diff --git a/workflows/bacterial_genomics/bacterial-quality-and-contamination-control-post-assembly/bacterial_quality_and_contamination_control_post_assembly-tests.yml b/workflows/bacterial_genomics/bacterial-quality-and-contamination-control-post-assembly/bacterial_quality_and_contamination_control_post_assembly-tests.yml index 262391cc02..218b1301c4 100644 --- a/workflows/bacterial_genomics/bacterial-quality-and-contamination-control-post-assembly/bacterial_quality_and_contamination_control_post_assembly-tests.yml +++ b/workflows/bacterial_genomics/bacterial-quality-and-contamination-control-post-assembly/bacterial_quality_and_contamination_control_post_assembly-tests.yml @@ -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: @@ -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: diff --git a/workflows/genome-assembly/quality-and-contamination-control-raw-reads/quality_and_contamination_control_raw_reads-tests.yml b/workflows/genome-assembly/quality-and-contamination-control-raw-reads/quality_and_contamination_control_raw_reads-tests.yml index d387a6876f..26e5793e6a 100644 --- a/workflows/genome-assembly/quality-and-contamination-control-raw-reads/quality_and_contamination_control_raw_reads-tests.yml +++ b/workflows/genome-assembly/quality-and-contamination-control-raw-reads/quality_and_contamination_control_raw_reads-tests.yml @@ -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: diff --git a/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/host-or-contamination-removal-on-long-reads-tests.yml b/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/host-or-contamination-removal-on-long-reads-tests.yml index 811693d354..282e4011ea 100644 --- a/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/host-or-contamination-removal-on-long-reads-tests.yml +++ b/workflows/microbiome/host-contamination-removal/host-contamination-removal-long-reads/host-or-contamination-removal-on-long-reads-tests.yml @@ -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: @@ -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: @@ -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: @@ -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: @@ -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: @@ -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: @@ -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: diff --git a/workflows/read-preprocessing/short-read-qc-trimming/short-read-quality-control-and-trimming-tests.yml b/workflows/read-preprocessing/short-read-qc-trimming/short-read-quality-control-and-trimming-tests.yml index c4b0b474c0..80568e68dc 100644 --- a/workflows/read-preprocessing/short-read-qc-trimming/short-read-quality-control-and-trimming-tests.yml +++ b/workflows/read-preprocessing/short-read-qc-trimming/short-read-quality-control-and-trimming-tests.yml @@ -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" diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation-tests.yml b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation-tests.yml index 2b09bc296c..0a5c7ab40b 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation-tests.yml +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation-tests.yml @@ -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\\)" diff --git a/workflows/variant-calling/ploidy-aware-genotype-calling/genotype-variant-calling-wgs-pe-test.yml b/workflows/variant-calling/ploidy-aware-genotype-calling/genotype-variant-calling-wgs-pe-test.yml index 491ec7805f..314ef60728 100644 --- a/workflows/variant-calling/ploidy-aware-genotype-calling/genotype-variant-calling-wgs-pe-test.yml +++ b/workflows/variant-calling/ploidy-aware-genotype-calling/genotype-variant-calling-wgs-pe-test.yml @@ -40,18 +40,18 @@ SnpEff variants: asserts: - has_text: + - that: has_text text: "##fileformat=VCFv4.2" - has_text: + - that: has_text text: "##contig=" - has_n_lines: + - that: has_n_lines n: 71 SnpEff eff reports: asserts: - has_text: + - that: has_text text: " Number of variants processed
(i.e. after filter and non-variants) " - has_text: + - that: has_text text: " 2 " Annotated Variants: