apply suggestions

Author: SusiJo

.github/workflows/nf-test.yml

@@ -99,8 +99,6 @@ jobs:
       - name: Run nf-test
         uses: ./.github/actions/nf-test
         env:
-          NFT_DIFF: ${{ env.NFT_DIFF }}
-          NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
           NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
         with:
           profile: ${{ matrix.profile }}

tests/.nftignore

@@ -12,3 +12,4 @@ shinyngs_app/**/data.rds
 .DS_Store
 *.dds.rld.rds
 **/**/*.dds.rld.rds
+**/**/*.limma.rds

tests/test_affy.nf.test.snap

@@ -222,7 +222,6 @@
             ],
             [
                 "raw._eset.rds:md5,8c6c7807ce6c5d8204bd681b941eeb0f",
-                "phenotype_uninvolved_lesional_GSE50790.MArrayLM.limma.rds:md5,b5ef9fc63c87a83bf925f9284d83663f",
                 "versions.yml:md5,225ced8832439345efa781c726cf2e5c",
                 "versions.yml:md5,d5f6ad8fe6242dcd75bc62b654d1d211",
                 "gene_sets_phenotype_uninvolved_lesional_GSE50790.h.all.v2022.1.Hs.symbols.HALLMARK_ADIPOGENESIS.tsv:md5,6dcf05651f6b0386fe089eaa421c3127",
@@ -284,7 +283,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.3"
         },
-        "timestamp": "2025-06-17T08:33:54.434923937"
+        "timestamp": "2025-06-17T09:35:13.777853554"
     },
     "Test affy profile - with toolsheet": {
         "content": [
@@ -509,7 +508,6 @@
             ],
             [
                 "raw._eset.rds:md5,8c6c7807ce6c5d8204bd681b941eeb0f",
-                "phenotype_uninvolved_lesional_GSE50790.MArrayLM.limma.rds:md5,b5ef9fc63c87a83bf925f9284d83663f",
                 "versions.yml:md5,225ced8832439345efa781c726cf2e5c",
                 "versions.yml:md5,d5f6ad8fe6242dcd75bc62b654d1d211",
                 "gene_sets_phenotype_uninvolved_lesional_GSE50790.h.all.v2022.1.Hs.symbols.HALLMARK_ADIPOGENESIS.tsv:md5,6dcf05651f6b0386fe089eaa421c3127",
@@ -571,6 +569,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.3"
         },
-        "timestamp": "2025-06-17T08:37:06.659194094"
+        "timestamp": "2025-06-17T09:38:26.821359936"
     }
 }