add default cpu and memory resources

deng-lab · Apr 13, 2023 · 471c32e · 471c32e
1 parent bd4387d
commit 471c32e
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Showing 5 changed files with 208 additions and 12 deletions.
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -3,7 +3,7 @@ name: Docker
 on:
   push:
     tags:
-      - 'v*'
+      # - 'v*'
       - 'docker*'
 
 jobs:

diff --git a/conf/test.config b/conf/test.config
@@ -20,8 +20,7 @@ params {
     max_time   = '24.h'
 
     // Input data for minimal test
-    // input = "https://raw.githubusercontent.com/deng-lab/viroprofiler/main/assets/samplesheet.csv"
-    input = "https://raw.githubusercontent.com/deng-lab/viroprofiler/dev2/assets/samplesheet.csv"
+    input = "https://raw.githubusercontent.com/deng-lab/viroprofiler/main/assets/samplesheet.csv"
     outdir = "output"
     mode = "all"
 

diff --git a/custom.config b/custom.config
@@ -162,7 +162,7 @@ process {
     }
 
     withName: SPADES {
-        cpu = { check_max( 4 * task.attempt, 'cpus') }
+        cpus = { check_max( 4 * task.attempt, 'cpus') }
         memory = { check_max( 20.GB * task.attempt, 'memory') }
     }
 

diff --git a/nextflow.config b/nextflow.config
@@ -14,13 +14,16 @@ params {
     input                      = null
     db                         = "${HOME}/viroprofiler"
     mode                       = 'all'                // ["setup", "all"]
+    input_contigs              = null
+    decontam                   = null
+    reads_type                 = "raw"                // ["raw", "clean"]
 
     // ViroProfiler modules
     use_abricate               = false
     use_decontam               = false
     use_eggnog                 = false
-    use_dram                   = false
-    use_iphop                  = false
+    use_dram                   = true
+    use_iphop                  = true
     use_kraken2                = false
     use_phamb                  = false
 
@@ -169,28 +172,185 @@ env {
 
 process {
     withLabel: setup {
-        cpus = 1
-        memory = "1 GB"
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 8.GB * task.attempt, 'memory') }
+        time = { check_max( 12.h * task.attempt, 'time') }
     }
-
+
+    withName: ABRICATE {
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 2.GB * task.attempt, 'memory') }
+    }
+
+    withName: ABUNDANCE {
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 1.GB * task.attempt, 'memory') }
+    }
+
     withName: BACPHLIP {
         ext.args = "--multi_fasta"
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 4.GB * task.attempt, 'memory') }
+    }
+
+    withName: CHECKV {
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 20.GB * task.attempt, 'memory') }
+    }
+
+    withName: CONTIGLIB {
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 2.GB * task.attempt, 'memory') }
+    }
+
+    withName: CONTIGLIB_CLUSTER {
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 4.GB * task.attempt, 'memory') }
+    }
+
+    withName: DB_DRAM {
+        cpus ={ check_max( 8 * task.attempt, 'cpus') }
+        memory = { check_max( 30.GB * task.attempt, 'memory') }
+    }
+
+    withName: DB_KRAKEN2 {
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 1.GB * task.attempt, 'memory') }
+    }
+
+    withName: DB_VIBRANT {
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 8.GB * task.attempt, 'memory') }
+    }
+
+    withName: DB_VIRSORTER2 {
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 8.GB * task.attempt, 'memory') }
+    }
+
+    withName: DB_VREFSEQ {
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 8.GB * task.attempt, 'memory') }
     }
 
     withName: DECONTAM {
         ext.args = 'maxindel=1 bwr=0.16 bw=12 quickmatch fast minhits=2 qtrim=rl trimq=10 pigz=True untrim'
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 2.GB * task.attempt, 'memory') }
+    }
+
+    withName: DRAMV {
+        cpus = { check_max( 8 * task.attempt, 'cpus') }
+        memory = { check_max( 50.GB * task.attempt, 'memory') }
+    }
+
+    withName: DVF {
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 4.GB * task.attempt, 'memory') }
+    }
+
+    withName: EMAPPER {
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 20.GB * task.attempt, 'memory') }
     }
 
