update malt/build module (#6994)

* update malt/build module * use stageAs for input fasta files * Try HTTPS rather than s3 * Trying manually restricting memory * Move config loading to the right place * Update modules/nf-core/malt/build/tests/main.nf.test Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * Update main.nf.test * Update nextflow.config * Get tests running * Adjust to VM minimum * And MALT_RUN * use process.resourceLimits defining the memory limit * Update modules/nf-core/malt/run/tests/nextflow.config Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * Update modules/nf-core/malt/run/tests/nextflow.config Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * Update modules/nf-core/malt/run/tests/nextflow.config Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * Update nextflow.config --------- Co-authored-by: James A. Fellows Yates <[email protected]> Co-authored-by: Mahesh Binzer-Panchal <[email protected]>
nf-core · Nov 27, 2024 · 47f728e · 47f728e
1 parent e24c973
commit 47f728e
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Showing 8 changed files with 44 additions and 43 deletions.
diff --git a/modules/nf-core/malt/build/environment.yml b/modules/nf-core/malt/build/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::malt=0.61
+  - bioconda::malt=0.62
diff --git a/modules/nf-core/malt/build/main.nf b/modules/nf-core/malt/build/main.nf
@@ -1,20 +1,18 @@
 process MALT_BUILD {
-
     label 'process_high'
-
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/malt:0.61--hdfd78af_0' :
-        'biocontainers/malt:0.61--hdfd78af_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/malt:0.62--hdfd78af_0'
+        : 'biocontainers/malt:0.62--hdfd78af_0'}"
 
     input:
-    path fastas
+    path fastas, stageAs: 'fa_folder/'
     path gff
     path mapping_db
 
     output:
-    path "malt_index/"   , emit: index
-    path "versions.yml"  , emit: versions
+    path "malt_index/", emit: index
+    path "versions.yml", emit: versions
     path "malt-build.log", emit: log
 
     when:
@@ -26,12 +24,12 @@ process MALT_BUILD {
 
     """
     malt-build \\
+        ${args} \\
         -v \\
-        --input ${fastas.join(' ')} \\
-        $igff \\
+        --input fa_folder \\
+        ${igff} \\
         -d 'malt_index/' \\
-        -t $task.cpus \\
-        $args \\
+        -t ${task.cpus} \\
         -mdb ${mapping_db}/*.db |&tee malt-build.log
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/nf-core/malt/build/meta.yml b/modules/nf-core/malt/build/meta.yml
@@ -51,5 +51,7 @@ output:
           pattern: "malt-build.log"
 authors:
   - "@jfy133"
+  - "@LilyAnderssonLee"
 maintainers:
   - "@jfy133"
+  - "@LilyAnderssonLee"
diff --git a/modules/nf-core/malt/build/tests/main.nf.test b/modules/nf-core/malt/build/tests/main.nf.test
@@ -3,7 +3,6 @@ nextflow_process {
     name "Test Process MALT_BUILD"
     script "../main.nf"
     process "MALT_BUILD"
-    config "./nextflow.config"
 
     tag "modules"
     tag "modules_nfcore"
@@ -16,18 +15,24 @@ nextflow_process {
             script "../../../unzip/main.nf"
             process {
                 """
-                input[0] = [[], file("s3://ngi-igenomes/test-data/createtaxdb/taxonomy/megan-nucl-Feb2022.db.zip", checkIfExists: true)]
+                input[0] = [[], file("https://ngi-igenomes.s3.eu-west-1.amazonaws.com/test-data/createtaxdb/taxonomy/megan-nucl-Feb2022.db.zip", checkIfExists: true)]
                 """
             }
         }
     }
 
     test("sarscov2 - fastq") {
-
+        config "./nextflow.config"
         when {
+            params {
+                module_args = '-J-Xmx6G --sequenceType DNA'
+            }
             process {
                 """
-                input[0] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+                def genome_1 = file(params.modules_testdata_base_path + 'genomics/prokaryotes/metagenome/fasta/sarscov2.fasta', checkIfExists: true )
+                def genome_2 = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true )
+
+                input[0] = [genome_1,genome_2]
                 input[1] = []
                 input[2] = UNZIP.out.unzipped_archive.map { it[1] }
                 """
@@ -59,13 +64,15 @@ nextflow_process {
     }
 
