From f4314b80012108983abc100b63ab8576d444abb5 Mon Sep 17 00:00:00 2001 From: Clea Siguret Date: Fri, 27 Sep 2024 10:41:51 +0200 Subject: [PATCH 1/4] Fix test syntax --- .../bacterial_genome_annotation-tests.yml | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) 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: From af8513cdda8081258cee610973c4dea581f958b3 Mon Sep 17 00:00:00 2001 From: Clea Siguret Date: Fri, 27 Sep 2024 11:45:27 +0200 Subject: [PATCH 2/4] Fix test for 5 outputs --- .../bacterial_genome_annotation-tests.yml | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) 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 c8e82d490..15aeb2599 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 @@ -13,28 +13,28 @@ text: "Writing out results for replicon" integronfinder2_summary: asserts: - has_n_columns: - n: 6 + has_text: + text: "contig00001" integronfinder2_results_tabular: asserts: - has_n_columns: - n: 14 + has_text: + text: "contig00009_42" bakta_hypothetical_tabular: asserts: - has_n_columns: - n: 9 + has_text: + text: "DHJLLP_04750" bakta_annotation_json: asserts: has_text: text: "aa_hexdigest" bakta_annotation_tabular: asserts: - has_n_columns: - n: 9 + has_text: + text: "Phosphotransferase system cellobiose-specific component IIC" isescan_results_tabular: asserts: - has_n_columns: - n: 24 + has_text: + text: "IS256_162" isescan_summary_tabular: asserts: has_text: @@ -58,4 +58,4 @@ has_text: text: "CALIN" has_text: - text: "insertion_sequence" + text: "PFAM" From a712636c6a95ee3fd569c7ea3eebbfb4b4ea8470 Mon Sep 17 00:00:00 2001 From: Clea Siguret Date: Fri, 27 Sep 2024 12:13:50 +0200 Subject: [PATCH 3/4] Fix has_text tests syntax --- .../bacterial_genome_annotation-tests.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) 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 15aeb2599..4fea58063 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 @@ -53,9 +53,9 @@ n: 8 tooldistillator_summarize: asserts: - has_text: + - that: "has_text" text: "CDS12738(DOp1)" - has_text: + - that: "has_text" text: "CALIN" - has_text: - text: "PFAM" + - that: "has_text" + text: "PFAM" \ No newline at end of file From e36b2ba7cf0f2bea79a227f26cd69eb55498faf4 Mon Sep 17 00:00:00 2001 From: Clea Siguret Date: Fri, 27 Sep 2024 15:21:34 +0200 Subject: [PATCH 4/4] Fix test --- .../bacterial_genome_annotation-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 4fea58063..7cc354b06 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 @@ -56,6 +56,6 @@ - that: "has_text" text: "CDS12738(DOp1)" - that: "has_text" - text: "CALIN" + text: "calin" - that: "has_text" text: "PFAM" \ No newline at end of file