diff --git a/CHANGELOG.md b/CHANGELOG.md
index 71bb6ef2..e17460c1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 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).
 
-## v2.3.0dev - [12-March-2025]
+## v2.3.0dev - [02-April-2025]
 
 ### `Added`
 
@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 2. The minimum required Nextflow version is now 24.10.5
 3. Now the pipeline parameters are presented in separate sections on the PARAMS summary page in the report
 4. Added parameter `hic_alphanumeric_sort` to allow disabling of FASTA sorting by sequence labels
+5. Added parameter `use_all_cpus` to allow multithreaded tasks to consume all the CPUs available on a machine. This behavior is desirable on [MM Cloud](https://www.mmcloud.io) but highly undesirable on AWS Batch, SLURM, etc.
 
 ### `Fixed`
 
diff --git a/conf/modules.config b/conf/modules.config
index 090ebd3a..e17c2742 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -417,3 +417,4 @@ process {
         ]
     }
 }
+process { ext.use_all_cpus = params.use_all_cpus }
diff --git a/docs/parameters.md b/docs/parameters.md
index 953b2e84..f0de04a0 100644
--- a/docs/parameters.md
+++ b/docs/parameters.md
@@ -131,3 +131,4 @@ Less common options for the pipeline, typically set in a config file.
 | `monochrome_logs`     | Do not use coloured log outputs.                                                                            | `boolean` |         |          | True   |
 | `hook_url`            | Incoming hook URL for messaging service                                                                     | `string`  |         |          | True   |
 | `trace_report_suffix` | Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss. | `string`  |         |          | True   |
+| `use_all_cpus`        | Use all the available CPUs for each task                                                                    | `boolean` |         |          |        |
diff --git a/modules/gallvp/bwa/mem/main.nf b/modules/gallvp/bwa/mem/main.nf
index d18cd936..3e07edcd 100644
--- a/modules/gallvp/bwa/mem/main.nf
+++ b/modules/gallvp/bwa/mem/main.nf
@@ -35,15 +35,19 @@ process BWA_MEM {
                     "bam"
     def reference = fasta && extension=="cram"  ? "--reference ${fasta}" : ""
     if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output"
-    """
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
+	"""
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
     INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'`
 
     bwa mem \\
         $args \\
-        -t $task.cpus \\
+        -t \${task_cpus} \\
         \$INDEX \\
         $reads \\
-        | samtools $samtools_command $args2 ${reference} --threads $task.cpus -o ${prefix}.${extension} -
+        | samtools $samtools_command $args2 ${reference} --threads \${task_cpus} -o ${prefix}.${extension} -
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/gallvp/cat/cat/main.nf b/modules/gallvp/cat/cat/main.nf
index 2862c64c..10b2f517 100644
--- a/modules/gallvp/cat/cat/main.nf
+++ b/modules/gallvp/cat/cat/main.nf
@@ -36,12 +36,16 @@ process CAT_CAT {
     out_zip  = prefix.endsWith('.gz')
     in_zip   = file_list[0].endsWith('.gz')
     command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
-    command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
+    command2 = (!in_zip && out_zip) ? "| pigz -c -p \${task_cpus} $args2" : ''
     if(file_list.contains(prefix.trim())) {
         error "The name of the input file can't be the same as for the output prefix in the " +
         "module CAT_CAT (currently `$prefix`). Please choose a different one."
     }
-    """
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
+	"""
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
     $command1 \\
         $args \\
         ${file_list.join(' ')} \\
diff --git a/modules/gallvp/ltrfinder/main.nf b/modules/gallvp/ltrfinder/main.nf
index 3e59e3c7..e17a2c92 100644
--- a/modules/gallvp/ltrfinder/main.nf
+++ b/modules/gallvp/ltrfinder/main.nf
@@ -21,10 +21,14 @@ process LTRFINDER {
     script:
     def args            = task.ext.args ?: ''
     def prefix          = task.ext.prefix ?: "${meta.id}"
-    """
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
+	"""
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
     LTR_FINDER_parallel \\
         -seq $fasta \\
-        -threads $task.cpus \\
+        -threads \${task_cpus} \\
         $args
 
     mv "${fasta}.finder.combine.scn"    "${prefix}.scn"
diff --git a/modules/gallvp/ltrharvest/main.nf b/modules/gallvp/ltrharvest/main.nf
index 1e5e06d2..8b89dc2d 100644
--- a/modules/gallvp/ltrharvest/main.nf
+++ b/modules/gallvp/ltrharvest/main.nf
@@ -21,11 +21,15 @@ process LTRHARVEST {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    """
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
+	"""
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
     LTR_HARVEST_parallel \\
         -seq $fasta \\
         $args \\
-        -threads $task.cpus
+        -threads \${task_cpus}
 
     mv "${fasta}.harvest.combine.gff3" \\
         "${prefix}.gff3"
diff --git a/modules/gallvp/ltrretriever/lai/main.nf b/modules/gallvp/ltrretriever/lai/main.nf
index 464b215b..00e5d7ea 100644
--- a/modules/gallvp/ltrretriever/lai/main.nf
+++ b/modules/gallvp/ltrretriever/lai/main.nf
@@ -27,12 +27,16 @@ process LTRRETRIEVER_LAI {
     def monoploid_param = monoploid_seqs    ? "-mono $monoploid_seqs"                       : ''
     def lai_output_name = monoploid_seqs    ? "${annotation_out}.${monoploid_seqs}.out.LAI" : "${annotation_out}.LAI"
     def VERSION         = 'beta3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
-    """
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
+	"""
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
     LAI \\
         -genome $fasta \\
         -intact $pass_list \\
         -all $annotation_out \\
-        -t $task.cpus \\
+        -t \${task_cpus} \\
         $monoploid_param \\
         $args \\
         > >(tee "${prefix}.LAI.log") \\
diff --git a/modules/gallvp/ltrretriever/ltrretriever/main.nf b/modules/gallvp/ltrretriever/ltrretriever/main.nf
index 8e1e2beb..59f25912 100644
--- a/modules/gallvp/ltrretriever/ltrretriever/main.nf
+++ b/modules/gallvp/ltrretriever/ltrretriever/main.nf
@@ -41,7 +41,11 @@ process LTRRETRIEVER_LTRRETRIEVER {
     //
     // This copy with permissions logic can be removed once https://github.com/oushujun/LTR_retriever/issues/176
     // has been resolved.
-    """
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
+	"""
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
     cp \\
         $genome \\
         $writable_genome
@@ -56,7 +60,7 @@ process LTRRETRIEVER_LTRRETRIEVER {
         $infinder \\
         $inmgescan \\
         $non_tgca_file \\
-        -threads $task.cpus \\
+        -threads \${task_cpus} \\
         $args \\
         &> >(tee "${prefix}.log" 2>&1) \\
         || echo "Errors from LTR_retriever printed to ${prefix}.log"
diff --git a/modules/gallvp/minimap2/align/main.nf b/modules/gallvp/minimap2/align/main.nf
index d82dc14d..cd87b53d 100644
--- a/modules/gallvp/minimap2/align/main.nf
+++ b/modules/gallvp/minimap2/align/main.nf
@@ -32,19 +32,23 @@ process MINIMAP2_ALIGN {
     def args4 = task.ext.args4 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def bam_index = bam_index_extension ? "${prefix}.bam##idx##${prefix}.bam.${bam_index_extension} --write-index" : "${prefix}.bam"
-    def bam_output = bam_format ? "-a | samtools sort -@ ${task.cpus-1} -o ${bam_index} ${args2}" : "-o ${prefix}.paf"
+    def bam_output = bam_format ? "-a | samtools sort -@ \$((task_cpus-1)) -o ${bam_index} ${args2}" : "-o ${prefix}.paf"
     def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
     def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
     def bam_input = "${reads.extension}".matches('sam|bam|cram')
-    def samtools_reset_fastq = bam_input ? "samtools reset --threads ${task.cpus-1} $args3 $reads | samtools fastq --threads ${task.cpus-1} $args4 |" : ''
+    def samtools_reset_fastq = bam_input ? "samtools reset --threads \$((task_cpus-1)) $args3 $reads | samtools fastq --threads \$((task_cpus-1)) $args4 |" : ''
     def query = bam_input ? "-" : reads
     def target = reference ?: (bam_input ? error("BAM input requires reference") : reads)
 
