rm fasta from bwameth index folder to be handled separately (#6780)

* rm fasta from bwameth index folder to be handled separately + update test + snaps * provide fasta separtely to index folder * add stub test
nf-core · Oct 16, 2024 · aa2f432 · aa2f432
1 parent 847683c
commit aa2f432
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Showing 8 changed files with 139 additions and 79 deletions.
diff --git a/modules/nf-core/bwameth/align/main.nf b/modules/nf-core/bwameth/align/main.nf
@@ -9,7 +9,8 @@ process BWAMETH_ALIGN {
 
     input:
     tuple val(meta), path(reads)
-    path index
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(index)
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -24,17 +25,16 @@ process BWAMETH_ALIGN {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
     """
-    INDEX=`find -L ${index} -name "*.bwameth.c2t" | sed 's/\\.bwameth.c2t\$//'`
-
     # Modify the timestamps so that bwameth doesn't complain about building the index
     # See https://github.com/nf-core/methylseq/pull/217
-    touch -c -- *
+    touch -c $index/*
+    mv $fasta $index/
 
     bwameth.py \\
         $args \\
         $read_group \\
         -t $task.cpus \\
-        --reference \$INDEX \\
+        --reference $index/$fasta \\
         $reads \\
         | samtools view $args2 -@ $task.cpus -bhS -o ${prefix}.bam -
 

diff --git a/modules/nf-core/bwameth/align/meta.yml b/modules/nf-core/bwameth/align/meta.yml
@@ -33,7 +33,20 @@ input:
         description: |
           List of input FastQ files of size 1 and 2 for single-end and paired-end data,
           respectively.
-  - - index:
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: Input genome fasta file
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - index:
         type: directory
         description: Directory containing bwameth genome index
 output:

diff --git a/modules/nf-core/bwameth/align/tests/main.nf.test b/modules/nf-core/bwameth/align/tests/main.nf.test
@@ -16,26 +16,29 @@ nextflow_process {
             script "../../../bwameth/index/main.nf"
             process {
                 """
-                input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
-
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
                 """
             }
         }
     }
 
-    test("test-bwameth-align-single-end") {
+    test("sarscov2 methylated single_end [fastq]") {
 
         when {
             process {
                 """
-                input[0] = [
-				    [ id:'test', single_end:true ], // meta map
-				    [
-				        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true)
-				    ]
-				]
-				input[1] = BWAMETH_INDEX.out.index
-
+                input[0] = Channel.of([
+                                [ id:'test', single_end:true ], // meta map
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true)
+				])
+                input[1] = Channel.of([
+                                [ id:'test' ], // meta map
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+				input[2] = BWAMETH_INDEX.out.index
                 """
             }
         }
@@ -52,20 +55,23 @@ nextflow_process {
         }
     }
 
-    test("test-bwameth-align-paired-end") {
+    test("sarscov2 methylated paired_end [fastq]") {
 
         when {
             process {
                 """
-                input[0] = [
-				    [ id:'test', single_end:false ], // meta map
-				    [
-				        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true),
-				        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true)
-				    ]
-				]
-				input[1] = BWAMETH_INDEX.out.index
-
+                input[0] = Channel.of([
+                                [ id:'test', single_end:false ], // meta map
+                                [
+                                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true),
+                                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true)
+                                ]
+				])
+				input[1] = Channel.of([
+                                [ id:'test' ], // meta map
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+				input[2] = BWAMETH_INDEX.out.index
                 """
             }
         }
@@ -88,15 +94,18 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [
-				    [ id:'test', single_end:false ], // meta map
-				    [
-				        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true),
-				        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true)
-				    ]
-				]
-				input[1] = BWAMETH_INDEX.out.index
-
+                input[0] = Channel.of([
+                                [ id:'test', single_end:false ], // meta map
+                                [
+                                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true),
+                                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true)
+                                ]
+				])
+				input[1] = Channel.of([
+                                [ id:'test' ], // meta map
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+				input[2] = BWAMETH_INDEX.out.index
                 """
             }
         }

diff --git a/modules/nf-core/bwameth/align/tests/main.nf.test.snap b/modules/nf-core/bwameth/align/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "test-bwameth-align-single-end": {
+    "sarscov2 methylated single_end [fastq]": {
         "content": [
             "5fdda0ada69daa3956c65a24c9d1c1e0",
             [
@@ -10,20 +10,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-04T20:43:02.509483"
-    },
-    "test-bwameth-align-paired-end": {
-        "content": [
-            "cbd5cfa8b446e26987898a45a94770ba",
-            [
-                "versions.yml:md5,c00660f78aeab4fabe00092c70656098"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-09-04T20:43:10.963043"
+        "timestamp": "2024-10-16T07:50:08.241201566"
     },
     "test-bwameth-align-paired-end-stub": {
         "content": [
@@ -58,6 +45,19 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-04T20:43:17.04632"
+        "timestamp": "2024-10-16T08:00:51.770330645"
+    },
+    "sarscov2 methylated paired_end [fastq]": {
+        "content": [
+            "cbd5cfa8b446e26987898a45a94770ba",
+            [
+                "versions.yml:md5,c00660f78aeab4fabe00092c70656098"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-16T07:50:20.75109829"
     }
 }
diff --git a/modules/nf-core/bwameth/index/main.nf b/modules/nf-core/bwameth/index/main.nf
@@ -8,19 +8,36 @@ process BWAMETH_INDEX {
         'biocontainers/bwameth:0.2.7--pyh7cba7a3_0' }"
 
     input:
-    path fasta, stageAs: "bwameth/*"
+    tuple val(meta), path(fasta)
 
     output:
-    path "bwameth"      , emit: index
-    path "versions.yml" , emit: versions
+    tuple val(meta), path("BwamethIndex"), emit: index
+    path "versions.yml"                  , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
     """
-    bwameth.py index $fasta
+    mkdir BwamethIndex
+    mv $fasta BwamethIndex/
+
+    bwameth.py index BwamethIndex/$fasta
+
+    rm BwamethIndex/$fasta
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bwameth: \$(bwameth.py --version | cut -f2 -d" ")
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    """
+    mkdir BwamethIndex
+    touch BwamethIndex/$fasta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/bwameth/index/meta.yml b/modules/nf-core/bwameth/index/meta.yml
@@ -19,12 +19,21 @@ tools:
       licence: ["MIT"]
       identifier: ""
 input:
-  - - fasta:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
         type: file
         description: Input genome fasta file
 output:
   - index:
-      - bwameth:
+      - meta:
+          type: directory
+          description: Directory containing bwameth genome index
+          pattern: "index"
+      - BwamethIndex:
           type: directory
           description: Directory containing bwameth genome index
           pattern: "index"
@@ -37,3 +46,4 @@ authors:
   - "@phue"
 maintainers:
   - "@phue"
+  - "@sateeshperi"
diff --git a/modules/nf-core/bwameth/index/tests/main.nf.test b/modules/nf-core/bwameth/index/tests/main.nf.test
@@ -10,12 +10,15 @@ nextflow_process {
     tag "bwameth"
     tag "bwameth/index"
 
-    test("test-bwameth-index") {
-        
+    test("sarscov2 genome [fasta]") {
+
         when {
             process {
                 """
-                input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
                 """
             }
         }
@@ -27,5 +30,5 @@ nextflow_process {
             )
         }
     }
-    
+
 }
diff --git a/modules/nf-core/bwameth/index/tests/main.nf.test.snap b/modules/nf-core/bwameth/index/tests/main.nf.test.snap
@@ -1,30 +1,38 @@
 {
-    "test-bwameth-index": {
+    "sarscov2 genome [fasta]": {
         "content": [
             {
                 "0": [
                     [
-                        "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6",
-                        "genome.fasta.bwameth.c2t:md5,98039984526a41d04d6bd92fcc040c62",
-                        "genome.fasta.bwameth.c2t.amb:md5,249a4195069071ce47cd0bae68abe376",
-                        "genome.fasta.bwameth.c2t.ann:md5,46524d4359dcdfb203a235ab3b930dbb",
-                        "genome.fasta.bwameth.c2t.bwt:md5,84f65df7d42dbe84c9ccfaddfdd5ea6b",
-                        "genome.fasta.bwameth.c2t.pac:md5,4d8e51cb0bbdeaf24576bdf0264d8653",
-                        "genome.fasta.bwameth.c2t.sa:md5,d25f6486f5134f57ed5b258f6fbb8673"
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "genome.fasta.bwameth.c2t:md5,98039984526a41d04d6bd92fcc040c62",
+                            "genome.fasta.bwameth.c2t.amb:md5,249a4195069071ce47cd0bae68abe376",
+                            "genome.fasta.bwameth.c2t.ann:md5,46524d4359dcdfb203a235ab3b930dbb",
+                            "genome.fasta.bwameth.c2t.bwt:md5,84f65df7d42dbe84c9ccfaddfdd5ea6b",
+                            "genome.fasta.bwameth.c2t.pac:md5,4d8e51cb0bbdeaf24576bdf0264d8653",
+                            "genome.fasta.bwameth.c2t.sa:md5,d25f6486f5134f57ed5b258f6fbb8673"
+                        ]
                     ]
                 ],
                 "1": [
                     "versions.yml:md5,0827d461c1a0b41bd533aea470843c2c"
                 ],
                 "index": [
                     [
-                        "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6",
-                        "genome.fasta.bwameth.c2t:md5,98039984526a41d04d6bd92fcc040c62",
-                        "genome.fasta.bwameth.c2t.amb:md5,249a4195069071ce47cd0bae68abe376",
-                        "genome.fasta.bwameth.c2t.ann:md5,46524d4359dcdfb203a235ab3b930dbb",
-                        "genome.fasta.bwameth.c2t.bwt:md5,84f65df7d42dbe84c9ccfaddfdd5ea6b",
-                        "genome.fasta.bwameth.c2t.pac:md5,4d8e51cb0bbdeaf24576bdf0264d8653",
-                        "genome.fasta.bwameth.c2t.sa:md5,d25f6486f5134f57ed5b258f6fbb8673"
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "genome.fasta.bwameth.c2t:md5,98039984526a41d04d6bd92fcc040c62",
+                            "genome.fasta.bwameth.c2t.amb:md5,249a4195069071ce47cd0bae68abe376",
+                            "genome.fasta.bwameth.c2t.ann:md5,46524d4359dcdfb203a235ab3b930dbb",
+                            "genome.fasta.bwameth.c2t.bwt:md5,84f65df7d42dbe84c9ccfaddfdd5ea6b",
+                            "genome.fasta.bwameth.c2t.pac:md5,4d8e51cb0bbdeaf24576bdf0264d8653",
+                            "genome.fasta.bwameth.c2t.sa:md5,d25f6486f5134f57ed5b258f6fbb8673"
+                        ]
                     ]
                 ],
                 "versions": [
@@ -33,9 +41,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
+            "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-28T13:57:11.602104"
+        "timestamp": "2024-10-14T20:32:13.750317299"
     }
 }