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fix some tests
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@nvnieuwk
nvnieuwk committed Jan 9, 2025
1 parent 717ca2a commit f54266e
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Showing 3 changed files with 39 additions and 39 deletions.
24 changes: 12 additions & 12 deletions subworkflows/local/vcf_annotate_all/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -22,15 +22,15 @@ workflow VCF_ANNOTATE_ALL {

main:
def ch_reports = Channel.empty()
def vcf_ann = Channel.empty()
def tab_ann = Channel.empty()
def json_ann = Channel.empty()
def vcf_annotated = Channel.empty()
def tab_annotated = Channel.empty()
def json_annotated = Channel.empty()
def ch_versions = Channel.empty()

if (tools.split(',').contains('bcfann')) {
VCF_ANNOTATE_BCFTOOLS(vcf)

vcf_ann = vcf_ann.mix(VCF_ANNOTATE_BCFTOOLS.out.vcf_tbi)
vcf_annotated = vcf_annotated.mix(VCF_ANNOTATE_BCFTOOLS.out.vcf_tbi)
ch_versions = ch_versions.mix(VCF_ANNOTATE_BCFTOOLS.out.versions)
}

Expand All @@ -39,7 +39,7 @@ workflow VCF_ANNOTATE_ALL {
VCF_ANNOTATE_SNPEFF(vcf, snpeff_db, snpeff_cache)

ch_reports = ch_reports.mix(VCF_ANNOTATE_SNPEFF.out.reports.map{ _meta, reports_ -> [ reports_ ] })
vcf_ann = vcf_ann.mix(VCF_ANNOTATE_SNPEFF.out.vcf_tbi)
vcf_annotated = vcf_annotated.mix(VCF_ANNOTATE_SNPEFF.out.vcf_tbi)
ch_versions = ch_versions.mix(VCF_ANNOTATE_SNPEFF.out.versions)
}

Expand All @@ -48,7 +48,7 @@ workflow VCF_ANNOTATE_ALL {
VCF_ANNOTATE_MERGE(vcf_ann_for_merge, fasta, vep_genome, vep_species, vep_cache_version, vep_cache, vep_extra_files)

ch_reports = ch_reports.mix(VCF_ANNOTATE_MERGE.out.reports)
vcf_ann = vcf_ann.mix(VCF_ANNOTATE_MERGE.out.vcf_tbi)
vcf_annotated = vcf_annotated.mix(VCF_ANNOTATE_MERGE.out.vcf_tbi)
ch_versions = ch_versions.mix(VCF_ANNOTATE_MERGE.out.versions)
}

Expand All @@ -57,16 +57,16 @@ workflow VCF_ANNOTATE_ALL {
VCF_ANNOTATE_ENSEMBLVEP(vcf_for_vep, fasta, vep_genome, vep_species, vep_cache_version, vep_cache, vep_extra_files)

ch_reports = ch_reports.mix(VCF_ANNOTATE_ENSEMBLVEP.out.reports)
vcf_ann = vcf_ann.mix(VCF_ANNOTATE_ENSEMBLVEP.out.vcf_tbi)
tab_ann = tab_ann.mix(VCF_ANNOTATE_ENSEMBLVEP.out.tab)
json_ann = json_ann.mix(VCF_ANNOTATE_ENSEMBLVEP.out.json)
vcf_annotated = vcf_annotated.mix(VCF_ANNOTATE_ENSEMBLVEP.out.vcf_tbi)
tab_annotated = tab_annotated.mix(VCF_ANNOTATE_ENSEMBLVEP.out.tab)
json_annotated = json_annotated.mix(VCF_ANNOTATE_ENSEMBLVEP.out.json)
ch_versions = ch_versions.mix(VCF_ANNOTATE_ENSEMBLVEP.out.versions)
}

emit:
vcf_ann // channel: [ val(meta), vcf.gz, vcf.gz.tbi ]
tab_ann
json_ann
vcf_ann = vcf_annotated // channel: [ val(meta), vcf.gz, vcf.gz.tbi ]
tab_ann = tab_annotated
json_ann = json_annotated
reports = ch_reports // path: *.html
versions = ch_versions // path: ch_versions.yml
}
18 changes: 9 additions & 9 deletions tests/all_inputs.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -31,29 +31,29 @@
"gatk4": "4.5.0.0"
},
"PICARD_MARKDUPLICATES": {
"picard": "3.1.1"
"picard": "3.3.0"
},
"SAMTOOLS_FLAGSTAT": {
"samtools": "1.19.2"
"samtools": 1.21
},
"SAMTOOLS_IDXSTATS": {
"samtools": "1.19.2"
"samtools": 1.21
},
"SAMTOOLS_INDEX": {
"samtools": "1.19.2"
"samtools": 1.21
},
"SAMTOOLS_MERGE": {
"samtools": "1.19.2"
},
"SAMTOOLS_SORT": {
"samtools": "1.19.2"
"samtools": 1.21
},
"SAMTOOLS_STATS": {
"samtools": "1.19.2"
"samtools": 1.21
},
"STAR_ALIGN": {
"star": "2.7.10a",
"samtools": 1.18,
"star": "2.7.11b",
"samtools": 1.21,
"gawk": "5.1.0"
},
"TABIX": {
Expand Down Expand Up @@ -128,6 +128,6 @@
"nf-test": "0.9.1",
"nextflow": "24.10.3"
},
"timestamp": "2025-01-08T13:56:22.79954652"
"timestamp": "2025-01-09T16:41:24.471237186"
}
}
36 changes: 18 additions & 18 deletions tests/annotation.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -297,29 +297,29 @@
"gatk4": "4.5.0.0"
},
"PICARD_MARKDUPLICATES": {
"picard": "3.1.1"
"picard": "3.3.0"
},
"SAMTOOLS_FLAGSTAT": {
"samtools": "1.19.2"
"samtools": 1.21
},
"SAMTOOLS_IDXSTATS": {
"samtools": "1.19.2"
"samtools": 1.21
},
"SAMTOOLS_INDEX": {
"samtools": "1.19.2"
"samtools": 1.21
},
"SAMTOOLS_MERGE": {
"samtools": "1.19.2"
},
"SAMTOOLS_SORT": {
"samtools": "1.19.2"
"samtools": 1.21
},
"SAMTOOLS_STATS": {
"samtools": "1.19.2"
"samtools": 1.21
},
"STAR_ALIGN": {
"star": "2.7.10a",
"samtools": 1.18,
"star": "2.7.11b",
"samtools": 1.21,
"gawk": "5.1.0"
},
"TABIX": {
Expand Down Expand Up @@ -504,7 +504,7 @@
"nf-test": "0.9.1",
"nextflow": "24.10.3"
},
"timestamp": "2025-01-08T13:37:37.774766173"
"timestamp": "2025-01-09T16:51:32.004274594"
},
"Run with profile test | annotation with snpeff": {
"content": [
Expand Down Expand Up @@ -538,32 +538,32 @@
"gatk4": "4.5.0.0"
},
"PICARD_MARKDUPLICATES": {
"picard": "3.1.1"
"picard": "3.3.0"
},
"SAMTOOLS_FLAGSTAT": {
"samtools": "1.19.2"
"samtools": 1.21
},
"SAMTOOLS_IDXSTATS": {
"samtools": "1.19.2"
"samtools": 1.21
},
"SAMTOOLS_INDEX": {
"samtools": "1.19.2"
"samtools": 1.21
},
"SAMTOOLS_MERGE": {
"samtools": "1.19.2"
},
"SAMTOOLS_SORT": {
"samtools": "1.19.2"
"samtools": 1.21
},
"SAMTOOLS_STATS": {
"samtools": "1.19.2"
"samtools": 1.21
},
"SNPEFF_SNPEFF": {
"snpeff": "5.1d"
},
"STAR_ALIGN": {
"star": "2.7.10a",
"samtools": 1.18,
"star": "2.7.11b",
"samtools": 1.21,
"gawk": "5.1.0"
},
"TABIX": {
Expand Down Expand Up @@ -644,6 +644,6 @@
"nf-test": "0.9.1",
"nextflow": "24.10.3"
},
"timestamp": "2025-01-08T13:31:39.422563362"
"timestamp": "2025-01-09T16:47:00.48306332"
}
}

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