-    """
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
+	"""
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
     $samtools_reset_fastq \\
     minimap2 \\
         $args \\
-        -t $task.cpus \\
+        -t \${task_cpus} \\
         $target \\
         $query \\
         $cigar_paf \\
diff --git a/modules/gallvp/seqkit/seq/main.nf b/modules/gallvp/seqkit/seq/main.nf
index 9d76da21..d19eadbe 100644
--- a/modules/gallvp/seqkit/seq/main.nf
+++ b/modules/gallvp/seqkit/seq/main.nf
@@ -29,10 +29,14 @@ process SEQKIT_SEQ {
     extension       = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
     def call_gzip   = extension.endsWith('.gz') ? "| gzip -c $args2" : ''
     if("${prefix}.${extension}" == "$fastx") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
-    """
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
+	"""
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
     seqkit \\
         seq \\
-        --threads $task.cpus \\
+        --threads \${task_cpus} \\
         $args \\
         $fastx \\
         $call_gzip \\
diff --git a/modules/local/juicer_sort.nf b/modules/local/juicer_sort.nf
index 4b0645bd..fbcd2f68 100644
--- a/modules/local/juicer_sort.nf
+++ b/modules/local/juicer_sort.nf
@@ -17,8 +17,12 @@ process JUICER_SORT {
     task.ext.when == null || task.ext.when
 
     script:
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
     """
-    sort --parallel=${task.cpus} \\
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
+    sort --parallel=\${task_cpus} \\
         -k2,2 -k6,6 \\
         $out_links_txt \\
         > out.sorted.links.txt
diff --git a/modules/local/kraken2.nf b/modules/local/kraken2.nf
index 53f722ac..2183fbd7 100644
--- a/modules/local/kraken2.nf
+++ b/modules/local/kraken2.nf
@@ -18,13 +18,17 @@ process KRAKEN2 {
     task.ext.when == null || task.ext.when
 
     script:
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
     """
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
     kraken2 \\
         --output "${asm_tag}.kraken2.cut" \\
         --report "${asm_tag}.kraken2.report" \\
         --use-names \\
         --db $db_path \\
-        --threads ${task.cpus} \\
+        --threads \${task_cpus} \\
         $fasta_file > kraken2.log
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/local/mummer.nf b/modules/local/mummer.nf
index 401dbaa1..1a1be4a8 100644
--- a/modules/local/mummer.nf
+++ b/modules/local/mummer.nf
@@ -15,10 +15,14 @@ process MUMMER {
     task.ext.when == null || task.ext.when
 
     script:
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
     """
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
     nucmer \
         --mum \\
-        -t ${task.cpus} \\
+        -t \${task_cpus} \\
         -p "${target}.on.${reference}" \\
         $ref_fasta \\
         $target_fasta
diff --git a/modules/local/ncbi_fcs_gx_screen_samples.nf b/modules/local/ncbi_fcs_gx_screen_samples.nf
index 24276f61..55df8882 100644
--- a/modules/local/ncbi_fcs_gx_screen_samples.nf
+++ b/modules/local/ncbi_fcs_gx_screen_samples.nf
@@ -22,8 +22,12 @@ process NCBI_FCS_GX_SCREEN_SAMPLES {
 
