From 23f3ecb9b92a2108f556b66ab671707232984566 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 23 Jun 2026 15:02:18 +0200 Subject: [PATCH 1/8] Expand resource usage guidance in documentation Added detailed resource usage guidance for nf-core/mag pipeline, including default resource requests for each module. --- docs/usage/resource_guidance.md | 123 ++++++++++++++++++++++++++++++++ 1 file changed, 123 insertions(+) create mode 100644 docs/usage/resource_guidance.md diff --git a/docs/usage/resource_guidance.md b/docs/usage/resource_guidance.md new file mode 100644 index 000000000..078eda81b --- /dev/null +++ b/docs/usage/resource_guidance.md @@ -0,0 +1,123 @@ +# Resource usage guidance + +**nf-core/mag** is a bioinformatics best-practice analysis pipeline for the assembly, binning, and annotation of metagenomes. + +Due to the nature of metagenomic samples, nf-core/mag can in some cases require large amounts of computational resources to execute. + +In this page we provide information and guidance on how nf-core/mag works by default, and in some cases how to optimise computational resource usage. + +## Grouping modules. + +By default, nf-core/mag aims to make the runtime as efficiently as possible on HPC and similar infrastructure through generating more but shorter running jobs. + +For example, all pre-assembly steps typically run one job per input FASTQ file. +After assembly, each step runs on a per assembly or contig. +After binning, each step runs on a per-bin basis. + +The only exception to this are report aggregation steps, which concatenate report tables from all samples together for a given step (e.g. CONCAT_QUAST_SUMMARY, or BIN_SUMMARY). +However these are computationally very light and should not impact a user. + +## Default resource requests + +The following table lists the default resource requests for every module in the pipeline. +Note that not all modules will run in every pipeline run, nor that the tool will necessarily actually use the requested amount. + +_Table generated for nf-core/mag v5.5, using Claude Haiku 4.5, and verified for accuracy by a human_ + +| Module Name | CPU | Memory | Time | Source | +|-------------|-----|--------|------|--------| +| ADAPTERREMOVAL | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | +| ADJUST_MAXBIN2_EXT | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | +| ALE | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| BBMAP_BBNORM | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | +| BCFTOOLS_CONSENSUS | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | +| BCFTOOLS_INDEX | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | +| BCFTOOLS_VIEW | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | +| BIN_SUMMARY | 1 * task.attempt | 7.GB * task.attempt | 4.h * task.attempt | Default | +| BOWTIE2_ASSEMBLY_ALIGN | 2 * task.attempt | 8.GB * task.attempt | 8.h * task.attempt | Named process | +| BOWTIE2_ASSEMBLY_BUILD | 1 * task.attempt | 7.GB * task.attempt | 4.h * task.attempt | Default | +| BOWTIE2_REMOVAL_ALIGN | 1 * task.attempt | 7.GB * task.attempt | 4.h * task.attempt | Default | +| BOWTIE2_REMOVAL_BUILD | 1 * task.attempt | 7.GB * task.attempt | 4.h * task.attempt | Default | +| BUSCO_BUSCO | 10 * task.attempt | 12.GB * task.attempt | 8.h * task.attempt | Named process | +| CATPACK_ADDNAMES | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| CATPACK_BINS | 6 * task.attempt | 120.GB * task.attempt | 8.h * task.attempt | Named process | +| CATPACK_CONTIGS | 6 * task.attempt | 60.GB * task.attempt | 8.h * task.attempt | Named process | +| CATPACK_DOWNLOAD | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| CATPACK_PREPARE | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | +| CATPACK_SUMMARISE | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| CAT_FASTQ | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| CHECKM2_DATABASEDOWNLOAD | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| CHECKM2_PREDICT | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | +| CHECKM_LINEAGEWF | 6 * task.attempt | 42.GB | 8.h * task.attempt | Named process | +| CHECKM_QA | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | +| CHOPPER | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | +| COMEBIN_RUNCOMEBIN | 12 * task.attempt | 72.GB * task.attempt | 16.h * task.attempt | Label: process_high | +| CONCOCT_CONCOCT | 12 * task.attempt | 72.GB * task.attempt | 16.h * task.attempt | Label: process_high | +| CONCOCT_CONCOCTCOVERAGETABLE | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| CONCOCT_CUTUPFASTA | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| CONCOCT_EXTRACTFASTABINS | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| CONCOCT_MERGECUTUPCLUSTERING | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| CONVERT_DEPTHS | 1 * task.attempt | 7.GB * task.attempt | 4.h * task.attempt | Default | +| DASTOOL_DASTOOL | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | +| DASTOOL_FASTATOCONTIG2BIN | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| FASTP | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | +| FASTQC | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | +| FILTLONG | 8 * task.attempt | 64.GB * (2 ** (task.attempt - 1)) | 24.h * (2 ** (task.attempt - 1)) | Named process | +| FIND_CONCATENATE | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | +| FLYE | 12 * task.attempt | 72.GB * (2 ** (task.attempt - 1)) | 24.h * (2 ** (task.attempt - 1)) | Named process | +| FREEBAYES | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| GENOMAD_DOWNLOAD | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| GENOMAD_ENDTOEND | 12 * task.attempt | 72.GB * task.attempt | 16.h * task.attempt | Label: process_high | +| GTDBTK_CLASSIFYWF | 10 * task.attempt | 140.GB * task.attempt | 12.h * task.attempt | Named process | +| GTDBTK_DB_PREPARATION | 1 * task.attempt | 7.GB * task.attempt | 4.h * task.attempt | Default | +| GTDBTK_SUMMARY | 1 * task.attempt | 7.GB * task.attempt | 4.h * task.attempt | Default | +| GUNC_DOWNLOADDB | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| GUNC_MERGECHECKM | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| GUNC_RUN | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | +| GUNZIP | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| MAG_DEPTHS | 1 * task.attempt | 16.GB * task.attempt | 4.h * task.attempt | Named process | +| MAG_DEPTHS_SUMMARY | 1 * task.attempt | 7.GB * task.attempt | 4.h * task.attempt | Default | +| MAXBIN2 | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | +| MEGAHIT | params.megahit_fix_cpu_1 ? 1 : (8 * task.attempt) | 40.GB * task.attempt | 16.h * task.attempt | Named process | +| METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | +| METABAT2_METABAT2 | 8 * task.attempt | 20.GB * task.attempt | 8.h * task.attempt | Named process | +| METABINNER_BINS | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | +| METABINNER_KMER | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | +| METABINNER_METABINNER | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | +| METABINNER_TOOSHORT | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | +| METAEUK_EASYPREDICT | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | +| METAMDBG_ASM | 12 * task.attempt | 72.GB * (2 ** (task.attempt - 1)) | 24.h * (2 ** (task.attempt - 1)) | Named process | +| MINIMAP2_ALIGN | 12 * task.attempt | 72.GB * task.attempt | 16.h * task.attempt | Label: process_high | +| MINIMAP2_INDEX | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | +| MMSEQS_DATABASES | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | +| MULTIQC | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| NANOLYSE | 2 * task.attempt | 10.GB * task.attempt | 3.h * task.attempt | Named process | +| NANOPLOT | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | +| NANOQ | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | +| PORECHOP_ABI | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | +| PORECHOP_PORECHOP | 4 * task.attempt | 30.GB * task.attempt | 4.h * task.attempt | Named process | +| PREPARE_BIGMAG_SUMMARY | 1 * task.attempt | 7.GB * task.attempt | 4.h * task.attempt | Default | +| PRODIGAL | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| PROKKA | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | +| PYDAMAGE_ANALYZE | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | +| PYDAMAGE_FILTER | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| PYPOLCA_RUN | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | +| QSV_CAT | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| QUAST | 1 * task.attempt | 7.GB * task.attempt | 4.h * task.attempt | Default | +| QUAST_BINS | 1 * task.attempt | 7.GB * task.attempt | 4.h * task.attempt | Default | +| RENAME_POSTDASTOOL | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | +| RENAME_PREDASTOOL | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | +| SAMTOOLS_FAIDX | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| SAMTOOLS_INDEX | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | +| SAMTOOLS_STATS | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| SAMTOOLS_UNMAPPED | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | +| SEMIBIN_SINGLEEASYBIN | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | +| SEQKIT_STATS | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | +| SEQTK_MERGEPE | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| SPADES | 12 * task.attempt | 72.GB * task.attempt | 16.h * task.attempt | Label: process_high | +| SPLIT_FASTA | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | +| SUMMARISE_PYDAMAGEBINS | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | +| TIARA_CLASSIFY | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +| TIARA_TIARA | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | +| TRIMMOMATIC | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | +| UNTAR | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | From a705b3262ac78a93d29ecca64a981aaff393876c Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 23 Jun 2026 15:02:52 +0200 Subject: [PATCH 2/8] Add link to Resource guidance in usage.md Updated usage documentation to include new resource guidance link. --- docs/usage.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/usage.md b/docs/usage.md index ea567130b..72ec5c681 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -11,6 +11,7 @@ In addition to this page, you can find additional usage information on the following pages: - [New to mag?](usage/new_to_mag.md) +- [Resource guidance](usage/resource_guidance.md) ## Input specifications From daf5e5d97ea78b400a89512011ad75d7c3b2eef4 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 23 Jun 2026 17:41:30 +0200 Subject: [PATCH 3/8] Add defaults table --- docs/usage/resource_guidance.md | 242 ++++++++++++++++++-------------- nextflow.config | 5 +- 2 files changed, 136 insertions(+), 111 deletions(-) diff --git a/docs/usage/resource_guidance.md b/docs/usage/resource_guidance.md index 078eda81b..84bb3211d 100644 --- a/docs/usage/resource_guidance.md +++ b/docs/usage/resource_guidance.md @@ -6,118 +6,142 @@ Due to the nature of metagenomic samples, nf-core/mag can in some cases require In this page we provide information and guidance on how nf-core/mag works by default, and in some cases how to optimise computational resource usage. -## Grouping modules. +## Multi-sample or bin