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 6c31172063..a6a3f8b867 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 9ed2a53ddd..8a5cfd2a7a 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 7c28a630e7..3f79a85b4b 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 1d9044cfbd..43888eb137 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 c7a1de448d..254a6b4035 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 96a7fc4de9..c8e82d4906 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 c514aa2093..5da14f26db 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 ac0808b9b3..35483d0f78 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 9078bd0a53..aad5280a15 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 3f21209d29..7484600c36 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 8f2ebcecb8..3a9ebbeb1e 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 1730620974..27a590032b 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 95a438d6b1..186fbb60f9 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 b184f0a508..e394d71efb 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 b5768ad0b0..adbe029d5a 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 eb13dcea93..c499aa9b02 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: ">subsample3[0-9].[0-9]% | |