     script:
     def VERSION = '0.5.4'
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
     """
-    export GX_NUM_CORES=$task.cpus
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
+    export GX_NUM_CORES=\${task_cpus}
 
     for sample_fasta in $samples;
     do
diff --git a/modules/nf-core/busco/busco/main.nf b/modules/nf-core/busco/busco/main.nf
index 17496910..b4c8381d 100644
--- a/modules/nf-core/busco/busco/main.nf
+++ b/modules/nf-core/busco/busco/main.nf
@@ -45,7 +45,11 @@ process BUSCO_BUSCO {
         : "--lineage_dataset ${lineage}"
     def busco_lineage_dir = busco_lineages_path ? "--download_path ${busco_lineages_path}" : ''
     def clean_cmd = clean_intermediates ? 'rm -fr ./*-busco/*/auto_lineage ./*-busco/*/**/{miniprot,hmmer,.bbtools}_output' : ''
-    """
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
+	"""
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
     # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
     # Check for container variable initialisation script and source it.
     if [ -f "/usr/local/env-activate.sh" ]; then
@@ -77,7 +81,7 @@ process BUSCO_BUSCO {
     cd ..
 
     busco \\
-        --cpu $task.cpus \\
+        --cpu \${task_cpus} \\
         --in "\$INPUT_SEQS" \\
         --out ${prefix}-busco \\
         --mode $mode \\
diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
index e1b9f565..cb94900f 100644
--- a/modules/nf-core/fastp/main.nf
+++ b/modules/nf-core/fastp/main.nf
@@ -35,14 +35,18 @@ process FASTP {
     def out_fq2 = discard_trimmed_pass ?: "--out2 ${prefix}_2.fastp.fastq.gz"
     // Added soft-links to original fastqs for consistent naming in MultiQC
     // Use single ended for interleaved. Add --interleaved_in in config.
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
     if ( task.ext.args?.contains('--interleaved_in') ) {
-        """
+	    """
+        n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+        task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
         [ ! -f  ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
 
         fastp \\
             --stdout \\
             --in1 ${prefix}.fastq.gz \\
-            --thread $task.cpus \\
+            --thread \${task_cpus} \\
             --json ${prefix}.fastp.json \\
             --html ${prefix}.fastp.html \\
             $adapter_list \\
@@ -58,12 +62,15 @@ process FASTP {
         """
     } else if (meta.single_end) {
         """
+        n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+        task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
         [ ! -f  ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
 
         fastp \\
             --in1 ${prefix}.fastq.gz \\
             $out_fq1 \\
-            --thread $task.cpus \\
+            --thread \${task_cpus} \\
             --json ${prefix}.fastp.json \\
             --html ${prefix}.fastp.html \\
             $adapter_list \\
@@ -79,6 +86,9 @@ process FASTP {
     } else {
         def merge_fastq = save_merged ? "-m --merged_out ${prefix}.merged.fastq.gz" : ''
         """
+        n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+        task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
         [ ! -f  ${prefix}_1.fastq.gz ] && ln -sf ${reads[0]} ${prefix}_1.fastq.gz
         [ ! -f  ${prefix}_2.fastq.gz ] && ln -sf ${reads[1]} ${prefix}_2.fastq.gz
         fastp \\
@@ -91,7 +101,7 @@ process FASTP {
             $adapter_list \\
             $fail_fastq \\
             $merge_fastq \\
-            --thread $task.cpus \\
+            --thread \${task_cpus} \\
             --detect_adapter_for_pe \\
             $args \\
             2> >(tee ${prefix}.fastp.log >&2)
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 033f4154..d6b9794d 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -33,14 +33,18 @@ process FASTQC {
     // FastQC memory value allowed range (100 - 10000)
     def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
 