     test("sarscov2 - fastq - stub") {
-
         options "-stub"
 
         when {
             process {
                 """
-                input[0] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+                def genome_1 = file(params.modules_testdata_base_path + 'genomics/prokaryotes/metagenome/fasta/sarscov2.fasta', checkIfExists: true )
+                def genome_2 = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true )
+
+                input[0] = [genome_1,genome_2]
                 input[1] = []
                 input[2] = UNZIP.out.unzipped_archive.map { it[1] }
                 """

diff --git a/modules/nf-core/malt/build/tests/main.nf.test.snap b/modules/nf-core/malt/build/tests/main.nf.test.snap
@@ -8,7 +8,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,52c299d59c90219b9b442ee54f1acc97"
+                    "versions.yml:md5,4ad582e415ed27dd4a275a149209961b"
                 ],
                 "2": [
                     "malt-build.log:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -22,33 +22,33 @@
                     "malt-build.log:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "versions": [
-                    "versions.yml:md5,52c299d59c90219b9b442ee54f1acc97"
+                    "versions.yml:md5,4ad582e415ed27dd4a275a149209961b"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-01-26T11:49:19.685017271"
+        "timestamp": "2024-11-15T12:14:24.942518"
     },
     "sarscov2 - fastq": {
         "content": [
-            "index0.idx:md5,1954f2c00b418d00112829b0a6adb8ce",
-            "ref.db:md5,772a09aeb162515485b037604399f2bd",
-            "ref.idx:md5,7dea362b3fac8e00956a4952a3d4f474",
-            "ref.inf:md5,b146842067cf278ef1d23e6c2e7c0c35",
-            "taxonomy.idx:md5,bb335e7c378a5bd85761b6eeed16d984",
+            "index0.idx:md5,0ba3d8bfb7ef28d08e2a005dd3405c55",
+            "ref.db:md5,6b36ae031c49feaae50f4cea07d9c7f4",
+            "ref.idx:md5,8ba66cdf65181c7efee1d366574cb9d7",
+            "ref.inf:md5,042712533a0187b6566db67c6503a71e",
+            "taxonomy.idx:md5,e7ce35e6238f39fa0c236fcf991546e4",
             "taxonomy.map:md5,5bb3f2192e925bca2e61e4b54f1671e0",
             "taxonomy.tre:md5,f76fb2d5aa9b0d637234d48175841e0e",
             [
-                "versions.yml:md5,52c299d59c90219b9b442ee54f1acc97"
+                "versions.yml:md5,4ad582e415ed27dd4a275a149209961b"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-06-30T19:04:45.72181253"
+        "timestamp": "2024-11-15T12:13:59.078459"
     }
 }
diff --git a/modules/nf-core/malt/build/tests/nextflow.config b/modules/nf-core/malt/build/tests/nextflow.config
@@ -1,8 +1,5 @@
 process {
-
-
     withName: MALT_BUILD {
-        ext.args = "--sequenceType DNA"
+        ext.args = params.module_args
     }
-
 }
diff --git a/modules/nf-core/malt/run/tests/main.nf.test b/modules/nf-core/malt/run/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_process {
             script "../../../unzip/main.nf"
             process {
                 """
-                input[0] = [[], file("s3://ngi-igenomes/test-data/createtaxdb/taxonomy/megan-nucl-Feb2022.db.zip", checkIfExists: true)]
+                input[0] = [[], file("https://ngi-igenomes.s3.eu-west-1.amazonaws.com/test-data/createtaxdb/taxonomy/megan-nucl-Feb2022.db.zip", checkIfExists: true)]
                 """
             }
         }

diff --git a/modules/nf-core/malt/run/tests/nextflow.config b/modules/nf-core/malt/run/tests/nextflow.config
@@ -1,13 +1,10 @@
 process {
 
-
-    withName: MALT_RUN {
-        ext.args = "-m BlastN -J-Xmx8G -a . -f SAM"
-        memory = 12.GB
-    }
-
     withName: MALT_BUILD {
-        ext.args = "--sequenceType DNA"
+        ext.args = { "-J-Xmx${task.memory.toGiga()}G --sequenceType DNA" }
     }
 
+    withName: MALT_RUN {
+        ext.args = { "-m BlastN -J-Xmx${task.memory.toGiga()}G -a . -f SAM" }
+    }
 }