From 07d11e07e9f470fbd05e999c9773d0b473b52a56 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Mon, 23 Sep 2024 14:48:39 -0400 Subject: [PATCH] Fix test syntax issues. --- .../Assembly-Hifi-HiC-phasing-VGP4-tests.yml | 8 ++--- .../Mitogenome-Assembly-VGP0-tests.yml | 4 +-- .../kmer-profiling-hifi-VGP1-tests.yml | 4 --- .../kmer-profiling-hifi-trio-VGP2-tests.yml | 3 -- .../amr_gene_detection-tests.yml | 34 +++++++++---------- .../bacterial_genome_annotation-tests.yml | 24 ++++++------- .../fragment-based-docking-scoring-tests.yml | 15 ++++---- .../gromacs-dctmd/gromacs-dctmd-tests.yml | 25 ++++++++------ .../gromacs-mmgbsa/gromacs-mmgbsa-tests.yml | 21 +++++++----- ...verage-bigwig-between-replicates-tests.yml | 4 +-- .../epigenetics/cutandrun/cutandrun-tests.yml | 20 ++++++----- .../chic-fastq-to-cool-hicup-cooler-tests.yml | 1 - .../hic-fastq-to-cool-hicup-cooler-tests.yml | 1 - .../bacterial_genome_assembly-tests.yml | 22 ++++++------ ...uality_and_contamination_control-tests.yml | 34 +++++++++---------- ...seq-fastq-to-matrix-10x-cellplex-tests.yml | 10 ++---- ...scrna-seq-fastq-to-matrix-10x-v3-tests.yml | 4 +-- 17 files changed, 115 insertions(+), 119 deletions(-) diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml index 6c3117206..a6a3f8b86 100644 --- a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml +++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml @@ -35,8 +35,8 @@ Database for Busco Lineage: v5 outputs: Hifiasm HiC hap1: - assert: - has_n_line: + asserts: + has_n_lines: n: 168 Estimated Genome size: 2288021 Busco Summary Hap1: @@ -49,8 +49,8 @@ value: 65000 delta: 10000 usable hap1 gfa: - assert: - has_n_line: + asserts: + has_n_lines: n: 173 Assembly statistics for Hap1 and Hap2: asserts: diff --git a/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0-tests.yml b/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0-tests.yml index 9ed2a53dd..8a5cfd2a7 100644 --- a/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0-tests.yml +++ b/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0-tests.yml @@ -25,6 +25,6 @@ value: 68000 delta: 5000 mitogenome_genbank: - assert: - has_n_line: + asserts: + has_n_lines: n: 480 diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1-tests.yml b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1-tests.yml index 7c28a630e..3f79a85b4 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1-tests.yml +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1-tests.yml @@ -12,22 +12,18 @@ Ploidy: 1 outputs: GenomeScope linear plot: - class: File file: test-data/GenomeScope_Linear_plot.png compare: sim_size delta: 10000 GenomeScope log plot: - class: File file: test-data/GenomeScope_Log_plot.png compare: sim_size delta: 10000 GenomeScope transformed linear plot: - class: File file: test-data/GenomeScope_Transformed_linear_plot.png compare: sim_size delta: 10000 GenomeScope transformed log plot: - class: File file: test-data/GenomeScope_Transformed_log_plot.png compare: sim_size delta: 10000 diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2-tests.yml b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2-tests.yml index 1d9044cfb..43888eb13 100644 --- a/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2-tests.yml +++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2-tests.yml @@ -36,17 +36,14 @@ Ploidy: 1 outputs: GenomeScope linear plot (maternal): - class: File file: test-data/GenomeScope_Linear_plot_maternal.png compare: sim_size delta: 15000 GenomeScope linear plot (paternal): - class: File file: test-data/GenomeScope_Linear_plot_paternal.png compare: sim_size delta: 15000 