-    """
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
+	"""
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
     printf "%s %s\\n" ${rename_to} | while read old_name new_name; do
         [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
     done
 
     fastqc \\
         ${args} \\
-        --threads ${task.cpus} \\
+        --threads \${task_cpus} \\
         --memory ${fastqc_memory} \\
         ${renamed_files}
 
diff --git a/modules/nf-core/gfastats/main.nf b/modules/nf-core/gfastats/main.nf
index 0fb31832..6e6f53d2 100644
--- a/modules/nf-core/gfastats/main.nf
+++ b/modules/nf-core/gfastats/main.nf
@@ -32,10 +32,14 @@ process GFASTATS {
     def ibed = include_bed ? "--include-bed $include_bed" : ""
     def ebed = exclude_bed ? "--exclude-bed $exclude_bed" : ""
     def sak  = instructions ? "--swiss-army-knife $instructions" : ""
-    """
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
+	"""
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
     gfastats \\
         $args \\
-        --threads $task.cpus \\
+        --threads \${task_cpus} \\
         $agp \\
         $ibed \\
         $ebed \\
diff --git a/modules/nf-core/merqury/merqury/main.nf b/modules/nf-core/merqury/merqury/main.nf
index ca8795a9..c6fb6916 100644
--- a/modules/nf-core/merqury/merqury/main.nf
+++ b/modules/nf-core/merqury/merqury/main.nf
@@ -37,7 +37,11 @@ process MERQURY_MERQURY {
     // def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = 1.3 // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
-    """
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
+	"""
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
     # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
     # Check for container variable initialisation script and source it.
     if [ -f "/usr/local/env-activate.sh" ]; then
@@ -46,7 +50,7 @@ process MERQURY_MERQURY {
         set -u
     fi
     # limit meryl to use the assigned number of cores.
-    export OMP_NUM_THREADS=$task.cpus
+    export OMP_NUM_THREADS=\${task_cpus}
 
     merqury.sh \\
         $meryl_db \\
diff --git a/modules/nf-core/meryl/count/main.nf b/modules/nf-core/meryl/count/main.nf
index c90079d6..ad3418e7 100644
--- a/modules/nf-core/meryl/count/main.nf
+++ b/modules/nf-core/meryl/count/main.nf
@@ -22,11 +22,15 @@ process MERYL_COUNT {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def reduced_mem = task.memory.multiply(0.9).toGiga()
-    """
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
+	"""
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
     for READ in ${reads}; do
         meryl count \\
             k=${kvalue} \\
-            threads=${task.cpus} \\
+            threads=\${task_cpus} \\
             memory=${reduced_mem} \\
             ${args} \\
             \$READ \\
diff --git a/modules/nf-core/meryl/unionsum/main.nf b/modules/nf-core/meryl/unionsum/main.nf
index bc2853b0..9a2d06f3 100644
--- a/modules/nf-core/meryl/unionsum/main.nf
+++ b/modules/nf-core/meryl/unionsum/main.nf
@@ -21,10 +21,14 @@ process MERYL_UNIONSUM {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    """
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
+	"""
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
     meryl union-sum \\
         k=$kvalue \\
-        threads=$task.cpus \\
+        threads=\${task_cpus} \\
         memory=${task.memory.toGiga()} \\
         $args \\
         output ${prefix}.unionsum.meryl \\
diff --git a/modules/nf-core/minimap2/align/main.nf b/modules/nf-core/minimap2/align/main.nf
index d82dc14d..cd87b53d 100644
--- a/modules/nf-core/minimap2/align/main.nf
+++ b/modules/nf-core/minimap2/align/main.nf
@@ -32,19 +32,23 @@ process MINIMAP2_ALIGN {
     def args4 = task.ext.args4 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def bam_index = bam_index_extension ? "${prefix}.bam##idx##${prefix}.bam.${bam_index_extension} --write-index" : "${prefix}.bam"
-    def bam_output = bam_format ? "-a | samtools sort -@ ${task.cpus-1} -o ${bam_index} ${args2}" : "-o ${prefix}.paf"
+    def bam_output = bam_format ? "-a | samtools sort -@ \$((task_cpus-1)) -o ${bam_index} ${args2}" : "-o ${prefix}.paf"
     def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
     def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
     def bam_input = "${reads.extension}".matches('sam|bam|cram')
-    def samtools_reset_fastq = bam_input ? "samtools reset --threads ${task.cpus-1} $args3 $reads | samtools fastq --threads ${task.cpus-1} $args4 |" : ''
+    def samtools_reset_fastq = bam_input ? "samtools reset --threads \$((task_cpus-1)) $args3 $reads | samtools fastq --threads \$((task_cpus-1)) $args4 |" : ''
     def query = bam_input ? "-" : reads
     def target = reference ?: (bam_input ? error("BAM input requires reference") : reads)
 
