skip pytests for new nf-test

nf-core · Nov 8, 2024 · c1f45b7 · c1f45b7
1 parent e8a7e81
commit c1f45b7
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Showing 5 changed files with 17 additions and 103 deletions.
diff --git a/tests/.nftignore b/tests/.nftignore
@@ -21,3 +21,4 @@ reports/markduplicates/**/*.md.cram.metrics
 reports/snpeff/*/*_snpEff.csv
 reports/snpeff/*/snpEff_summary.html
 variant_calling/**/*.vcf.{gz,gz.tbi}
+.DS_Store
diff --git a/tests/config/pytesttags.yml b/tests/config/pytesttags.yml
@@ -35,21 +35,6 @@ sentieon/bwamem:
   - tests/csv/3.0/fastq_single.csv
   - tests/test_sentieon_aligner_bwamem.yml
 
-## markduplicates
-gatk4/markduplicates:
-  - conf/modules/markduplicates.config
-  - modules/nf-core/gatk4/markduplicates/**
-  - modules/nf-core/mosdepth/**
-  - modules/nf-core/samtools/convert/**
-  - modules/nf-core/samtools/index/**
-  - modules/nf-core/samtools/stats/**
-  - subworkflows/local/bam_markduplicates/**
-  - subworkflows/local/cram_qc_mosdepth_samtools/**
-  - tests/csv/3.0/mapped_single_bam.csv
-  - tests/csv/3.0/mapped_single_cram.csv
-  - tests/test_markduplicates_from_bam.yml
-  - tests/test_markduplicates_from_cram.yml
-
 ## sentieon/dedup
 sentieon/dedup:
   - conf/modules/sentieon_dedup.config
@@ -64,34 +49,6 @@ sentieon/dedup:
   - tests/test_sentieon_dedup_from_bam.yml
   - tests/test_sentieon_dedup_from_cram.yml
 
-## prepare_recalibration
-prepare_recalibration:
-  - conf/modules/prepare_recalibration.config
-  - modules/nf-core/gatk4/baserecalibrator/**
-  - modules/nf-core/gatk4/gatherbqsrreports/**
-  - modules/nf-core/mosdepth/**
-  - modules/nf-core/samtools/convert/**
-  - subworkflows/local/bam_baserecalibrator/**
-  - tests/csv/3.0/mapped_single_bam.csv
-  - tests/csv/3.0/mapped_single_cram.csv
-  - tests/test_prepare_recalibration_from_bam.yml
-  - tests/test_prepare_recalibration_from_cram.yml
-
-## recalibrate
-recalibrate:
-  - conf/modules/recalibrate.config
-  - modules/nf-core/gatk4/applybqsr/**
-  - modules/nf-core/samtools/convert/**
-  - modules/nf-core/samtools/index/**
-  - modules/nf-core/samtools/merge/**
-  - modules/nf-core/mosdepth/**
-  - subworkflows/local/bam_applybqsr/**
-  - subworkflows/local/cram_merge_index_samtools/**
-  - tests/csv/3.0/prepare_recalibration_single_bam.csv
-  - tests/csv/3.0/prepare_recalibration_single_cram.csv
-  - tests/test_recalibrate_from_bam.yml
-  - tests/test_recalibrate_from_cram.yml
-
 ## intervals
 intervals:
   - conf/modules/prepare_intervals.config