GenomeScope linear plot (child): - class: File file: test-data/GenomeScope_Linear_plot_child.png compare: sim_size delta: 15000 diff --git a/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection-tests.yml b/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection-tests.yml index c7a1de448..254a6b403 100644 --- a/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection-tests.yml +++ b/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection-tests.yml @@ -5,55 +5,55 @@ path: https://zenodo.org/records/11488310/files/shovill_contigs_fasta outputs: staramr_detailed_summary: - assert: - has_text: - text: "Resistance" - has_n_columns: - n: 12 + asserts: + has_text: + text: "Resistance" + has_n_columns: + n: 12 staramr_resfinder_report: - assert: - has_text: - text: "tetracycline" - has_n_columns: - n: 13 + asserts: + has_text: + text: "tetracycline" + has_n_columns: + n: 13 staramr_mlst_report: - assert: + asserts: has_text: text: "efaecalis" has_n_columns: n: 10 staramr_plasmidfinder_report: - assert: + asserts: has_text: text: "CP002494" has_n_columns: n: 9 staramr_summary: - assert: + asserts: has_text: text: "streptomycin" has_n_columns: n: 12 amrfinderplus_report: - assert: + asserts: has_text: text: "Enterococcus faecalis quinolone resistant ParC" has_n_columns: n: 23 amrfinderplus_mutation: - assert: + asserts: has_text: text: "cardiolipin synthase Cls" has_n_columns: n: 23 abricate_virulence_report: - assert: + asserts: has_text: text: "endocarditis specific antigen" has_n_columns: n: 15 tooldistillator_summarize: - assert: + asserts: has_text: text: "% Identity to reference sequence" has_text: diff --git a/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation-tests.yml b/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation-tests.yml index 96a7fc4de..c8e82d490 100644 --- a/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation-tests.yml +++ b/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation-tests.yml @@ -8,51 +8,51 @@ Select a AMRFinderPlus database: amrfinderplus_V3.12_2024-05-02.2 outputs: integronfinder2_logfile_text: - assert: + asserts: has_text: text: "Writing out results for replicon" integronfinder2_summary: - assert: + asserts: has_n_columns: n: 6 integronfinder2_results_tabular: - assert: + asserts: has_n_columns: n: 14 bakta_hypothetical_tabular: - assert: + asserts: has_n_columns: n: 9 bakta_annotation_json: - assert: + asserts: has_text: text: "aa_hexdigest" bakta_annotation_tabular: - assert: + asserts: has_n_columns: n: 9 isescan_results_tabular: - assert: + asserts: has_n_columns: n: 24 isescan_summary_tabular: - assert: + asserts: has_text: text: "nIS" isescan_logfile_text: - assert: + asserts: has_text: text: "Both complete and partial IS elements are reported." plasmidfinder_result_json: - assert: + asserts: has_text: text: "positions_in_contig" plasmidfinder_results_tabular: - assert: + asserts: has_n_columns: n: 8 tooldistillator_summarize: - assert: + asserts: has_text: text: "CDS12738(DOp1)" has_text: diff --git a/workflows/computational-chemistry/fragment-based-docking-scoring/fragment-based-docking-scoring-tests.yml b/workflows/computational-chemistry/fragment-based-docking-scoring/fragment-based-docking-scoring-tests.yml index c514aa209..5da14f26d 100644 --- a/workflows/computational-chemistry/fragment-based-docking-scoring/fragment-based-docking-scoring-tests.yml +++ b/workflows/computational-chemistry/fragment-based-docking-scoring/fragment-based-docking-scoring-tests.yml @@ -21,10 +21,11 @@ SuCOS threshold: 0 outputs: Scored and filtered poses: - class: File - assert: - has_line: "$$$$" - n: 4 - assert: - has_test: "SuCOS_Score" - n: 4 + asserts: + has_line: + line: "$$$$" + n: 4 + asserts: + has_text: + text: "SuCOS_Score" + n: 4 diff --git a/workflows/computational-chemistry/gromacs-dctmd/gromacs-dctmd-tests.yml b/workflows/computational-chemistry/gromacs-dctmd/gromacs-dctmd-tests.yml index ac0808b9b..35483d0f7 100644 --- a/workflows/computational-chemistry/gromacs-dctmd/gromacs-dctmd-tests.yml +++ b/workflows/computational-chemistry/gromacs-dctmd/gromacs-dctmd-tests.yml @@ -21,16 +21,19 @@ XTC files: element_tests: split_file_000000.txt: - assert: - has_size: 138900 - delta: 500 + asserts: + has_size: + size: 138900 + delta: 500 Free energy data: - class: 'File' - assert: - has_n_lines: 101 - has_n_columns: 5 + asserts: + has_n_lines: + n: 101 + has_n_columns: + n: 5 Friction data: - class: 'File' - assert: - has_n_lines: 101 - has_n_columns: 5 + asserts: + has_n_lines: + n: 101 + has_n_columns: + n: 5 diff --git a/workflows/computational-chemistry/gromacs-mmgbsa/gromacs-mmgbsa-tests.yml b/workflows/computational-chemistry/gromacs-mmgbsa/gromacs-mmgbsa-tests.yml index 9078bd0a5..aad5280a1 100644 --- a/workflows/computational-chemistry/gromacs-mmgbsa/gromacs-mmgbsa-tests.yml +++ b/workflows/computational-chemistry/gromacs-mmgbsa/gromacs-mmgbsa-tests.yml @@ -15,18 +15,21 @@ Salt concentration: 0.1 outputs: MMGBSA free energy: - class: 'File' - assert: - has_n_lines: 2 + asserts: + has_n_lines: + n: 2 MMGBSA statistics: element_tests: split_file_000000.txt: - assert: - has_text: 'DELTA TOTAL' - has_text: 'Generalized Born ESURF calculated using LCPO' + asserts: + - that: has_text + text: 'DELTA TOTAL' + - that: has_text + text: 'Generalized Born ESURF calculated using LCPO' XTC files: element_tests: split_file_000000.txt: - assert: - has_size: 138900 - delta: 500 + asserts: + has_size: + size: 138900 + delta: 500 diff --git a/workflows/epigenetics/average-bigwig-between-replicates/average-bigwig-between-replicates-tests.yml b/workflows/epigenetics/average-bigwig-between-replicates/average-bigwig-between-replicates-tests.yml index 3f21209d2..7484600c3 100644 --- a/workflows/epigenetics/average-bigwig-between-replicates/average-bigwig-between-replicates-tests.yml +++ b/workflows/epigenetics/average-bigwig-between-replicates/average-bigwig-between-replicates-tests.yml @@ -23,8 +23,8 @@ bin_size: 50 outputs: average_bigwigs: - class: Collection - collection_type: list + attributes: + collection_type: list element_tests: ATAC_HH19_PT: asserts: diff --git a/workflows/epigenetics/cutandrun/cutandrun-tests.yml b/workflows/epigenetics/cutandrun/cutandrun-tests.yml index 8f2ebcecb..3a9ebbeb1 100644 --- a/workflows/epigenetics/cutandrun/cutandrun-tests.yml +++ b/workflows/epigenetics/cutandrun/cutandrun-tests.yml @@ -46,13 +46,15 @@ MACS2 summits: element_tests: Rep1: - has_n_lines: - n: 1856 + asserts: + has_n_lines: + n: 1856 MACS2 narrowPeak: element_tests: Rep1: - has_n_lines: - n: 1856 + asserts: + has_n_lines: + n: 1856 MACS2 peaks xls: element_tests: Rep1: @@ -109,13 +111,15 @@ MACS2 summits: element_tests: Rep1: - has_n_lines: - n: 3261 + asserts: + has_n_lines: + n: 3261 MACS2 narrowPeak: element_tests: Rep1: - has_n_lines: - n: 3261 + asserts: + has_n_lines: + n: 3261 MACS2 peaks xls: element_tests: Rep1: diff --git a/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler-tests.yml b/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler-tests.yml index 173062097..27a590032 100644 --- a/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler-tests.yml +++ b/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler-tests.yml @@ -81,7 +81,6 @@ value: 47830 delta: 