-    """
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
+	"""
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
     $samtools_reset_fastq \\
     minimap2 \\
         $args \\
-        -t $task.cpus \\
+        -t \${task_cpus} \\
         $target \\
         $query \\
         $cigar_paf \\
diff --git a/modules/nf-core/orthofinder/main.nf b/modules/nf-core/orthofinder/main.nf
index a47c4dea..e799b5d9 100644
--- a/modules/nf-core/orthofinder/main.nf
+++ b/modules/nf-core/orthofinder/main.nf
@@ -24,12 +24,16 @@ process ORTHOFINDER {
     prefix = task.ext.prefix ?: "${meta.id}"
     def include_command = prior_run   ? "-b $prior_run" : ''
 
-    """
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
+	"""
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
     mkdir temp_pickle
 
     orthofinder \\
-        -t $task.cpus \\
-        -a $task.cpus \\
+        -t \${task_cpus} \\
+        -a \${task_cpus} \\
         -p temp_pickle \\
         -f input \\
         -n $prefix \\
diff --git a/modules/nf-core/seqkit/rmdup/main.nf b/modules/nf-core/seqkit/rmdup/main.nf
index f943a76f..393a45c0 100644
--- a/modules/nf-core/seqkit/rmdup/main.nf
+++ b/modules/nf-core/seqkit/rmdup/main.nf
@@ -29,10 +29,14 @@ process SEQKIT_RMDUP {
     extension       = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
     // SeqKit/rmdup takes care of compressing the output: https://bioinf.shenwei.me/seqkit/usage/#rmdup
     if("${prefix}.${extension}" == "$fastx") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
-    """
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
+	"""
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
     seqkit \\
         rmdup \\
-        --threads $task.cpus \\
+        --threads \${task_cpus} \\
         $args \\
         $fastx \\
         -o ${prefix}.${extension} \\
diff --git a/modules/nf-core/seqkit/seq/main.nf b/modules/nf-core/seqkit/seq/main.nf
index 9d76da21..d19eadbe 100644
--- a/modules/nf-core/seqkit/seq/main.nf
+++ b/modules/nf-core/seqkit/seq/main.nf
@@ -29,10 +29,14 @@ process SEQKIT_SEQ {
     extension       = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
     def call_gzip   = extension.endsWith('.gz') ? "| gzip -c $args2" : ''
     if("${prefix}.${extension}" == "$fastx") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
-    """
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
+	"""
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
     seqkit \\
         seq \\
-        --threads $task.cpus \\
+        --threads \${task_cpus} \\
         $args \\
         $fastx \\
         $call_gzip \\
diff --git a/modules/nf-core/seqkit/sort/main.nf b/modules/nf-core/seqkit/sort/main.nf
index 19f5a1a4..e4be2546 100644
--- a/modules/nf-core/seqkit/sort/main.nf
+++ b/modules/nf-core/seqkit/sort/main.nf
@@ -29,10 +29,14 @@ process SEQKIT_SORT {
     extension       = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
     def call_gzip   = extension.endsWith('.gz') ? "| gzip -c $args2 " : ''
     if("${prefix}.${extension}" == "$fastx") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
-    """
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
+	"""
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
     seqkit \\
         sort \\
-        --threads $task.cpus \\
+        --threads \${task_cpus} \\
         $args \\
         $fastx \\
         $call_gzip \\
diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf
index d5b65bab..11af28e3 100644
--- a/modules/nf-core/sratools/fasterqdump/main.nf
+++ b/modules/nf-core/sratools/fasterqdump/main.nf
@@ -33,12 +33,16 @@ process SRATOOLS_FASTERQDUMP {
     } else if (certificate.toString().endsWith('.ngc')) {
         key_file += " --ngc ${certificate}"
     }
-    """
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
+	"""
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+
     export NCBI_SETTINGS="\$PWD/${ncbi_settings}"
 
