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fixed failig test case
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@mattheww95
mattheww95 committed Nov 12, 2024
1 parent 6ba57b0 commit a2c56a8
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Showing 2 changed files with 42 additions and 46 deletions.
4 changes: 0 additions & 4 deletions modules/local/report.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -41,9 +41,7 @@ process REPORT{
def report_tag = test_in[i+1]
def report_value = test_in[i+2]

println meta_data
if(!sample_data.containsKey(meta_data.sample)){
// Todo issue grabbing correct tag is here
sample_data[meta_data.sample] = [:]
sample_data[meta_data.sample]["meta"] = [:]
}
Expand Down Expand Up @@ -680,8 +678,6 @@ def generate_qc_data(data, search_phrases, qc_species_tag){
def species_tag_location = 0
for(k in data){
if(!k.value.meta.metagenomic){
println k.value
println k.key
def species = get_species(k.value[k.key][top_hit_tag], search_phrases, shortest_token)
// update coverage first so its values can be used in generating qc messages
generate_coverage_data(data[k.key], params.coverage_calc_fields.bp_field, species)
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84 changes: 42 additions & 42 deletions tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -155,45 +155,45 @@ nextflow_pipeline {
// parse output json file
def json = path("$launchDir/results/FinalReports/Aggregated/Json/final_report.json").json

assert json.short.short.RawReadSummary.R1."total_bp".equals(118750)
assert json.short.short.RawReadSummary.R1."total_reads".equals(475)
assert json.short.short.RawReadSummary.R1."read_qual_mean".equals(40.0)
assert json.short.short.RawReadSummary.R1."mean_sequence_length".equals(250.0)

assert json.short.short.FastP.summary.sequencing.equals("paired end (250 cycles + 250 cycles)")
assert json.short.short.FastP.summary.before_filtering.total_reads.equals(950)
assert json.short.short.FastP.filtering_result.passed_filter_reads.equals(950)
assert json.short.short.FastP.filtering_result.low_quality_reads.equals(0)
assert json.short.short.FastP.insert_size.peak.equals(347)

//assert json.short.meta.metagenomic.equals(false) // Currently, this is "null".
assert json.short.meta.assembly.equals(false)
assert json.short.meta.hybrid.equals(false)
assert json.short.meta.single_end.equals(false)
assert json.short.meta.merge.equals(false)
assert json.short.meta.downsampled.equals(false)

assert json.short.short.AssemblyCompleted.equals(true)
assert json.short.short.QUAST."0"."Total length (>= 0 bp)".equals("4949")
assert json.short.short.QUAST."0"."Largest contig".equals("4949")
assert json.short.short.QUAST."0"."GC (%)".equals("52.96")
assert json.short.short.QUAST."0"."Avg. coverage depth".equals("47")
assert json.INX.INX.RawReadSummary.R1."total_bp".equals(118750)
assert json.INX.INX.RawReadSummary.R1."total_reads".equals(475)
assert json.INX.INX.RawReadSummary.R1."read_qual_mean".equals(40.0)
assert json.INX.INX.RawReadSummary.R1."mean_sequence_length".equals(250.0)

assert json.INX.INX.FastP.summary.sequencing.equals("paired end (250 cycles + 250 cycles)")
assert json.INX.INX.FastP.summary.before_filtering.total_reads.equals(950)
assert json.INX.INX.FastP.filtering_result.passed_filter_reads.equals(950)
assert json.INX.INX.FastP.filtering_result.low_quality_reads.equals(0)
assert json.INX.INX.FastP.insert_size.peak.equals(347)

//assert json.INX.meta.metagenomic.equals(false) // Currently, this is "null".
assert json.INX.meta.assembly.equals(false)
assert json.INX.meta.hybrid.equals(false)
assert json.INX.meta.single_end.equals(false)
assert json.INX.meta.merge.equals(false)
assert json.INX.meta.downsampled.equals(false)

assert json.INX.INX.AssemblyCompleted.equals(true)
assert json.INX.INX.QUAST."0"."Total length (>= 0 bp)".equals("4949")
assert json.INX.INX.QUAST."0"."Largest contig".equals("4949")
assert json.INX.INX.QUAST."0"."GC (%)".equals("52.96")
assert json.INX.INX.QUAST."0"."Avg. coverage depth".equals("47")

