RUNASSEMBLYVISUALIZER is now single threaded for successful execution…

… on both Linux and MacOS

CHANGELOG.md

@@ -3,14 +3,15 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## 2.0.0 - [30-April-2024]
+## 2.0.0 - [01-May-2024]
 
 ### `Added`
 
 1. Updated modules and sub-workflows
 2. Updated nf-core/template to 2.13.1
 3. Removed release-announcements GitHub workflow
 4. Added a list of nf-core contributors
+5. Added a launcher script for local testing `local_assemblyqc`
 
 ### `Fixed`
 
@@ -19,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 3. Fixed n-core linting
 4. Updated `tower.yml`
 5. Updated LICENSE copyright to Copyright (c) 2024 The New Zealand Institute for Plant and Food Research Limited
+6. `RUNASSEMBLYVISUALIZER` is now single threaded for successful execution on both Linux and MacOS
 
 ### `Dependencies`
 

conf/test_full.config

@@ -20,7 +20,7 @@ params {
     ncbi_fcs_adaptor_empire     = 'euk'
 
     ncbi_fcs_gx_skip            = true // Skipping this step as the dataset is humengous (500 GB). Please download the dataset manually
-    // ncbi_fcs_gx_tax_id       = 35717
+    ncbi_fcs_gx_tax_id          = 35717
     // ncbi_fcs_gx_db_path      = 'https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/r2023-01-24'
 
     busco_skip                  = false

local_assemblyqc

@@ -0,0 +1,27 @@
+#!/usr/bin/env bash
+
+NO_FORMAT="\033[0m"
+C_RED="\033[38;5;9m"
+F_BOLD="\033[1m"
+
+[[ $1 == '-stub' ]] \
+    && stub='-stub' \
+    || stub=''
+
+[[ $1 == '-stub' ]] \
+    && echo 'Executing with -stub' \
+    || echo -e "${C_RED}${F_BOLD}Executing without -stub${NO_FORMAT}"
+
+nextflow run \
+    main.nf \
+    -profile docker,test_full \
+    -resume \
+    $stub \
+    --max_cpus 8 \
+    --max_memory '32.GB' \
+    --ncbi_fcs_gx_skip false \
+    --ncbi_fcs_gx_db_path ../dbs/gxdb/test \
+    --busco_download_path ../dbs/busco \
+    --kraken2_skip false \
+    --kraken2_db_path ../dbs/kraken2db/k2_minusb \
+    --hic "$(realpath ../test-data/assemblyqc/hic)/SRR8238190_{1,2}.fastq.gz"

modules/local/runassemblyvisualizer.nf

@@ -1,6 +1,6 @@
 process RUNASSEMBLYVISUALIZER {
     tag "$sample_id_on_tag"
-    label 'process_medium'
+    label 'process_single'
 
     container "docker.io/gallvp/3d-dna:63029aa"
 
@@ -15,12 +15,12 @@ process RUNASSEMBLYVISUALIZER {
     task.ext.when == null || task.ext.when
 
     script:
-    // -p true/false    Use GNU Parallel to speed up computation (default is true).
     """
     assembly_tag=\$(echo $sample_id_on_tag | sed 's/.*\\.on\\.//g')
     file_name="${agp_assembly_file}"
 
     /usr/src/3d-dna/visualize/run-assembly-visualizer.sh \\
+        -p false \\
         $agp_assembly_file $sorted_links_txt_file
 
     mv "\${file_name%.*}.hic" "\${assembly_tag}.hic"