make changes based on code review

EBI-Metagenomics · Apr 17, 2024 · 10f526d · 10f526d
1 parent f9c6373
commit 10f526d
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Showing 4 changed files with 9 additions and 144 deletions.
diff --git a/modules/ebi-metagenomics/mapseq2biom/main.nf b/modules/ebi-metagenomics/mapseq2biom/main.nf
@@ -10,7 +10,7 @@ process MAPSEQ2BIOM {
 
     input:
     tuple val(meta), path(msq)
-    tuple path(db_fasta), path(db_tax), path(db_otu), path(db_mscluster), val(db_label)
+    tuple path(db_otu), val(db_label)
 
     output:
     tuple val(meta), path("${meta.id}.txt")         , emit: krona_input
@@ -25,14 +25,13 @@ process MAPSEQ2BIOM {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
-
     """
     mapseq2biom \
-        $args \
+        ${args} \
         --krona ${prefix}.txt \
         --no-tax-id-file ${prefix}.notaxid.tsv \
-        --label $db_label \
-        --query $msq \
+        --label ${db_label} \
+        --query ${msq} \
         --otu-table ${db_otu} \
         --out-file ${prefix}.tsv
 

diff --git a/modules/ebi-metagenomics/mapseq2biom/meta.yml b/modules/ebi-metagenomics/mapseq2biom/meta.yml
@@ -16,7 +16,6 @@ tools:
       licence: ["Apache-2.0"]
 
 input:
-  # Only when we have meta
   - meta:
       type: map
       description: |
@@ -26,28 +25,15 @@ input:
       type: file
       description: MAPseq output file
       pattern: "*.mseq"
-  - db_fasta:
-      type: file
-      description: Processed reference database fasta file
-      pattern: "*.{fasta, fasta.gz}"
-  - db_tax:
-      type: file
-      description: Processed reference database taxonomy file
-      pattern: "*.txt"
   - db_otu:
       type: file
       description: Processed reference database otu file
       pattern: "*.otu"
-  - db_mscluster:
-      type: file
-      description: Pre-computed MAPseq cluster file
-      pattern: "*.mscluster"
   - db_label:
       type: string
       description: Reference database label
 
 output:
-  #Only when we have meta
   - meta:
       type: map
       description: |

diff --git a/modules/ebi-metagenomics/mapseq2biom/tests/main.nf.test b/modules/ebi-metagenomics/mapseq2biom/tests/main.nf.test
@@ -20,10 +20,7 @@ nextflow_process {
                     file("${moduleDir}/tests/test.mseq", checkIfExists: true)
                     ]
                 input[1] = [
-                    file("${moduleDir}/tests/silva_ssu/test.fasta", checkIfExists: true),
-                    file("${moduleDir}/tests/silva_ssu/test.txt", checkIfExists: true),
                     file("${moduleDir}/tests/silva_ssu/test.otu", checkIfExists: true),
-                    file("${moduleDir}/tests/silva_ssu/test.mscluster", checkIfExists: true),
                     "SILVA-SSU"
                 ]
                 """
@@ -33,10 +30,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
-                { assert snapshot(process.out.krona_input).match("krona_input") },
-                { assert snapshot(process.out.biom_out).match("biom_out") },
-                { assert snapshot(process.out.biom_out).match("biom_notaxid_out") }
+                { assert snapshot(process.out).match() }
             )
         }
 
@@ -54,10 +48,7 @@ nextflow_process {
                     file("${moduleDir}/tests/test.mseq", checkIfExists: true)
                     ]
                 input[1] = [
-                    file("${moduleDir}/tests/silva_ssu/test.fasta", checkIfExists: true),
-                    file("${moduleDir}/tests/silva_ssu/test.txt", checkIfExists: true),
                     file("${moduleDir}/tests/silva_ssu/test.otu", checkIfExists: true),
-                    file("${moduleDir}/tests/silva_ssu/test.mscluster", checkIfExists: true),
                     "SILVA-SSU"
                 ]
                 """
@@ -67,10 +58,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() },
-                { assert snapshot(process.out.krona_input).match("krona_input_stub") },
-                { assert snapshot(process.out.biom_out).match("biom_out_stub") },
-                { assert snapshot(process.out.biom_out).match("biom_notaxid_out_stub") }
+                { assert snapshot(process.out).match() }
             )
         }
 

diff --git a/modules/ebi-metagenomics/mapseq2biom/tests/main.nf.test.snap b/modules/ebi-metagenomics/mapseq2biom/tests/main.nf.test.snap
@@ -8,7 +8,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.txt:md5,fa3ef8980608011a1ecdd15f93889c0a"
+                        "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -56,7 +56,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.txt:md5,fa3ef8980608011a1ecdd15f93889c0a"
+                        "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
@@ -68,79 +68,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-04-11T09:35:26.295587"
-    },
-    "biom_notaxid_out_stub": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
-                ]
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-04-11T09:40:59.430421"
-    },
-    "biom_notaxid_out": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.tsv:md5,627ca596232e79fe2777f0e9352df993"
-                ]
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-04-11T09:35:09.690135"
-    },
-    "krona_input": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.txt:md5,fa3ef8980608011a1ecdd15f93889c0a"
-                ]
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-04-10T16:01:39.324767"
-    },
-    "biom_out": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.tsv:md5,627ca596232e79fe2777f0e9352df993"
-                ]
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-04-11T09:35:09.683552"
+        "timestamp": "2024-04-11T15:15:47.935539"
     },
     "test_silva - mseq": {
         "content": [
@@ -212,41 +140,5 @@
             "nextflow": "23.10.1"
         },
         "timestamp": "2024-04-11T09:35:09.669445"
-    },
-    "biom_out_stub": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
-                ]
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-04-11T09:35:26.305058"
-    },
-    "krona_input_stub": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.txt:md5,fa3ef8980608011a1ecdd15f93889c0a"
-                ]
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-04-10T16:09:22.893604"
     }
 }