Merge pull request #93 from sanger-bentley-group/feature/assembler_th…

…read

Allow optional assembler thread count option

README.md

@@ -210,9 +210,12 @@ The pipeline is compatible with [Launchpad](https://help.tower.nf/23.2/launch/la
   | `--depth` | Any integer or float value<br />(Default: `20.00`) | Minimum sequencing depth to pass Assembly QC. |
 
 ## Assembly
+> ℹ️ The output of SPAdes-based assembler is deterministic for a given count of threads. Hence, using `--assembler_thread` with a specific value can guarantee the generated assemblies will be reproducible for others using the same value.
+<!-- -->
   | Option | Values | Description |
   | --- | ---| --- |
   | `--assembler` | `"shovill"` or `"unicycler"`<br />(Default: `"shovill"`)| Using which SPAdes-based assembler to assemble the reads. |
+  | `--assembler_thread` | Any integer value<br />(Default: `0`) | Number of threads used by the assembler. `0` means all available. |
   | `--min_contig_length` | Any integer value<br />(Default: `500`) | Minimum legnth of contig to be included in the assembly. |
 
 ## Mapping

modules/assembly.nf

@@ -13,16 +13,25 @@ process ASSEMBLY_UNICYCLER {
     input:
     tuple val(sample_id), path(read1), path(read2), path(unpaired)
     val min_contig_length
+    val assembler_thread
 
     output:
     tuple val(sample_id), path(fasta)
 
     script:
     fasta="${sample_id}.contigs.fasta"
-    """
-    unicycler -1 "$read1" -2 "$read2" -s "$unpaired" -o results -t "`nproc`" --min_fasta_length "$min_contig_length"
-    mv results/assembly.fasta "${fasta}"
-    """
+    thread="$assembler_thread"
+
+    if ( thread.toInteger() == 0 )
+        """
+        unicycler -1 "$read1" -2 "$read2" -s "$unpaired" -o results -t "`nproc`" --min_fasta_length "$min_contig_length"
+        mv results/assembly.fasta "${fasta}"
+        """
+    else   
+        """
+        unicycler -1 "$read1" -2 "$read2" -s "$unpaired" -o results -t "$thread" --min_fasta_length "$min_contig_length"
+        mv results/assembly.fasta "${fasta}"
+        """
 }
 
 // Run Shovill to get assembly
@@ -40,16 +49,25 @@ process ASSEMBLY_SHOVILL {
     input:
     tuple val(sample_id), path(read1), path(read2), path(unpaired)
     val min_contig_length
+    val assembler_thread
 
     output:
     tuple val(sample_id), path(fasta)
 
     script:
     fasta="${sample_id}.contigs.fasta"
-    """
-    shovill --R1 "$read1" --R2 "$read2" --outdir results --cpus "`nproc`" --minlen "$min_contig_length" --force
-    mv results/contigs.fa "${fasta}"
-    """
+    thread="$assembler_thread"
+
+    if ( thread.toInteger() == 0 )
+        """
+        shovill --R1 "$read1" --R2 "$read2" --outdir results --cpus "`nproc`" --minlen "$min_contig_length" --force
+        mv results/contigs.fa "${fasta}"
+        """
+    else
+        """
+        shovill --R1 "$read1" --R2 "$read2" --outdir results --cpus "$thread" --minlen "$min_contig_length" --force
+        mv results/contigs.fa "${fasta}"
+        """
 }
 
 // Run quast to assess assembly quality

modules/info.nf

@@ -368,6 +368,7 @@ process SAVE {
     |${assemblerTextRow('Option', 'Value')}
     |╠═══════════════════════════╪═════════════════════════════════════════════════════════════════════╣
     |${assemblerTextRow('Assembler', params.assembler.capitalize())}
+    |${assemblerTextRow('Assembler Thread', params.assembler_thread == 0 ? "0 (All Available)" : params.assembler_thread)}
     |${assemblerTextRow('Minimum contig length', params.min_contig_length)}
     |╚═══════════════════════════╧═════════════════════════════════════════════════════════════════════╝
     |""".stripMargin()

modules/validate.nf

@@ -8,6 +8,7 @@ validParams = [
     db: 'path',
     assembler: 'assembler',
     min_contig_length: 'int',
+    assembler_thread: 'int',
     assembly_publish: 'publish_mode',
     seroba_db_remote: 'url_targz',
     seroba_kmer: 'int',
@@ -39,7 +40,7 @@ void validate(Map params) {
             |(Only one of --init, --version, --help should be used at one time)
             '''.stripMargin())
         System.exit(1)
-}
+    }
 
     // Skip validation when help option is used
     if (params.help) {

nextflow.config

@@ -19,6 +19,8 @@ params {
 
     // Default assembler
     assembler = "shovill"
+    // Default assembler thread count (0 means all)
+    assembler_thread = 0
     // Default minimum contig length
     min_contig_length = 500
     // Default assembly publish mode

nextflow_schema.json

@@ -133,6 +133,11 @@
                         "unicycler"
                     ]
                 },
+                "assembler_thread": {
+                    "type": "integer",
+                    "description": "Number of threads used by the assembler. 0 means all available.",
+                    "hidden": true
+                },
                 "min_contig_length": {
                     "type": "integer",
                     "description": "Minimum legnth of contig to be included in the assembly.",
@@ -142,7 +147,8 @@
             },
             "required": [
                 "assembler",
-                "min_contig_length"
+                "min_contig_length",
+                "assembler_thread"
             ]
         },
         "mapping": {

workflows/pipeline.nf

@@ -58,11 +58,11 @@ workflow PIPELINE {
     // Output into Channel ASSEMBLY_ch, and hardlink (default) the assemblies to $params.output directory
     switch (params.assembler) {
         case 'shovill':
-            ASSEMBLY_ch = ASSEMBLY_SHOVILL(READ_QC_PASSED_READS_ch, params.min_contig_length)
+            ASSEMBLY_ch = ASSEMBLY_SHOVILL(READ_QC_PASSED_READS_ch, params.min_contig_length, params.assembler_thread)
             break
 
         case 'unicycler':
-            ASSEMBLY_ch = ASSEMBLY_UNICYCLER(READ_QC_PASSED_READS_ch, params.min_contig_length)
+            ASSEMBLY_ch = ASSEMBLY_UNICYCLER(READ_QC_PASSED_READS_ch, params.min_contig_length, params.assembler_thread)
             break
     }