// Below two values should be empty
assert json.short.short.StarAMR."0"."Genotype".equals("None")
assert json.short.short.StarAMR."0"."Predicted Phenotype".equals("Susceptible")
assert json.short.short.StarAMR."0"."Genome Length".equals("4949")
assert json.INX.INX.StarAMR."0"."Genotype".equals("None")
assert json.INX.INX.StarAMR."0"."Predicted Phenotype".equals("Susceptible")
assert json.INX.INX.StarAMR."0"."Genome Length".equals("4949")

assert json.short.short.CheckM."0"."# genomes".equals("5656")
assert json.short.short.CheckM."0"."# markers".equals("56")
assert json.short.short.CheckM."0"."# marker sets".equals("24")
assert json.short.short.CheckM."0".Contamination.equals("0.00")
assert json.INX.INX.CheckM."0"."# genomes".equals("5656")
assert json.INX.INX.CheckM."0"."# markers".equals("56")
assert json.INX.INX.CheckM."0"."# marker sets".equals("24")
assert json.INX.INX.CheckM."0".Contamination.equals("0.00")

assert json.short.short.SevenGeneMLSTReport[0].filename.equals("short.filtered.fasta.gz")
assert json.INX.INX.SevenGeneMLSTReport[0].filename.equals("short.filtered.fasta.gz")

assert json.short.short.Abricate."0".RESISTANCE.equals("NoData") // All Abricate results for this are "NoData".
assert json.INX.INX.Abricate."0".RESISTANCE.equals("NoData") // All Abricate results for this are "NoData".

def assembly_path = "$launchDir/results/Assembly/FinalAssembly/short/short.final.filtered.assembly.fasta.gz"
def assembly_path = "$launchDir/results/Assembly/FinalAssembly/INX/short.final.filtered.assembly.fasta.gz"
assert path(assembly_path).exists()

// parse assembly file
Expand All @@ -209,17 +209,17 @@ nextflow_pipeline {
// output files
assert iridanext_global.findAll { it.path == "FinalReports/Aggregated/Json/final_report.json" }.size() == 1
assert iridanext_global.findAll { it.path == "FinalReports/Aggregated/Tables/final_report.tsv" }.size() == 1
assert iridanext_samples.short.findAll { it.path == "Assembly/FinalAssembly/short/short.final.filtered.assembly.fasta.gz" }.size() == 1
assert iridanext_samples.short.findAll { it.path == "Assembly/Quality/QUAST/short/short.transposed_short.quast.quality.tsv" }.size() == 1
assert iridanext_samples.short.findAll { it.path == "Assembly/Quality/SeqKitStats/short.seqkit.stats.summary.tsv" }.size() == 1
assert iridanext_samples.short.findAll { it.path == "Assembly/PostProcessing/Speciation/MashScreen/short.mash.screen.taxa.screen.screen" }.size() == 1
assert iridanext_samples.short.findAll { it.path == "Reads/Quality/Trimmed/MashScreen/short.mash.screen.reads.screen.screen" }.size() == 1
assert iridanext_samples.short.findAll { it.path == "Reads/Quality/Trimmed/FastP/short.fastp.summary.json" }.size() == 1
assert iridanext_samples.short.findAll { it.path == "Reads/Quality/RawReadQuality/short.read.scan.summary.json" }.size() == 1
assert iridanext_samples.short.findAll { it.path == "FinalReports/FlattenedReports/short.flat_sample.json.gz" }.size() == 1
assert iridanext_samples.INX.findAll { it.path == "Assembly/FinalAssembly/INX/short.final.filtered.assembly.fasta.gz" }.size() == 1
assert iridanext_samples.INX.findAll { it.path == "Assembly/Quality/QUAST/short/short.transposed_short.quast.quality.tsv" }.size() == 1
assert iridanext_samples.INX.findAll { it.path == "Assembly/Quality/SeqKitStats/short.seqkit.stats.summary.tsv" }.size() == 1
assert iridanext_samples.INX.findAll { it.path == "Assembly/PostProcessing/Speciation/MashScreen/short.mash.screen.taxa.screen.screen" }.size() == 1
assert iridanext_samples.INX.findAll { it.path == "Reads/Quality/Trimmed/MashScreen/short.mash.screen.reads.screen.screen" }.size() == 1
assert iridanext_samples.INX.findAll { it.path == "Reads/Quality/Trimmed/FastP/short.fastp.summary.json" }.size() == 1
assert iridanext_samples.INX.findAll { it.path == "Reads/Quality/RawReadQuality/short.read.scan.summary.json" }.size() == 1
assert iridanext_samples.INX.findAll { it.path == "FinalReports/FlattenedReports/INX.flat_sample.json.gz" }.size() == 1

// output metadata
assert iridanext_metadata.short."QC Status" == "PASSED"
assert iridanext_metadata.INX."QC Status" == "PASSED"

}

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