diff --git a/tests/germline_small.nf.test.snap b/tests/germline_small.nf.test.snap index a99138b..e1a3bb6 100644 --- a/tests/germline_small.nf.test.snap +++ b/tests/germline_small.nf.test.snap @@ -1,7 +1,7 @@ { "-stub": { "content": [ - 76, + 77, { "BCFTOOLS_DEDUP": { "bcftools": 1.18 @@ -33,6 +33,9 @@ "MERGE_REPORTS": { "python": "3.8.6" }, + "PICARD_CREATESEQUENCEDICTIONARY": { + "picard": "3.2.0-1-g3948afb6b" + }, "PLOTS": { "r-base": "4.3.1" }, @@ -62,6 +65,8 @@ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", "references", + "references/dictionary", + "references/dictionary/genome.dict", "references/rtgtools", "references/rtgtools/genome.sdf", "small", @@ -231,11 +236,11 @@ "nf-test": "0.9.0", "nextflow": "24.10.2" }, - "timestamp": "2024-11-28T16:47:47.024615694" + "timestamp": "2024-12-04T10:12:17.779754389" }, "Params: --analysis 'germline' --variant_type 'small' --method 'happy,rtgtools'": { "content": [ - 76, + 77, { "BCFTOOLS_DEDUP": { "bcftools": 1.18 @@ -267,6 +272,9 @@ "MERGE_REPORTS": { "python": "3.8.6" }, + "PICARD_CREATESEQUENCEDICTIONARY": { + "picard": "3.2.0-1-g3948afb6b" + }, "PLOTS": { "r-base": "4.3.1" }, @@ -296,6 +304,8 @@ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", "references", + "references/dictionary", + "references/dictionary/genome.dict", "references/rtgtools", "references/rtgtools/genome.sdf", "references/rtgtools/genome.sdf/done", @@ -575,6 +585,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.2" }, - "timestamp": "2024-11-28T16:45:26.990755841" + "timestamp": "2024-12-04T10:10:09.338722844" } } \ No newline at end of file diff --git a/tests/germline_sv.nf.test.snap b/tests/germline_sv.nf.test.snap index b566380..5181ca9 100644 --- a/tests/germline_sv.nf.test.snap +++ b/tests/germline_sv.nf.test.snap @@ -1,7 +1,7 @@ { "Params: --analysis 'germline' --variant_type 'structural' --method 'truvari,svbenchmark,wittyer'": { "content": [ - 144, + 145, { "BCFTOOLS_DEDUP": { "bcftools": 1.18 @@ -30,6 +30,9 @@ "MERGE_REPORTS": { "python": "3.8.6" }, + "PICARD_CREATESEQUENCEDICTIONARY": { + "picard": "3.2.0-1-g3948afb6b" + }, "PLOTS": { "r-base": "4.3.1" }, @@ -79,6 +82,9 @@ [ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", + "references", + "references/dictionary", + "references/dictionary/genome.dict", "structural", "structural/HG002", "structural/HG002/preprocess", @@ -357,11 +363,11 @@ "nf-test": "0.9.0", "nextflow": "24.10.2" }, - "timestamp": "2024-11-28T16:51:57.386421371" + "timestamp": "2024-12-04T10:22:09.959009433" }, "-stub": { "content": [ - 144, + 145, { "BCFTOOLS_DEDUP": { "bcftools": 1.18 @@ -390,6 +396,9 @@ "MERGE_REPORTS": { "python": "3.8.6" }, + "PICARD_CREATESEQUENCEDICTIONARY": { + "picard": "3.2.0-1-g3948afb6b" + }, "PLOTS": { "r-base": "4.3.1" }, @@ -439,6 +448,9 @@ [ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", + "references", + "references/dictionary", + "references/dictionary/genome.dict", "structural", "structural/HG002", "structural/HG002/preprocess", @@ -656,6 +668,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.2" }, - "timestamp": "2024-11-28T16:54:34.483191183" + "timestamp": "2024-12-04T10:24:27.339868009" } } \ No newline at end of file diff --git a/tests/somatic_indel.nf.test.snap b/tests/somatic_indel.nf.test.snap index 6107271..2e1d10b 100644 --- a/tests/somatic_indel.nf.test.snap +++ b/tests/somatic_indel.nf.test.snap @@ -1,7 +1,7 @@ { "Params: --analysis 'somatic' --variant_type 'indel' --method 'sompy'": { "content": [ - 27, + 28, { "BCFTOOLS_REHEADER": { "bcftools": 1.18 @@ -30,6 +30,9 @@ "MERGE_REPORTS": { "python": "3.8.6" }, + "PICARD_CREATESEQUENCEDICTIONARY": { + "picard": "3.2.0-1-g3948afb6b" + }, "PLOTS": { "r-base": "4.3.1" }, @@ -165,7 +168,10 @@ "indel/test2/stats/bcftools", "indel/test2/stats/bcftools/test2.strelka.bcftools_stats.txt", "pipeline_info", - "pipeline_info/nf_core_pipeline_software_mqc_versions.yml" + "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", + "references", + "references/dictionary", + "references/dictionary/genome.dict" ], [ "SEQC2.bcftools_stats.txt:md5,e530daf4f6a4923f1cd85c51893d5747", @@ -175,8 +181,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-22T12:53:42.07320983" + "timestamp": "2024-12-04T09:59:41.934881268" } } \ No newline at end of file diff --git a/tests/somatic_snv.nf.test.snap b/tests/somatic_snv.nf.test.snap index 4c4cccb..20188bb 100644 --- a/tests/somatic_snv.nf.test.snap +++ b/tests/somatic_snv.nf.test.snap @@ -1,7 +1,7 @@ { "-stub": { "content": [ - 38, + 39, { "BCFTOOLS_REHEADER": { "bcftools": 1.18 @@ -30,6 +30,9 @@ "MERGE_REPORTS": { "python": "3.8.6" }, + "PICARD_CREATESEQUENCEDICTIONARY": { + "picard": "3.2.0-1-g3948afb6b" + }, "PLOTS": { "r-base": "4.3.1" }, @@ -46,6 +49,9 @@ [ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", + "references", + "references/dictionary", + "references/dictionary/genome.dict", "snv", "snv/SEQC2", "snv/SEQC2/stats", @@ -125,8 +131,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.10.1" + "nextflow": "24.10.2" }, - "timestamp": "2024-11-22T12:57:55.883023408" + "timestamp": "2024-12-04T09:53:59.901867572" } } \ No newline at end of file diff --git a/tests/somatic_sv.nf.test.snap b/tests/somatic_sv.nf.test.snap index fabf609..539def8 100644 --- a/tests/somatic_sv.nf.test.snap +++ b/tests/somatic_sv.nf.test.snap @@ -1,7 +1,7 @@ { "Params: --analysis 'somatic' --variant_type 'structural' --method 'truvari,svbenchmark'": { "content": [ - 69, + 70, { "BCFTOOLS_REHEADER": { "bcftools": 1.18 @@ -30,6 +30,9 @@ "MERGE_REPORTS": { "python": "3.8.6" }, + "PICARD_CREATESEQUENCEDICTIONARY": { + "picard": "3.2.0-1-g3948afb6b" + }, "PLOTS": { "r-base": "4.3.1" }, @@ -61,6 +64,9 @@ [ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", + "references", + "references/dictionary", + "references/dictionary/genome.dict", "structural", "structural/SEQC2", "structural/SEQC2/stats", @@ -206,6 +212,6 @@ "nf-test": "0.9.0", "nextflow": "24.10.2" }, - "timestamp": "2024-11-28T16:58:12.671419675" + "timestamp": "2024-12-04T09:56:29.305188123" } } \ No newline at end of file