update bcftools pluginsplit (#7013)

* update bcftools pluginsplit * Add error test * Fix test and meta * Fix test * Change extension detection * Change file renaming * Fix renaming * Update modules/nf-core/bcftools/pluginsplit/main.nf Co-authored-by: Felix Lenner <[email protected]> * Update bcftools pluginsplit * Stage input in folder * Fix meta.yml * Update input * Update error report --------- Co-authored-by: Felix Lenner <[email protected]> Co-authored-by: Louis Le Nezet <[email protected]> Co-authored-by: LouisLeNezet <[email protected]>
nf-core · Nov 21, 2024 · 14c910a · 14c910a
1 parent ffd452a
commit 14c910a
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diff --git a/modules/nf-core/bcftools/pluginsplit/main.nf b/modules/nf-core/bcftools/pluginsplit/main.nf
@@ -8,7 +8,7 @@ process BCFTOOLS_PLUGINSPLIT {
         'biocontainers/bcftools:1.20--h8b25389_0' }"
 
     input:
-    tuple val(meta), path(vcf), path(tbi)
+    tuple val(meta), path(vcf, stageAs: "input/*"), path(tbi, stageAs: "input/*")
     path(samples)
     path(groups)
     path(regions)
@@ -25,7 +25,6 @@ process BCFTOOLS_PLUGINSPLIT {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
 
     def samples_arg = samples ? "--samples-file ${samples}" : ""
     def groups_arg  = groups  ? "--groups-file ${groups}"   : ""
@@ -40,9 +39,7 @@ process BCFTOOLS_PLUGINSPLIT {
         ${groups_arg} \\
         ${regions_arg} \\
         ${targets_arg} \\
-        --output ${prefix}
-
-    mv ${prefix}/* .
+        --output .
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -52,7 +49,6 @@ process BCFTOOLS_PLUGINSPLIT {
 
     stub:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
 
     def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
                 args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
@@ -65,11 +61,15 @@ process BCFTOOLS_PLUGINSPLIT {
                 ""
     def determination_file = samples ?: targets
     def create_cmd = extension.matches("vcf|bcf") ? "touch " : "echo '' | gzip > "
-    def create_files = "cut -f 3 ${determination_file} | sed -e 's/\$/.${extension}/' > files.txt; while IFS= read -r filename; do ${create_cmd} \"\$filename\"; done < files.txt"
-    def create_index = index.matches("csi|tbi") ? "cut -f 3 ${determination_file} | sed -e 's/\$/.${extension}.${index}/' > indices.txt; touch \$(<indices.txt)" : ""
     """
-    ${create_files}
-    ${create_index}
+    cut -f 3 ${determination_file} | sed -e 's/\$/.${extension}/' > files.txt
+    while IFS= read -r filename;
+        do ${create_cmd} "./\$filename";
+        if [ -n "${index}" ]; then
+            index_file=\$(sed -e 's/\$/.${index}/' <<< \$filename);
+            touch ./\$index_file;
+        fi;
+    done < files.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
@@ -67,7 +67,6 @@ nextflow_process {
     }
 
     test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi") {
-
         config "./nextflow.config"
 
         when {
@@ -91,16 +90,43 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.vcf,
-                    process.out.tbi.get(0).get(1).find { file(it).name.matches("normal.vcf.gz.tbi|tumor.vcf.gz.tbi") },
-                ) }
+                    process.out.vcf.collect{ it[1].collect { file(it).name } },
+                    process.out.tbi.collect{ it[1].collect { file(it).name } },
+                ).match() }
             )
         }
 
     }
 
-    test("homo_sapiens - [ vcf, tbi ], samples, [], [], [] -stub") {
+    test("homo_sapiens - [ vcf, tbi ], [], [], [], [], - error no sample") {
+        config "./nextflow.config"
 
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                input[4] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.failed },
+                { assert process.errorReport.contains("No samples to split: input/dbsnp_146.hg38.vcf.gz") }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [ vcf, tbi ], samples, [], [], [] -stub") {
         options "-stub"
 
         when {
@@ -130,7 +156,6 @@ nextflow_process {
     }
 
     test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets -stub") {
-
         options "-stub"
 
         when {
@@ -160,7 +185,6 @@ nextflow_process {
     }
 
     test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi -stub") {
-
         config "./nextflow.config"
         options "-stub"
 

diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
@@ -47,18 +47,39 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-07-09T15:56:42.307673651"
+        "timestamp": "2024-11-20T14:56:54.383979416"
+    },
+    "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi": {
+        "content": [
+            [
+                [
+                    "normal.vcf.gz",
+                    "tumour.vcf.gz"
+                ]
+            ],
+            [
+                [
+                    "normal.vcf.gz.tbi",
+                    "tumour.vcf.gz.tbi"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-20T14:56:44.796391578"
     },
     "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets": {
         "content": null,
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-07-09T15:56:21.498991402"
+        "timestamp": "2024-11-20T14:56:36.709842966"
     },
     "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi -stub": {
         "content": [
@@ -126,10 +147,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-07-09T15:57:04.483688966"
+        "timestamp": "2024-11-20T14:57:11.163588435"
     },
     "homo_sapiens - [ vcf, tbi ], samples, [], [], []": {
         "content": [
@@ -179,10 +200,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-07-09T15:56:10.033818589"
+        "timestamp": "2024-11-20T14:56:27.978161766"
     },
     "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets -stub": {
         "content": [
@@ -232,9 +253,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-07-09T15:56:53.641165787"
+        "timestamp": "2024-11-20T14:57:02.456908152"
     }
 }