     withName: FASTQC {
         ext.args = '--quiet'
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 2.GB * task.attempt, 'memory') }
+    }
+
+    withName: FASTP {
+        ext.args = "-f 15 -t 1 -F 15 -T 1 --detect_adapter_for_pe -p -n 1 -l 30 -5 -W 4 -M 20 -r -c -g -x"
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 2.GB * task.attempt, 'memory') }
+    }
+
+    withName: GENEPRED {
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 2.GB * task.attempt, 'memory') }
+    }
+
+    withName: MAPPING2CONTIGS {
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 4.GB * task.attempt, 'memory') }
+    }
+
+    withName: MICOMPLETEDB {
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 8.GB * task.attempt, 'memory') }
+    }
+
+    withName: MULTIQC {
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 1.GB * task.attempt, 'memory') }
+    }
+
+    withName: NRSEQS {
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 8.GB * task.attempt, 'memory') }
+    }
+
+    withName: PHAMB_RF {
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 8.GB * task.attempt, 'memory') }
+    }
+
+    withName: REPLIDEC {
+        cpus = { check_max( 2 * task.attempt, 'cpus') }
+        memory = { check_max( 8.GB * task.attempt, 'memory') }
     }
 
     withName: SPADES {
         ext.args = "--meta"
+        cpus = { check_max( 4 * task.attempt, 'cpus') }
+        memory = { check_max( 20.GB * task.attempt, 'memory') }
+    }
+
+    withName: TAXONOMY_MERGE {
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 1.GB * task.attempt, 'memory') }
+    }
+
+    withName: TAXONOMY_MMSEQS {
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 20.GB * task.attempt, 'memory') }
+    }
+
+    withName: TAXONOMY_VCONTACT {
+        cpus = { check_max( 8 * task.attempt, 'cpus') }
+        memory = { check_max( 20.GB * task.attempt, 'memory') }
+    }
+
+    withName: VAMB {
+        cpus = { check_max( 4 * task.attempt, 'cpus') }
+        memory = { check_max( 8.GB * task.attempt, 'memory') }
+    }
+
+    withName: VIBRANT {
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 8.GB * task.attempt, 'memory') }
+    }
+
+    withName: VIRALHOST_IPHOP {
+        cpus = { check_max( 12 * task.attempt, 'cpus') }
+        memory = { check_max( 8.GB * task.attempt, 'memory') }
+    }
+
+    withName: VIRSORTER2 {
+        cpus = { check_max( 8 * task.attempt, 'cpus') }
+        memory = { check_max( 8.GB * task.attempt, 'memory') }
+    }
+
+    withName: VOGDB {
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 8.GB * task.attempt, 'memory') }
     }
 
     withName: VRHYME {
         ext.args = "--method longest"
+        cpus = { check_max( 1 * task.attempt, 'cpus') }
+        memory = { check_max( 8.GB * task.attempt, 'memory') }
     }
 }
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -126,10 +126,10 @@
                 }
             }
         },
-        "gene_library_parameters": {
-            "title": "Gene library parameters",
+        "prot_library_parameters": {
+            "title": "Protein library parameters",
             "type": "object",
-            "description": "Parameters for creating gene library",
+            "description": "Parameters for creating protein library",
             "default": "",
             "properties": {
                 "prot_cluster_min_similarity": {
@@ -144,6 +144,24 @@
                 }
             }
         },
+        "gene_library_parameters": {
+            "title": "Gene library parameters",
+            "type": "object",
+            "description": "Parameters for creating gene library",
+            "default": "",
+            "properties": {
+                "gene_cluster_min_similarity": {
+                    "type": "number",
+                    "description": "Minimum similarity of genes in a gene cluster",
+                    "default": 0.9
+                },
+                "gene_cluster_min_coverage": {
+                    "type": "number",
+                    "description": "Minimum coverage of the shorter gene in a gene cluster",
+                    "default": 0.9
+                }
+            }
+        },
         "binning_parameters": {
             "title": "Binning parameters",
             "type": "object",
@@ -270,6 +288,25 @@
                     "type": "boolean",
                     "description": "Use DRAM for metabolic reconstruction",
                     "default": false
+                },
+                "input_contigs": {
+                    "type": "string",
+                    "description": "Input contigs file",
+                    "default": null
+                },
+                "decontam": {
+                    "type": "string",
+                    "description": "Input contigs file",
+                    "default": null
+                },
+                "reads_type": {
+                    "type": "string",
+                    "description": "Type of reads",
+                    "default": "raw",
+                    "enum": [
+                        "raw",
+                        "clean"
+                    ]
                 }
             }
         },