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Convert duplicate-keyed asserts blocks to list form (passing subset) #1275

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Merged
mvdbeek merged 1 commit into from
Jul 13, 2026
Merged

Convert duplicate-keyed asserts blocks to list form (passing subset) #1275

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10 changes: 5 additions & 5 deletions ...control-post-assembly/bacterial_quality_and_contamination_control_post_assembly-tests.yml
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Expand Up @@ -28,10 +28,10 @@
n: 6
Kraken2 sequence assignation:
asserts:
has_text:
- that: has_text
text: "contig00001"
has_text:
text: "contig00359"
- that: has_text
text: "contig00359"
Kraken2 tabular report:
asserts:
has_text:
Expand All @@ -56,9 +56,9 @@
element_tests:
E-coli3_S194.fasta:
asserts:
has_text:
- that: has_text
text: ">contig00001_1"
has_text:
- that: has_text
text: ">contig00358_1"
Tooldistillator summarize control:
asserts:
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4 changes: 2 additions & 2 deletions ...and-contamination-control-raw-reads/quality_and_contamination_control_raw_reads-tests.yml
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Expand Up @@ -12,9 +12,9 @@
outputs:
fastp_report_json:
asserts:
has_text:
- that: has_text
text: "fastp_version"
has_text:
- that: has_text
text: "read2_before_filtering"
kraken_report_tabular:
asserts:
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36 changes: 18 additions & 18 deletions ...st-contamination-removal-long-reads/host-or-contamination-removal-on-long-reads-tests.yml
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Expand Up @@ -21,9 +21,9 @@
elements:
genome_results:
asserts:
has_text:
- that: has_text
text: "Spike3bBarcode10"
has_text:
- that: has_text
text: "586,300,787 bp"
coverage_across_reference:
asserts:
Expand All @@ -45,15 +45,15 @@
value: 51
duplication_rate_histogram:
asserts:
has_text:
- that: has_text
text: "#Duplication rate"
has_text:
- that: has_text
text: "17.0"
homopolymer_indels:
asserts:
has_text:
- that: has_text
text: "#Type of indel"
has_text:
- that: has_text
text: "polyN"
insert_size_across_reference:
asserts:
Expand All @@ -65,9 +65,9 @@
value: 0
mapped_reads_clipping_profile:
asserts:
has_text:
- that: has_text
text: "#Read position (bp)"
has_text:
- that: has_text
text: "38.123"
mapped_reads_gc-content_distribution:
asserts:
Expand Down Expand Up @@ -95,9 +95,9 @@
elements:
genome_results:
asserts:
has_text:
- that: has_text
text: "Spike3bBarcode12"
has_text:
- that: has_text
text: "586,300,787 bp"
coverage_across_reference:
asserts:
Expand All @@ -119,15 +119,15 @@
value: 51
duplication_rate_histogram:
asserts:
has_text:
- that: has_text
text: "#Duplication rate"
has_text:
- that: has_text
text: "8.0"
homopolymer_indels:
asserts:
has_text:
- that: has_text
text: "#Type of indel"
has_text:
- that: has_text
text: "polyN"
insert_size_across_reference:
asserts:
Expand All @@ -139,9 +139,9 @@
value: 0
mapped_reads_clipping_profile:
asserts:
has_text:
- that: has_text
text: "#Read position (bp)"
has_text:
- that: has_text
text: "0.03930972"
mapped_reads_gc-content_distribution:
asserts:
Expand All @@ -167,9 +167,9 @@
value: 4
MultiQC HTML Report:
asserts:
has_text:
- that: has_text
text: "Spike3bBarcode10"
has_text:
- that: has_text
text: "Spike3bBarcode12"
Reads without Host or Contamination:
element_tests:
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12 changes: 6 additions & 6 deletions ...ad-preprocessing/short-read-qc-trimming/short-read-quality-control-and-trimming-tests.yml
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Expand Up @@ -24,19 +24,19 @@
outputs:
MultiQC HTML report:
asserts:
has_text:
- that: has_text
text: "Filtered Reads"
has_text:
- that: has_text
text: "pair"
fastp JSON report:
element_tests:
pair:
asserts:
has_text:
- that: has_text
text: "paired end (301 cycles + 301 cycles)"
has_text:
- that: has_text
text: "300000"
has_text:
- that: has_text
text: "295680"
has_text:
- that: has_text
text: "59230948"
8 changes: 4 additions & 4 deletions ...variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation-tests.yml
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Expand Up @@ -32,11 +32,11 @@
element_tests:
SRR11578257:
asserts:
has_line:
- that: has_line
line: "##fileformat=VCFv4.0"
has_line:
- that: has_line
line: "#CHROM POS ID REF ALT QUAL FILTER INFO"
has_text_matching:
- that: has_text_matching
expression: "NC_045512.2\t174\t.\tG\tC\t[0-9]*\tPASS"
has_text_matching:
- that: has_text_matching
expression: "NC_045512.2\t20209\t.\tAGTAGAAATT\tA\t[0-9]*\tPASS\tDP=[0-9]*;AF=0.9[0-9]*;SB=24;DP4=[0-9]*,[0-9]*,[0-9]*,[0-9]*;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION\\(MODERATE||agtagaaattta/ata|SRNL6649I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A\\),CODON_CHANGE_PLUS_CODON_DELETION\\(MODERATE||agtagaaattta/ata|SRNL197I|345|ORF1ab|protein_coding|CODING|YP_009725310.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON\\)"
10 changes: 5 additions & 5 deletions ...ws/variant-calling/ploidy-aware-genotype-calling/genotype-variant-calling-wgs-pe-test.yml
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Expand Up @@ -40,18 +40,18 @@

SnpEff variants:
asserts:
has_text:
- that: has_text
text: "##fileformat=VCFv4.2"
has_text:
- that: has_text
text: "##contig=<ID=chr1,length=2000>"
has_n_lines:
- that: has_n_lines
n: 71

SnpEff eff reports:
asserts:
has_text:
- that: has_text
text: "<td valign=top> <b> Number of variants processed <br> (i.e. after filter and non-variants) </b> </td>"
has_text:
- that: has_text
text: "<td> 2 </td>"

Annotated Variants:
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