Update nf-test sbwf

nf-core · Nov 13, 2024 · 0a5cb05 · 0a5cb05
1 parent 1262ef2
commit 0a5cb05
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Showing 2 changed files with 2 additions and 14 deletions.
diff --git a/subworkflows/local/vcf_split_bcftools/tests/main.nf.test b/subworkflows/local/vcf_split_bcftools/tests/main.nf.test
@@ -115,9 +115,7 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.failed },
-                { assert snapshot(
-                    workflow.errorReport
-                ).match()
+                { assert workflow.errorReport.contains("No samples to split: dbsnp_146.hg38.vcf.gz")
                 }
             )
         }

diff --git a/subworkflows/local/vcf_split_bcftools/tests/main.nf.test.snap b/subworkflows/local/vcf_split_bcftools/tests/main.nf.test.snap
@@ -20,16 +20,6 @@
         },
         "timestamp": "2024-11-13T14:06:59.745818945"
     },
-    "Split no sample vcf file": {
-        "content": [
-            "Error executing process > 'VCF_SPLIT_BCFTOOLS:BCFTOOLS_PLUGINSPLIT (dbsnp_146.hg38)'\n\nCaused by:\n  Process `VCF_SPLIT_BCFTOOLS:BCFTOOLS_PLUGINSPLIT (dbsnp_146.hg38)` terminated with an error exit status (255)\n\n\nCommand executed:\n\n  bcftools plugin split \\\n      --write-index=tbi --output-type z \\\n      dbsnp_146.hg38.vcf.gz \\\n       \\\n       \\\n       \\\n       \\\n      --output dbsnp_146.hg38\n  \n  for file in dbsnp_146.hg38/*; do\n      # Extract the basename\n      base_name=$(basename \"$file\")\n      # Extract the part of the basename before the first dot\n      name_before_dot=\"${base_name%%.*}\"\n      # Extract the extension\n      extension=\"${base_name#${name_before_dot}}\"\n      # Construct the new name\n      new_name=\"${name_before_dot}${extension}\"\n      mv \"$file\" \"dbsnp_146.hg38/$new_name\"\n  done\n  \n  cat <<-END_VERSIONS > versions.yml\n  \"VCF_SPLIT_BCFTOOLS:BCFTOOLS_PLUGINSPLIT\":\n      bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*$//')\n  END_VERSIONS\n\nCommand exit status:\n  255\n\nCommand output:\n  (empty)\n\nCommand error:\n  INFO:    Converting SIF file to temporary sandbox...\n  No samples to split: dbsnp_146.hg38.vcf.gz\n  INFO:    Cleaning up image...\n\nWork dir:\n  /mnt/s/Users/Main/Documents/Louis/Travail/IGDR/Repositories/phaseimpute/.nf-test/tests/b9ce286d296c103157404c17538dfd38/work/e7/a5c43f2b2e65cccdc595ff4665a569\n\nContainer:\n  /mnt/s/Users/Main/Documents/Louis/Travail/IGDR/Repositories/phaseimpute/.nf-test/tests/b9ce286d296c103157404c17538dfd38/work/singularity/depot.galaxyproject.org-singularity-bcftools-1.20--h8b25389_0.img\n\nTip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`"
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.0"
-        },
-        "timestamp": "2024-11-13T14:07:08.772813678"
-    },
     "Split multiple vcf file": {
         "content": [
             [
@@ -70,4 +60,4 @@
         },
         "timestamp": "2024-11-11T14:42:48.076610625"
     }
-}
+}