4000 plot with pyGenomeTracks: - class: File file: test-data/plot_chic.png compare: sim_size delta: 1500 diff --git a/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml index 95a438d6b..186fbb60f 100644 --- a/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml +++ b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml @@ -79,7 +79,6 @@ value: 149349 delta: 10000 plot with pyGenomeTracks: - class: File file: test-data/plot_hic.png compare: sim_size delta: 1500 diff --git a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly-tests.yml b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly-tests.yml index b184f0a50..e394d71ef 100644 --- a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly-tests.yml +++ b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly-tests.yml @@ -10,44 +10,44 @@ filetype: fastqsanger.gz outputs: shovill_contigs_graph: - assert: + asserts: has_n_lines: n: 18 shovill_logfile: - assert: + asserts: has_text: text: "[shovill] Done." shovill_contigs_fasta: - assert: + asserts: has_text: text: ">contig00001" quast_report_tabular: - assert: + asserts: has_n_columns: n: 2 has_text: text: "shovill_contigs_fasta" quast_log: - assert: + asserts: has_text: text: "Thank you for using QUAST!" refseqmasher_report_tabular: - assert: + asserts: has_text: text: "Enterococcus faecalis" has_n_columns: n: 21 bandage_contig_graph_stats: - assert: + asserts: has_text: text: "Total length orphaned nodes (bp):" has_n_columns: n: 2 tooldistillator_summarize: - assert: - has_text: + asserts: + - that: has_text text: "\"Assembly\": \"shovill_contigs_fasta\"" - has_text: + - that: has_text text: "Enterococcus faecalis EnGen0295" - has_text: + - that: has_text text: "bandage_plot_path" diff --git a/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control-tests.yml b/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control-tests.yml index b5768ad0b..adbe029d5 100644 --- a/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control-tests.yml +++ b/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control-tests.yml @@ -12,52 +12,52 @@ Select a NCBI taxonomy database: "2022-03-08" outputs: fastp_report_json: - assert: + asserts: has_text: text: "fastp_version" has_text: text: "read2_before_filtering" kraken_report_tabular: - assert: + asserts: has_text: text: "Enterococcus avium" - has_n_column: + has_n_columns: n: 6 kraken_report_reads: - assert: + asserts: has_text: text: "M07044:90:000000000-JRJWP:1:1119:23974:4461" - has_n_column: + has_n_columns: n: 5 bracken_kraken_report: - assert: + asserts: has_text: text: "Enterococcus gallinarum" - has_n_column: + has_n_columns: n: 6 bracken_report_tsv: - assert: + asserts: has_text: text: "Escherichia coli" - has_n_column: + has_n_columns: n: 7 recentrifuge_data_tabular: - assert: + asserts: has_text: text: "Enterococcus faecalis" - has_n_column: + has_n_columns: n: 6 recentrifuge_stats_tabular: - assert: + asserts: has_text: text: "input_dir/kraken_report_reads" - has_n_column: + has_n_columns: n: 2 tooldistillator_summarize: - assert: - has_text: + asserts: + - that: has_text text: "fastp_report" - has_text: + - that: has_text text: "ncbi_taxonomic_id" - has_text: + - that: has_text text: "kraken2_report" diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml index eb13dcea9..c499aa9b0 100644 --- a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml +++ b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml @@ -54,15 +54,13 @@ Number of expected cells: 500 outputs: MultiQC_STARsolo: - class: File asserts: - that: "has_text_matching" expression: ">subsample
3[0-9].[0-9]%
subsample
3[0-9].[0-9]%