diff --git a/tests/start_from_markduplicates.nf.test.snap b/tests/start_from_markduplicates.nf.test.snap
@@ -122,7 +122,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-11-08T17:29:52.524459"
+        "timestamp": "2024-11-08T23:31:20.98766"
     },
     "Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --tools null ": {
         "content": [
@@ -301,7 +301,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-11-08T17:25:13.758062"
+        "timestamp": "2024-11-08T23:20:24.032921"
     },
     "Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --skip_tools markduplicates --tools null ": {
         "content": [
@@ -449,7 +449,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-11-08T17:36:56.432752"
+        "timestamp": "2024-11-08T23:38:03.780921"
     },
     "Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --tools null ": {
         "content": [
@@ -628,6 +628,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-11-08T17:33:38.41786"
+        "timestamp": "2024-11-08T23:34:58.814577"
     }
 }
diff --git a/tests/start_from_preparerecalibration.nf.test.snap b/tests/start_from_preparerecalibration.nf.test.snap
@@ -62,7 +62,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-11-08T18:12:30.69818"
+        "timestamp": "2024-11-08T19:02:04.839416"
     },
     "Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step prepare_recalibration --skip_tools baserecalibrator --tools strelka ": {
         "content": [
@@ -150,18 +150,7 @@
                 "reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary",
                 "reports/vcftools/strelka/test/test.strelka.variants.TsTv.count",
                 "reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual",
-                [
-                    ".DS_Store:md5,2e1453fbce51b095eea24106216f98f8",
-                    [
-                        "HCC1395N.strelka.genome.vcf.gz.tbi:md5,3a576ad9170e09f9c661bb3c9bda8e73",
-                        "HCC1395N.strelka.variants.vcf.gz.tbi:md5,79777af316475651498251f64ce87a1f"
-                    ],
-                    [
-                        "HCC1395T_vs_HCC1395N.strelka.somatic_indels.vcf.gz:md5,721a05b2ae643841c02f8df286dcc570",
-                        "HCC1395T_vs_HCC1395N.strelka.somatic_indels.vcf.gz.tbi:md5,cd5bd7d40770eb4542b4955b797d7ec6",
-                        "HCC1395T_vs_HCC1395N.strelka.somatic_snvs.vcf.gz.tbi:md5,62bc80362a1f2563e89d098a67e93260"
-                    ]
-                ],
+                "variant_calling",
                 "variant_calling/strelka",
                 "variant_calling/strelka/test",
                 "variant_calling/strelka/test/test.strelka.genome.vcf.gz",
@@ -193,7 +182,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-11-08T18:13:45.816277"
+        "timestamp": "2024-11-08T19:03:26.637555"
     },
     "Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step prepare_recalibration --skip_tools baserecalibrator --tools strelka ": {
         "content": [
@@ -281,18 +270,7 @@
                 "reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary",
                 "reports/vcftools/strelka/test/test.strelka.variants.TsTv.count",
                 "reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual",
-                [
-                    ".DS_Store:md5,2e1453fbce51b095eea24106216f98f8",
-                    [
-                        "HCC1395N.strelka.genome.vcf.gz.tbi:md5,3a576ad9170e09f9c661bb3c9bda8e73",
-                        "HCC1395N.strelka.variants.vcf.gz.tbi:md5,79777af316475651498251f64ce87a1f"
-                    ],
-                    [
-                        "HCC1395T_vs_HCC1395N.strelka.somatic_indels.vcf.gz:md5,721a05b2ae643841c02f8df286dcc570",
-                        "HCC1395T_vs_HCC1395N.strelka.somatic_indels.vcf.gz.tbi:md5,cd5bd7d40770eb4542b4955b797d7ec6",
-                        "HCC1395T_vs_HCC1395N.strelka.somatic_snvs.vcf.gz.tbi:md5,62bc80362a1f2563e89d098a67e93260"
-                    ]
-                ],
+                "variant_calling",
                 "variant_calling/strelka",
                 "variant_calling/strelka/test",
                 "variant_calling/strelka/test/test.strelka.genome.vcf.gz",
@@ -324,7 +302,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-11-08T18:17:25.766735"
+        "timestamp": "2024-11-08T19:07:48.175425"
     },
     "Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step prepare_recalibration --tools null ": {
         "content": [
@@ -417,6 +395,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-11-08T18:16:08.915809"
+        "timestamp": "2024-11-08T19:06:29.729137"
     }
 }
diff --git a/tests/start_from_recalibration.nf.test.snap b/tests/start_from_recalibration.nf.test.snap
@@ -64,7 +64,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-11-08T18:21:49.913569"
+        "timestamp": "2024-11-08T23:43:36.719177"
     },
     "Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step recalibrate --skip_tools baserecalibrator --tools strelka ": {
         "content": [
@@ -152,18 +152,7 @@
                 "reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary",
                 "reports/vcftools/strelka/test/test.strelka.variants.TsTv.count",
                 "reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual",
-                [
-                    ".DS_Store:md5,2e1453fbce51b095eea24106216f98f8",
-                    [
-                        "HCC1395N.strelka.genome.vcf.gz.tbi:md5,3a576ad9170e09f9c661bb3c9bda8e73",
-                        "HCC1395N.strelka.variants.vcf.gz.tbi:md5,79777af316475651498251f64ce87a1f"
-                    ],
-                    [
-                        "HCC1395T_vs_HCC1395N.strelka.somatic_indels.vcf.gz:md5,721a05b2ae643841c02f8df286dcc570",
-                        "HCC1395T_vs_HCC1395N.strelka.somatic_indels.vcf.gz.tbi:md5,cd5bd7d40770eb4542b4955b797d7ec6",
-                        "HCC1395T_vs_HCC1395N.strelka.somatic_snvs.vcf.gz.tbi:md5,62bc80362a1f2563e89d098a67e93260"
-                    ]
-                ],
+                "variant_calling",
                 "variant_calling/strelka",
                 "variant_calling/strelka/test",
                 "variant_calling/strelka/test/test.strelka.genome.vcf.gz",
@@ -195,7 +184,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-11-08T18:20:40.219765"
+        "timestamp": "2024-11-08T23:42:27.247547"
     },
     "Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step recalibrate --skip_tools baserecalibrator --tools strelka ": {
         "content": [
@@ -283,18 +272,7 @@
                 "reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary",
                 "reports/vcftools/strelka/test/test.strelka.variants.TsTv.count",
                 "reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual",
-                [
-                    ".DS_Store:md5,2e1453fbce51b095eea24106216f98f8",
-                    [
-                        "HCC1395N.strelka.genome.vcf.gz.tbi:md5,3a576ad9170e09f9c661bb3c9bda8e73",
-                        "HCC1395N.strelka.variants.vcf.gz.tbi:md5,79777af316475651498251f64ce87a1f"
-                    ],
-                    [
-                        "HCC1395T_vs_HCC1395N.strelka.somatic_indels.vcf.gz:md5,721a05b2ae643841c02f8df286dcc570",
-                        "HCC1395T_vs_HCC1395N.strelka.somatic_indels.vcf.gz.tbi:md5,cd5bd7d40770eb4542b4955b797d7ec6",
-                        "HCC1395T_vs_HCC1395N.strelka.somatic_snvs.vcf.gz.tbi:md5,62bc80362a1f2563e89d098a67e93260"
-                    ]
-                ],
+                "variant_calling",
                 "variant_calling/strelka",
                 "variant_calling/strelka/test",
                 "variant_calling/strelka/test/test.strelka.genome.vcf.gz",
@@ -326,7 +304,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-11-08T18:23:09.076851"
+        "timestamp": "2024-11-08T23:44:51.527726"
     },
     "Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step recalibrate --tools null ": {
         "content": [
@@ -365,6 +343,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-11-08T18:19:16.169004"
+        "timestamp": "2024-11-08T23:41:01.835335"
     }
 }