From 300ee2b04cea9e6d9afb2eb5114ca49a627215f0 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 14 Nov 2024 16:31:57 +0100 Subject: [PATCH] fix more workflow tests --- .../local/vcf_annotation/tests/main.nf.test | 8 ++++---- .../vcf_annotation/tests/main.nf.test.snap | 20 +++++++++---------- .../vcf_dbsnp_vcfanno/tests/main.nf.test | 2 +- .../vcf_dbsnp_vcfanno/tests/main.nf.test.snap | 6 +++--- .../tests/main.nf.test | 4 ++-- .../tests/main.nf.test.snap | 16 +++++++-------- 6 files changed, 28 insertions(+), 28 deletions(-) diff --git a/subworkflows/local/vcf_annotation/tests/main.nf.test b/subworkflows/local/vcf_annotation/tests/main.nf.test index 84835994..48757069 100644 --- a/subworkflows/local/vcf_annotation/tests/main.nf.test +++ b/subworkflows/local/vcf_annotation/tests/main.nf.test @@ -44,9 +44,9 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.annotated_vcfs.collect { it.collect { it instanceof Map ? it.groupTarget : file(it).name } }, + workflow.out.annotated_vcfs.collect { [ it[0].groupTarget, it[1][-7..-1] ]}, workflow.out.reports - ).match("default") } + ).match() } ) } @@ -87,9 +87,9 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.annotated_vcfs.collect { it.collect { it instanceof Map ? it.groupTarget : file(it).name } }, + workflow.out.annotated_vcfs.collect { [ it[0].groupTarget, it[1][-7..-1] ] }, workflow.out.reports - ).match("vcfanno") } + ).match() } ) } diff --git a/subworkflows/local/vcf_annotation/tests/main.nf.test.snap b/subworkflows/local/vcf_annotation/tests/main.nf.test.snap index d3ebc487..1e808b5d 100644 --- a/subworkflows/local/vcf_annotation/tests/main.nf.test.snap +++ b/subworkflows/local/vcf_annotation/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "default": { + "vcf_annotation - default": { "content": [ [ [ @@ -9,7 +9,7 @@ "family_samples": "NA24143", "caller": "haplotypecaller" }, - "NA24143.haplotypecaller.vcf.gz" + ".vcf.gz" ] ], [ @@ -19,12 +19,12 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-05T17:39:23.107888975" + "timestamp": "2024-11-14T16:27:10.638204373" }, - "vcfanno": { + "vcf_annotation - vcfanno": { "content": [ [ [ @@ -34,7 +34,7 @@ "family_samples": "NA24143", "caller": "haplotypecaller" }, - "NA24143.haplotypecaller.vcf.gz" + ".vcf.gz" ] ], [ @@ -44,9 +44,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-05T17:39:39.640344999" + "timestamp": "2024-11-14T16:27:36.089100362" } } \ No newline at end of file diff --git a/subworkflows/local/vcf_dbsnp_vcfanno/tests/main.nf.test b/subworkflows/local/vcf_dbsnp_vcfanno/tests/main.nf.test index 77f8c579..3461e963 100644 --- a/subworkflows/local/vcf_dbsnp_vcfanno/tests/main.nf.test +++ b/subworkflows/local/vcf_dbsnp_vcfanno/tests/main.nf.test @@ -37,7 +37,7 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.vcfs.collect { [ it[0], "${file(it[1]).name},variantsMD5:${path(it[1]).vcf.variantsMD5}", file(it[2]).name ] } + workflow.out.vcfs.collect { [ it[0], "variantsMD5:${path(it[1]).vcf.variantsMD5}", it[2][-4..-1] ] } ).match() } ) } diff --git a/subworkflows/local/vcf_dbsnp_vcfanno/tests/main.nf.test.snap b/subworkflows/local/vcf_dbsnp_vcfanno/tests/main.nf.test.snap index 43ea8318..64683b8a 100644 --- a/subworkflows/local/vcf_dbsnp_vcfanno/tests/main.nf.test.snap +++ b/subworkflows/local/vcf_dbsnp_vcfanno/tests/main.nf.test.snap @@ -9,8 +9,8 @@ "family_samples": "NA24143", "caller": "haplotypecaller" }, - "NA24143.vcf.gz,variantsMD5:b4f76bc67ba0e159489393d4788349b3", - "NA24143.vcf.gz.tbi" + "variantsMD5:b4f76bc67ba0e159489393d4788349b3", + ".tbi" ] ] ], @@ -18,6 +18,6 @@ "nf-test": "0.9.1", "nextflow": "24.10.0" }, - "timestamp": "2024-11-05T14:44:22.532988474" + "timestamp": "2024-11-14T16:28:22.613197067" } } \ No newline at end of file diff --git a/subworkflows/local/vcf_extract_relate_somalier/tests/main.nf.test b/subworkflows/local/vcf_extract_relate_somalier/tests/main.nf.test index 7c4d9351..2e14eda3 100644 --- a/subworkflows/local/vcf_extract_relate_somalier/tests/main.nf.test +++ b/subworkflows/local/vcf_extract_relate_somalier/tests/main.nf.test @@ -38,7 +38,7 @@ nextflow_workflow { workflow.out.pairs_tsv, workflow.out.samples_tsv, workflow.out.peds - ).match("default - peds") } + ).match() } ) } @@ -74,7 +74,7 @@ nextflow_workflow { workflow.out.pairs_tsv, workflow.out.samples_tsv, workflow.out.peds - ).match("default - no peds") } + ).match() } ) } diff --git a/subworkflows/local/vcf_extract_relate_somalier/tests/main.nf.test.snap b/subworkflows/local/vcf_extract_relate_somalier/tests/main.nf.test.snap index 49d14e7c..002b354a 100644 --- a/subworkflows/local/vcf_extract_relate_somalier/tests/main.nf.test.snap +++ b/subworkflows/local/vcf_extract_relate_somalier/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "default - peds": { + "vcf_extract_relate_somalier - default - peds": { "content": [ [ [ @@ -62,12 +62,12 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-05T17:39:52.526057891" + "timestamp": "2024-11-14T16:29:26.72882236" }, - "default - no peds": { + "vcf_extract_relate_somalier - default - no peds": { "content": [ [ [ @@ -130,9 +130,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-09-05T17:40:03.603049023" + "timestamp": "2024-11-14T16:29:46.729601248" } } \ No newline at end of file