fix linting

nf-core · Jul 19, 2024 · cd5632c · cd5632c
1 parent aba93ac
commit cd5632c
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Showing 4 changed files with 35 additions and 84 deletions.
diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml
@@ -1,8 +1,10 @@
 name: tabix_tabix
+
 channels:
   - conda-forge
   - bioconda
   - defaults
+
 dependencies:
-  - bioconda::tabix=1.11
   - bioconda::htslib=1.20
+  - bioconda::tabix=1.11
diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf
@@ -36,8 +36,8 @@ process TABIX_TABIX {
     """
     touch ${tab}.tbi
     touch ${tab}.csi
-    cat <<-END_VERSIONS > versions.yml
 
+    cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
     END_VERSIONS

diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test
@@ -25,11 +25,10 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out).match() },
                 { assert snapshot(
-                            file(process.out.tbi[0][1]).name
-                                ).match("tbi_bed")
-                }
+                    process.out,
+                    file(process.out.tbi[0][1]).name
+                ).match() }
             )
         }
     }
@@ -50,11 +49,9 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out).match() },
                 { assert snapshot(
-                            file(process.out.tbi[0][1]).name
-                                ).match("tbi_gff")
-                }
+                    process.out,
+                    file(process.out.tbi[0][1]).name).match() }
             )
         }
 
@@ -76,11 +73,10 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out).match() },
                 { assert snapshot(
-                            file(process.out.tbi[0][1]).name
-                                ).match("tbi_vcf")
-                }
+                    process.out,
+                    file(process.out.tbi[0][1]).name
+                ).match() }
             )
         }
 
@@ -102,11 +98,10 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out).match() },
                 { assert snapshot(
-                            file(process.out.csi[0][1]).name
-                                ).match("vcf_csi")
-                }
+                    process.out,
+                    file(process.out.csi[0][1]).name
+                ).match() }
             )
         }
 
@@ -129,11 +124,10 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out).match() },
                 { assert snapshot(
-                            file(process.out.csi[0][1]).name
-                                ).match("vcf_csi_stub")
-                }
+                    process.out,
+                    file(process.out.csi[0][1]).name
+                ).match() }
             )
         }
 

diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
@@ -1,24 +1,4 @@
 {
-    "vcf_csi_stub": {
-        "content": [
-            "test.vcf.gz.csi"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-03-04T14:51:59.788002"
-    },
-    "tbi_gff": {
-        "content": [
-            "genome.gff3.gz.tbi"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-02-19T14:53:37.420216"
-    },
     "sarscov2_gff_tbi": {
         "content": [
             {
@@ -50,13 +30,14 @@
                 "versions": [
                     "versions.yml:md5,07064637fb8a217174052be8e40234e2"
                 ]
-            }
+            },
+            "genome.gff3.gz.tbi"
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-07-19T11:30:08.097194659"
+        "timestamp": "2024-07-19T12:06:25.653807564"
     },
     "sarscov2_bedgz_tbi": {
         "content": [
@@ -89,33 +70,14 @@
                 "versions": [
                     "versions.yml:md5,07064637fb8a217174052be8e40234e2"
                 ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-07-19T11:29:56.691350166"
-    },
-    "tbi_vcf": {
-        "content": [
-            "test.vcf.gz.tbi"
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-02-19T14:53:46.402522"
-    },
-    "vcf_csi": {
-        "content": [
-            "test.vcf.gz.csi"
+            },
+            "test.bed.gz.tbi"
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-02-19T14:53:54.921189"
+        "timestamp": "2024-07-19T12:06:09.754082161"
     },
     "sarscov2_vcf_tbi": {
         "content": [
@@ -148,13 +110,14 @@
                 "versions": [
                     "versions.yml:md5,07064637fb8a217174052be8e40234e2"
                 ]
-            }
+            },
+            "test.vcf.gz.tbi"
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-07-19T11:30:19.881620622"
+        "timestamp": "2024-07-19T12:06:40.042648294"
     },
     "sarscov2_vcf_csi_stub": {
         "content": [
@@ -176,7 +139,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,9f0a973d840bf1ff116773f51b89ac1b"
+                    "versions.yml:md5,07064637fb8a217174052be8e40234e2"
                 ],
                 "csi": [
                     [
@@ -195,15 +158,16 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,9f0a973d840bf1ff116773f51b89ac1b"
+                    "versions.yml:md5,07064637fb8a217174052be8e40234e2"
                 ]
-            }
+            },
+            "test.vcf.gz.csi"
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-07-19T11:30:42.00245281"
+        "timestamp": "2024-07-19T12:07:08.700367261"
     },
     "sarscov2_vcf_csi": {
         "content": [
@@ -236,22 +200,13 @@
                 "versions": [
                     "versions.yml:md5,07064637fb8a217174052be8e40234e2"
                 ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-07-19T11:30:31.015047391"
-    },
-    "tbi_bed": {
-        "content": [
-            "test.bed.gz.tbi"
+            },
+            "test.vcf.gz.csi"
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-02-19T14:53:28.947628"
+        "timestamp": "2024-07-19T12:06:55.362067748"
     }
 }