     fasterq-dump \\
         $args \\
-        --threads $task.cpus \\
+        --threads \${task_cpus} \\
         --outfile $outfile \\
         ${key_file} \\
         ${sra}
@@ -48,7 +52,7 @@ process SRATOOLS_FASTERQDUMP {
     pigz \\
         $args2 \\
         --no-name \\
-        --processes $task.cpus \\
+        --processes \${task_cpus} \\
         *.fastq
 
     cat <<-END_VERSIONS > versions.yml
@@ -73,7 +77,11 @@ process SRATOOLS_FASTERQDUMP {
         key_file += " --ngc ${certificate}"
     }
     def touch_outfiles = meta.single_end ? "${prefix}.fastq" : "${prefix}_1.fastq ${prefix}_2.fastq"
-    """
+    def use_all_cpus = task.ext.use_all_cpus ? 'yes' : 'no'
+	"""
+    n_proc=\$(nproc 2>/dev/null || < /proc/cpuinfo grep '^process' -c)
+    task_cpus=\$([ "$use_all_cpus" = "yes" ] && echo "\$n_proc" || echo "$task.cpus")
+    
     touch $touch_outfiles
 
     export NCBI_SETTINGS="\$PWD/${ncbi_settings}"
@@ -81,7 +89,7 @@ process SRATOOLS_FASTERQDUMP {
     echo \\
     "fasterq-dump \\
         $args \\
-        --threads $task.cpus \\
+        --threads \${task_cpus} \\
         --outfile $outfile \\
         ${key_file} \\
         ${sra}"
@@ -91,7 +99,7 @@ process SRATOOLS_FASTERQDUMP {
     pigz \\
         $args2 \\
         --no-name \\
-        --processes $task.cpus \\
+        --processes \${task_cpus} \\
         *.fastq
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/nextflow.config b/nextflow.config
index b2fc814c..454d34c7 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -91,6 +91,7 @@ params {
     help_full                           = false
     show_hidden                         = false
     trace_report_suffix                 = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options
+    use_all_cpus                        = false
 
     // Config options
     config_profile_name                 = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index eaaa6d1c..5a1a99c4 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -460,6 +460,11 @@
                     "fa_icon": "far calendar",
                     "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
                     "hidden": true
+                },
+                "use_all_cpus": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-microchip",
+                    "description": "Use all the available CPUs for each task"
                 }
             }
         }
diff --git a/subworkflows/local/utils_nfcore_assemblyqc_pipeline/main.nf b/subworkflows/local/utils_nfcore_assemblyqc_pipeline/main.nf
index 3ef50014..01715cda 100644
--- a/subworkflows/local/utils_nfcore_assemblyqc_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_assemblyqc_pipeline/main.nf
@@ -171,7 +171,7 @@ workflow PIPELINE_INITIALISATION {
     maternal_reads                          = ch_maternal_reads
     paternal_reads                          = ch_paternal_reads
     params_as_json                          = ch_params_as_json
-    summary_params_as_json                  = ch_summary_params_as_json | view
+    summary_params_as_json                  = ch_summary_params_as_json
     versions                                = ch_versions
 }