…
aidaanva Jun 21, 2024
4317d13
Merge branch 'master' into multivcfanalyzer_fix_meta
aidaanva Jun 21, 2024
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60 changes: 44 additions & 16 deletions modules/nf-core/multivcfanalyzer/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -8,30 +8,30 @@ process MULTIVCFANALYZER {
'biocontainers/multivcfanalyzer:0.85.2--hdfd78af_1' }"

input:
path vcfs
path fasta
path snpeff_results
path gff
tuple val(meta), path(vcfs)
tuple val(meta2), path(fasta)
tuple val(meta3), path(snpeff_results)
tuple val(meta4), path(gff)
val allele_freqs
val genotype_quality
val coverage
val homozygous_freq
val heterozygous_freq
path gff_exclude
tuple val(meta5), path(gff_exclude)


output:
path('fullAlignment.fasta.gz') , emit: full_alignment
path('info.txt') , emit: info_txt
path('snpAlignment.fasta.gz') , emit: snp_alignment
path('snpAlignmentIncludingRefGenome.fasta.gz') , emit: snp_genome_alignment
path('snpStatistics.tsv') , emit: snpstatistics
path('snpTable.tsv') , emit: snptable
path('snpTableForSnpEff.tsv') , emit: snptable_snpeff
path('snpTableWithUncertaintyCalls.tsv') , emit: snptable_uncertainty
path('structureGenotypes.tsv') , emit: structure_genotypes
path('structureGenotypes_noMissingData-Columns.tsv') , emit: structure_genotypes_nomissing
path('MultiVCFAnalyzer.json') , emit: json
tuple val(meta), path('fullAlignment.fasta.gz') , emit: full_alignment
tuple val(meta), path('info.txt') , emit: info_txt
tuple val(meta), path('snpAlignment.fasta.gz') , emit: snp_alignment
tuple val(meta), path('snpAlignmentIncludingRefGenome.fasta.gz') , emit: snp_genome_alignment
tuple val(meta), path('snpStatistics.tsv') , emit: snpstatistics
tuple val(meta), path('snpTable.tsv') , emit: snptable
tuple val(meta), path('snpTableForSnpEff.tsv') , emit: snptable_snpeff
tuple val(meta), path('snpTableWithUncertaintyCalls.tsv') , emit: snptable_uncertainty
tuple val(meta), path('structureGenotypes.tsv') , emit: structure_genotypes
tuple val(meta), path('structureGenotypes_noMissingData-Columns.tsv') , emit: structure_genotypes_nomissing
tuple val(meta), path('MultiVCFAnalyzer.json') , emit: json
path "versions.yml" , emit: versions

when:
Expand Down Expand Up @@ -69,4 +69,32 @@ process MULTIVCFANALYZER {
multivcfanalyzer: \$(echo \$(multivcfanalyzer --help | head -n 1) | cut -f 3 -d ' ' )
END_VERSIONS
"""
stub:

def args2 = task.ext.args2 ?: ''

def cmd_snpeff_results = snpeff_results ? "${snpeff_results}" : "NA"
def cmd_gff = gff ? "${gff}" : "NA"
def cmd_allele_freqs = allele_freqs ? "T" : "F"
def cmd_gff_exclude = gff_exclude ? "${gff}" : "NA"

"""
echo "" | gzip > fullAlignment.fasta.gz
touch info.txt
echo "" | gzip > snpAlignment.fasta.gz
echo "" | gzip > snpAlignmentIncludingRefGenome.fasta.gz
touch snpStatistics.tsv
touch snpTable.tsv
touch snpTableForSnpEff.tsv
touch snpTableWithUncertaintyCalls.tsv
touch structureGenotypes.tsv
touch structureGenotypes_noMissingData-Columns.tsv
touch MultiVCFAnalyzer.json

cat <<-END_VERSIONS > versions.yml
"${task.process}":
multivcfanalyzer: \$(echo \$(multivcfanalyzer --help | head -n 1) | cut -f 3 -d ' ' )
END_VERSIONS

"""
}
124 changes: 124 additions & 0 deletions modules/nf-core/multivcfanalyzer/tests/main.nf.test
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@@ -0,0 +1,124 @@
nextflow_process {

name "Test Process MULTIVCFANALYZER"
script "../main.nf"
process "MULTIVCFANALYZER"

tag "modules"
tag "modules_nfcore"
tag "multivcfanalyzer"

setup {
run("GATK_UNIFIEDGENOTYPER") {
script "../../gatk/unifiedgenotyper/main.nf"
process{
"""
input[0] = Channel.of([ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
],
[ [ id:'test2' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true)
]
)
input[1] = [ [],
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
input[2] = [ [],
file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
]
input[3] = [ [],
file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
]
input[4] = [[],[]]
input[5] = [[],[]]
input[6] = [[],[]]
input[7] = [[],[]]
"""
}
}
run("GUNZIP") {
script "../../gunzip/main.nf"
process{
"""
input[0] = GATK_UNIFIEDGENOTYPER.out.vcf
"""
}
}
}

test("sarscov2 - vcf") {

when {
process {
"""
input[0] = GUNZIP.out.gunzip.collect{ meta, vcf -> vcf }.map{ vcf -> [[ id: 'testVCF'], vcf]}
input[1] = [ [] ,
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
input[2] = [[],[]]
input[3] = [[],[]]
input[4] = true
input[5] = 30
input[6] = 5
input[7] = 0.8
input[8] = 0.2
input[9] = [[],[]]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out.full_alignment,
process.out.snp_alignment,
process.out.snp_genome_alignment,
process.out.snpstatistics,
process.out.snptable,
process.out.snptable_snpeff,
process.out.snptable_uncertainty,
process.out.structure_genotypes,
process.out.structure_genotypes_nomissing,
process.out.json,
process.out.versions,
file(process.out.info_txt[0][1]).readLines().any { it.contains('Run finished:') }).match() }
)
}

}

test("sarscov2 - vcf - stub") {

options "-stub"

when {
process {
"""
input[0] = GUNZIP.out.gunzip.collect{ meta, vcf -> vcf }.map{ vcf -> [[ id: 'testVCF'], vcf]}
input[1] = [ [] ,
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
input[2] = [[],[]]
input[3] = [[],[]]
input[4] = true
input[5] = 30
input[6] = 5
input[7] = 0.8
input[8] = 0.2
input[9] = [[],[]]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}

}

}
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