Merge pull request #104 from sanger-bentley-group/feature/print_actua…

…l_thread_count Save actual assembler thread count when all available are used
sanger-bentley-group · May 29, 2024 · a612211 · a612211
2 parents 9aeb349 + 2b51ea5
commit a612211
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Showing 2 changed files with 24 additions and 7 deletions.
diff --git a/bin/save_tools_info.sh b/bin/save_tools_info.sh
@@ -4,11 +4,15 @@ add_version () {
     jq -n --arg version "$1" '.version = $version'
 }
 
+add_version_and_nproc_value () {
+    jq -n --arg version "$1" --arg nproc_value "$2" '.version = $version | .nproc_value = $nproc_value'
+}
+
 jq -n \
     --argjson python "$(add_version "$PYTHON_VERSION")" \
     --argjson fastp "$(add_version "$FASTP_VERSION")" \
-    --argjson unicycler "$(add_version "$UNICYCLER_VERSION")" \
-    --argjson shovill "$(add_version "$SHOVILL_VERSION")" \
+    --argjson unicycler "$(add_version_and_nproc_value "$UNICYCLER_VERSION" "$UNICYCLER_NPROC_VALUE")" \
+    --argjson shovill "$(add_version_and_nproc_value "$SHOVILL_VERSION" "$SHOVILL_NPROC_VALUE")" \
     --argjson quast "$(add_version "$QUAST_VERSION")" \
     --argjson bwa "$(add_version "$BWA_VERSION")" \
     --argjson samtools "$(add_version "$SAMTOOLS_VERSION")" \

diff --git a/modules/info.nf b/modules/info.nf
@@ -75,8 +75,8 @@ process TOOLS {
     input:
     val python_version
     val fastp_version
-    val unicycler_version
-    val shovill_version
+    tuple  val(unicycler_version), val(unicycler_nproc_value)
+    tuple  val(shovill_version), val(shovill_nproc_value)
     val quast_version
     val bwa_version
     val samtools_version
@@ -96,7 +96,9 @@ process TOOLS {
     PYTHON_VERSION="$python_version"
     FASTP_VERSION="$fastp_version"
     UNICYCLER_VERSION="$unicycler_version"
+    UNICYCLER_NPROC_VALUE="$unicycler_nproc_value"
     SHOVILL_VERSION="$shovill_version"
+    SHOVILL_NPROC_VALUE="$shovill_nproc_value"
     QUAST_VERSION="$quast_version"
     BWA_VERSION="$bwa_version"
     SAMTOOLS_VERSION="$samtools_version"
@@ -153,12 +155,19 @@ process PARSE {
     val dbText
     val toolText
     val imageText
+    val nprocValue
 
     exec:
     def jsonSlurper = new JsonSlurper()
 
     def json = jsonSlurper.parse(new File("${json_file}"))
 
+    if (params.assembler == 'unicycler') {
+        nprocValue = json.unicycler.nproc_value
+    } else if (params.assembler == 'shovill') {
+        nprocValue = json.shovill.nproc_value
+    }
+
     def textRow = { leftSpace, rightSpace, leftContent, rightContent ->
         String.format("║ %-${leftSpace}s │ %-${rightSpace}s ║", leftContent, rightContent)
     }
@@ -305,6 +314,7 @@ process PRINT {
     val dbText
     val toolText
     val imageText
+    val nprocValue
 
     exec:
     log.info(
@@ -332,6 +342,7 @@ process SAVE {
     val dbText
     val toolText
     val imageText
+    val nprocValue
 
     output:
     path "info.txt", emit: info
@@ -368,7 +379,7 @@ process SAVE {
     |${assemblerTextRow('Option', 'Value')}
     |╠═══════════════════════════╪═════════════════════════════════════════════════════════════════════╣
     |${assemblerTextRow('Assembler', params.assembler.capitalize())}
-    |${assemblerTextRow('Assembler Thread', params.assembler_thread == 0 ? "0 (All Available)" : params.assembler_thread)}
+    |${assemblerTextRow('Assembler Thread', params.assembler_thread == 0 ? "${nprocValue} (All Available)" : params.assembler_thread)}
     |${assemblerTextRow('Minimum contig length', params.min_contig_length)}
     |╚═══════════════════════════╧═════════════════════════════════════════════════════════════════════╝
     |""".stripMargin()
@@ -464,11 +475,12 @@ process UNICYCLER_VERSION {
     label 'farm_low'
 
     output:
-    env VERSION
+    tuple env(VERSION), env(THREAD)
 
     shell:
     $/
     VERSION=$(unicycler --version | sed -r "s/.*\sv(.+)/\1/")
+    THREAD=$(nproc)
     /$
 }
 
@@ -477,11 +489,12 @@ process SHOVILL_VERSION {
     label 'farm_low'
 
     output:
-    env VERSION
+    tuple env(VERSION), env(THREAD)
 
     shell:
     $/
     VERSION=$(shovill -v | sed -r "s/.*\s(.+)/\1/")
+    THREAD=$(nproc)
     /$
 }