executing modules -By default, nf-core/mag aims to make the runtime as efficiently as possible on HPC and similar infrastructure through generating more but shorter running jobs. +By default, nf-core/mag aims to make the runtime as efficiently as possible on HPC and similar infrastructure through generating more but shorter running jobs. -For example, all pre-assembly steps typically run one job per input FASTQ file. -After assembly, each step runs on a per assembly or contig. -After binning, each step runs on a per-bin basis. +In most cases, all pre-assembly steps typically run one job per input FASTQ file. +After assembly, most steps run on a per assembly or contig. +After binning, each step runs on a per-bin basis, and so forth. -The only exception to this are report aggregation steps, which concatenate report tables from all samples together for a given step (e.g. CONCAT_QUAST_SUMMARY, or BIN_SUMMARY). -However these are computationally very light and should not impact a user. +There are a few exceptions to this. +In the following cases, depending on the options you set in the pipeline, you may see some steps running as a single job with multiple samples. + +- Multiple samples processed in one job: + - If `--coassemble_group`: all reads across all samples will be pooled into one assembly job (e.g. MEGAHIT, metaSPAdes) + - If `--gtdbtk_single_job`: all bins across all samples will be pooled into a single GTDBTk classification job ## Default resource requests -The following table lists the default resource requests for every module in the pipeline. -Note that not all modules will run in every pipeline run, nor that the tool will necessarily actually use the requested amount. - -_Table generated for nf-core/mag v5.5, using Claude Haiku 4.5, and verified for accuracy by a human_ - -| Module Name | CPU | Memory | Time | Source | -|-------------|-----|--------|------|--------| -| ADAPTERREMOVAL | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | -| ADJUST_MAXBIN2_EXT | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | -| ALE | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| BBMAP_BBNORM | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | -| BCFTOOLS_CONSENSUS | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | -| BCFTOOLS_INDEX | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | -| BCFTOOLS_VIEW | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | -| BIN_SUMMARY | 1 * task.attempt | 7.GB * task.attempt | 4.h * task.attempt | Default | -| BOWTIE2_ASSEMBLY_ALIGN | 2 * task.attempt | 8.GB * task.attempt | 8.h * task.attempt | Named process | -| BOWTIE2_ASSEMBLY_BUILD | 1 * task.attempt | 7.GB * task.attempt | 4.h * task.attempt | Default | -| BOWTIE2_REMOVAL_ALIGN | 1 * task.attempt | 7.GB * task.attempt | 4.h * task.attempt | Default | -| BOWTIE2_REMOVAL_BUILD | 1 * task.attempt | 7.GB * task.attempt | 4.h * task.attempt | Default | -| BUSCO_BUSCO | 10 * task.attempt | 12.GB * task.attempt | 8.h * task.attempt | Named process | -| CATPACK_ADDNAMES | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| CATPACK_BINS | 6 * task.attempt | 120.GB * task.attempt | 8.h * task.attempt | Named process | -| CATPACK_CONTIGS | 6 * task.attempt | 60.GB * task.attempt | 8.h * task.attempt | Named process | -| CATPACK_DOWNLOAD | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| CATPACK_PREPARE | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | -| CATPACK_SUMMARISE | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| CAT_FASTQ | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| CHECKM2_DATABASEDOWNLOAD | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| CHECKM2_PREDICT | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | -| CHECKM_LINEAGEWF | 6 * task.attempt | 42.GB | 8.h * task.attempt | Named process | -| CHECKM_QA | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | -| CHOPPER | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | -| COMEBIN_RUNCOMEBIN | 12 * task.attempt | 72.GB * task.attempt | 16.h * task.attempt | Label: process_high | -| CONCOCT_CONCOCT | 12 * task.attempt | 72.GB * task.attempt | 16.h * task.attempt | Label: process_high | -| CONCOCT_CONCOCTCOVERAGETABLE | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| CONCOCT_CUTUPFASTA | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| CONCOCT_EXTRACTFASTABINS | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| CONCOCT_MERGECUTUPCLUSTERING | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| CONVERT_DEPTHS | 1 * task.attempt | 7.GB * task.attempt | 4.h * task.attempt | Default | -| DASTOOL_DASTOOL | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | -| DASTOOL_FASTATOCONTIG2BIN | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| FASTP | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | -| FASTQC | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | -| FILTLONG | 8 * task.attempt | 64.GB * (2 ** (task.attempt - 1)) | 24.h * (2 ** (task.attempt - 1)) | Named process | -| FIND_CONCATENATE | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | -| FLYE | 12 * task.attempt | 72.GB * (2 ** (task.attempt - 1)) | 24.h * (2 ** (task.attempt - 1)) | Named process | -| FREEBAYES | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| GENOMAD_DOWNLOAD | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| GENOMAD_ENDTOEND | 12 * task.attempt | 72.GB * task.attempt | 16.h * task.attempt | Label: process_high | -| GTDBTK_CLASSIFYWF | 10 * task.attempt | 140.GB * task.attempt | 12.h * task.attempt | Named process | -| GTDBTK_DB_PREPARATION | 1 * task.attempt | 7.GB * task.attempt | 4.h * task.attempt | Default | -| GTDBTK_SUMMARY | 1 * task.attempt | 7.GB * task.attempt | 4.h * task.attempt | Default | -| GUNC_DOWNLOADDB | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| GUNC_MERGECHECKM | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| GUNC_RUN | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | -| GUNZIP | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| MAG_DEPTHS | 1 * task.attempt | 16.GB * task.attempt | 4.h * task.attempt | Named process | -| MAG_DEPTHS_SUMMARY | 1 * task.attempt | 7.GB * task.attempt | 4.h * task.attempt | Default | -| MAXBIN2 | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | -| MEGAHIT | params.megahit_fix_cpu_1 ? 1 : (8 * task.attempt) | 40.GB * task.attempt | 16.h * task.attempt | Named process | -| METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | -| METABAT2_METABAT2 | 8 * task.attempt | 20.GB * task.attempt | 8.h * task.attempt | Named process | -| METABINNER_BINS | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | -| METABINNER_KMER | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | -| METABINNER_METABINNER | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | -| METABINNER_TOOSHORT | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | -| METAEUK_EASYPREDICT | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | -| METAMDBG_ASM | 12 * task.attempt | 72.GB * (2 ** (task.attempt - 1)) | 24.h * (2 ** (task.attempt - 1)) | Named process | -| MINIMAP2_ALIGN | 12 * task.attempt | 72.GB * task.attempt | 16.h * task.attempt | Label: process_high | -| MINIMAP2_INDEX | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | -| MMSEQS_DATABASES | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | -| MULTIQC | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| NANOLYSE | 2 * task.attempt | 10.GB * task.attempt | 3.h * task.attempt | Named process | -| NANOPLOT | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | -| NANOQ | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | -| PORECHOP_ABI | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | -| PORECHOP_PORECHOP | 4 * task.attempt | 30.GB * task.attempt | 4.h * task.attempt | Named process | -| PREPARE_BIGMAG_SUMMARY | 1 * task.attempt | 7.GB * task.attempt | 4.h * task.attempt | Default | -| PRODIGAL | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| PROKKA | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | -| PYDAMAGE_ANALYZE | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | -| PYDAMAGE_FILTER | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| PYPOLCA_RUN | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | -| QSV_CAT | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| QUAST | 1 * task.attempt | 7.GB * task.attempt | 4.h * task.attempt | Default | -| QUAST_BINS | 1 * task.attempt | 7.GB * task.attempt | 4.h * task.attempt | Default | -| RENAME_POSTDASTOOL | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | -| RENAME_PREDASTOOL | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | -| SAMTOOLS_FAIDX | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| SAMTOOLS_INDEX | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | -| SAMTOOLS_STATS | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| SAMTOOLS_UNMAPPED | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | -| SEMIBIN_SINGLEEASYBIN | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | -| SEQKIT_STATS | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | -| SEQTK_MERGEPE | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| SPADES | 12 * task.attempt | 72.GB * task.attempt | 16.h * task.attempt | Label: process_high | -| SPLIT_FASTA | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | -| SUMMARISE_PYDAMAGEBINS | 2 * task.attempt | 12.GB * task.attempt | 4.h * task.attempt | Label: process_low | -| TIARA_CLASSIFY | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | -| TIARA_TIARA | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | -| TRIMMOMATIC | 6 * task.attempt | 36.GB * task.attempt | 8.h * task.attempt | Label: process_medium | -| UNTAR | 1 | 6.GB * task.attempt | 4.h * task.attempt | Label: process_single | +The following table lists the default resources that Nextflow will request from a machine on it's first execution attempt for a given module. +It summaries information recorded in the file `conf/base.conf` and the module files themselves `modules`. + +To customise these resource requests, see the central [nf-core instructions](https://nf-co.re/docs/running/configuration/nextflow-for-your-system#customize-process-resources). + +Please also note the following: + +- Not all modules in this table will run in every pipeline run, nor that the tool will necessarily actually _use_ the requested amount. +- On certain module execution failures (such as out of memory), Nextflow will try and resubmit with increased resources with the equation ` * task.attempt`, up to a certain number of retries. See `conf/base.conf` for more information. +- Some modules have a dedicate flag to fix the number of CPUs for reproducibility reasons (e.g. `--megahit_fix_cpu_1`). See the [parameters page](https://nf-co.re/mag/dev/parameters). + +The table is ordered first by 'memory', then 'Source' of defaults by specificity of definition, and then 'Module name' by alphabetical order. + +| Module Name | CPU | Memory | Time | Source | +| ------------------------------------ | --- | ------ | ---- | --------------------- | +| GTDBTK_CLASSIFYWF | 10 | 140.GB | 12.h | Named customisation | +| CATPACK_BINS | 6 | 120.GB | 8.h | Named customisation | +| FLYE | 12 | 72.GB | 24.h | Named customisation | +| METAMDBG_ASM | 12 | 72.GB | 24.h | Named customisation | +| FILTLONG | 8 | 64.GB | 24.h | Named customisation | +| CATPACK_CONTIGS | 6 | 60.GB | 8.h | Named customisation | +| CHECKM_LINEAGEWF | 6 | 42.GB | 8.h | Named customisation | +| MEGAHIT | 8 | 40.GB | 16.h | Named customisation | +| METASPADES | 10 | 40.GB | 16.h | Named customisation | +| METASPADESHYBRID | 10 | 40.GB | 16.h | Named customisation | +| PORECHOP_PORECHOP | 4 | 30.GB | 4.h | Named customisation | +| BOWTIE2_HOST_REMOVAL_BUILD | 10 | 20.GB | 4.h | Named customisation | +| METABAT2_METABAT2 | 8 | 20.GB | 8.h | Named customisation | +| MAG_DEPTHS | 1 | 16.GB | 4.h | Named customisation | +| BUSCO_BUSCO | 10 | 12.GB | 8.h | Named customisation | +| BOWTIE2_HOST_REMOVAL_ALIGN | 10 | 10.GB | 6.h | Named customisation | +| NANOLYSE | 2 | 10.GB | 3.h | Named customisation | +| BOWTIE2_ASSEMBLY_ALIGN | 2 | 8.GB | 8.h | Named customisation | +| BOWTIE2_PHIX_REMOVAL_ALIGN | 4 | 8.GB | 6.h | Named customisation | +| BOWTIE2_ASSEMBLY_BUILD | 1 | 7.GB | 4.h | Named customisation | +| CONCAT_BUSCO_TSV | 1 | 1.GB | 4.h | Named customisation | +| CONCAT_CHECKM_TSV | 1 | 1.GB | 4.h | Named customisation | +| CONCAT_CHECKM2_TSV | 1 | 1.GB | 4.h | Named customisation | +| CONCAT_GUNC_CHECKM_TSV | 1 | 1.GB | 4.h | Named customisation | +| CONCAT_GUNC_TSV | 1 | 1.GB | 4.h | Named customisation | +| COMEBIN_RUNCOMEBIN | 12 | 72.GB | 16.h | Label: process_high | +| CONCOCT_CONCOCT | 12 | 72.GB | 16.h | Label: process_high | +| GENOMAD_ENDTOEND | 12 | 72.GB | 16.h | Label: process_high | +| MINIMAP2_ALIGN | 12 | 72.GB | 16.h | Label: process_high | +| ADAPTERREMOVAL | 6 | 36.GB | 8.h | Label: process_medium | +| BBMAP_BBNORM | 6 | 36.GB | 8.h | Label: process_medium | +| BCFTOOLS_CONSENSUS | 6 | 36.GB | 8.h | Label: process_medium | +| BCFTOOLS_VIEW | 6 | 36.GB | 8.h | Label: process_medium | +| CATPACK_PREPARE | 6 | 36.GB | 8.h | Label: process_medium | +| CHECKM2_PREDICT | 6 | 36.GB | 8.h | Label: process_medium | +| CHOPPER | 6 | 36.GB | 8.h | Label: process_medium | +| DASTOOL_DASTOOL | 6 | 36.GB | 8.h | Label: process_medium | +| FASTP | 6 | 36.GB | 8.h | Label: process_medium | +| GUNC_RUN | 6 | 36.GB | 8.h | Label: process_medium | +| MAXBIN2 | 6 | 36.GB | 8.h | Label: process_medium | +| METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS | 6 | 36.GB | 8.h | Label: process_medium | +| METABINNER_METABINNER | 6 | 36.GB | 8.h | Label: process_medium | +| METAEUK_EASYPREDICT | 6 | 36.GB | 8.h | Label: process_medium | +| MMSEQS_DATABASES | 6 | 36.GB | 8.h | Label: process_medium | +| PORECHOP_ABI | 6 | 36.GB | 8.h | Label: process_medium | +| PYDAMAGE_ANALYZE | 6 | 36.GB | 8.h | Label: process_medium | +| SEMIBIN_SINGLEEASYBIN | 6 | 36.GB | 8.h | Label: process_medium | +| TIARA_TIARA | 6 | 36.GB | 8.h | Label: process_medium | +| TRIMMOMATIC | 6 | 36.GB | 8.h | Label: process_medium | +| ADJUST_MAXBIN2_EXT | 2 | 12.GB | 4.h | Label: process_low | +| BCFTOOLS_INDEX | 2 | 12.GB | 4.h | Label: process_low | +| CHECKM_QA | 2 | 12.GB | 4.h | Label: process_low | +| FASTQC | 2 | 12.GB | 4.h | Label: process_low | +| FIND_CONCATENATE | 2 | 12.GB | 4.h | Label: process_low | +| METABINNER_BINS | 2 | 12.GB | 4.h | Label: process_low | +| METABINNER_KMER | 2 | 12.GB | 4.h | Label: process_low | +| METABINNER_TOOSHORT | 2 | 12.GB | 4.h | Label: process_low | +| MINIMAP2_INDEX | 2 | 12.GB | 4.h | Label: process_low | +| NANOPLOT | 2 | 12.GB | 4.h | Label: process_low | +| NANOQ | 2 | 12.GB | 4.h | Label: process_low | +| PROKKA | 2 | 12.GB | 4.h | Label: process_low | +| PYPOLCA_RUN | 2 | 12.GB | 4.h | Label: process_low | +| RENAME_POSTDASTOOL | 2 | 12.GB | 4.h | Label: process_low | +| RENAME_PREDASTOOL | 2 | 12.GB | 4.h | Label: process_low | +| SAMTOOLS_INDEX | 2 | 12.GB | 4.h | Label: process_low | +| SAMTOOLS_UNMAPPED | 2 | 12.GB | 4.h | Label: process_low | +| SEQKIT_STATS | 2 | 12.GB | 4.h | Label: process_low | +| SPLIT_FASTA | 2 | 12.GB | 4.h | Label: process_low | +| SUMMARISE_PYDAMAGEBINS | 2 | 12.GB | 4.h | Label: process_low | +| ALE | 1 | 6.GB | 4.h | Label: process_single | +| CAT_FASTQ | 1 | 6.GB | 4.h | Label: process_single | +| CATPACK_ADDNAMES | 1 | 6.GB | 4.h | Label: process_single | +| CATPACK_DOWNLOAD | 1 | 6.GB | 4.h | Label: process_single | +| CATPACK_SUMMARISE | 1 | 6.GB | 4.h | Label: process_single | +| CHECKM2_DATABASEDOWNLOAD | 1 | 6.GB | 4.h | Label: process_single | +| CONCOCT_CONCOCTCOVERAGETABLE | 1 | 6.GB | 4.h | Label: process_single | +| CONCOCT_CUTUPFASTA | 1 | 6.GB | 4.h | Label: process_single | +| CONCOCT_EXTRACTFASTABINS | 1 | 6.GB | 4.h | Label: process_single | +| CONCOCT_MERGECUTUPCLUSTERING | 1 | 6.GB | 4.h | Label: process_single | +| DASTOOL_FASTATOCONTIG2BIN | 1 | 6.GB | 4.h | Label: process_single | +| FREEBAYES | 1 | 6.GB | 4.h | Label: process_single | +| GENOMAD_DOWNLOAD | 1 | 6.GB | 4.h | Label: process_single | +| GUNC_DOWNLOADDB | 1 | 6.GB | 4.h | Label: process_single | +| GUNC_MERGECHECKM | 1 | 6.GB | 4.h | Label: process_single | +| GUNZIP | 1 | 6.GB | 4.h | Label: process_single | +| MULTIQC | 1 | 6.GB | 4.h | Label: process_single | +| PRODIGAL | 1 | 6.GB | 4.h | Label: process_single | +| PYDAMAGE_FILTER | 1 | 6.GB | 4.h | Label: process_single | +| QSV_CAT | 1 | 6.GB | 4.h | Label: process_single | +| SAMTOOLS_FAIDX | 1 | 6.GB | 4.h | Label: process_single | +| SAMTOOLS_STATS | 1 | 6.GB | 4.h | Label: process_single | +| SEQTK_MERGEPE | 1 | 6.GB | 4.h | Label: process_single | +| TIARA_CLASSIFY | 1 | 6.GB | 4.h | Label: process_single | +| UNTAR | 1 | 6.GB | 4.h | Label: process_single | +| BIN_SUMMARY | 1 | 7.GB | 4.h | Default | +| BOWTIE2_PHIX_REMOVAL_BUILD | 1 | 7.GB | 4.h | Default | +| CONVERT_DEPTHS | 1 | 7.GB | 4.h | Default | +| GTDBTK_DB_PREPARATION | 1 | 7.GB | 4.h | Default | +| GTDBTK_SUMMARY | 1 | 7.GB | 4.h | Default | +| MAG_DEPTHS_SUMMARY | 1 | 7.GB | 4.h | Default | +| PREPARE_BIGMAG_SUMMARY | 1 | 7.GB | 4.h | Default | +| QUAST | 1 | 7.GB | 4.h | Default | +| QUAST_BINS | 1 | 7.GB | 4.h | Default | + +_Table generated for nf-core/mag v5.5, using Claude Haiku 4.5, and corrected for accuracy by a human._ + + diff --git a/nextflow.config b/nextflow.config index 095771607..857e2bcf1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -110,7 +110,8 @@ params { gtdbtk_pplacer_useram = false gtdbtk_use_full_tree = false gtdbtk_place_species = false - gtdbtk_skip_aniscreen = false // DEPRECATED: use gtdbtk_place_species instead + gtdbtk_skip_aniscreen = false + // DEPRECATED: use gtdbtk_place_species instead gtdbtk_single_job = false // long read preprocessing options @@ -529,7 +530,7 @@ manifest { // Nextflow plugins plugins { - id 'nf-schema@2.5.1' + id 'nf-schema@2.7.2' } validation { From 62ae4fcda7dd145315a11447a06d14ca08e19c03 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 23 Jun 2026 17:47:42 +0200 Subject: [PATCH 4/8] update CHANGELOG --- CHANGELOG.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 93730b041..8052a671e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1044](https://github.com/nf-core/mag/pull/1044) - Add new `--gtdbtk_place_species` parameter (by @dialvarezs) - [#1047](https://github.com/nf-core/mag/issues/1007) - Add `--gtdbtk_single_job` to run GTDB-Tk classification for all bins in a single job (requested by @sarah-shah-bioinf, by @dialvarezs) - [#1048](https://github.com/nf-core/mag/pull/1048) - Add optional PyPOLCA polishing for long-read assemblies via `--run_pypolca` (by @Harshita-sriv) +- [#1055](https://github.com/nf-core/mag/pull/1055) - Add dedicated page describing resource usage (by @jfy133) ### `Changed` @@ -37,9 +38,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Dependencies` -| Tool | Previous version | New version | -| ------- | ---------------- | ----------- | -| GTDB-Tk | 2.5.2 | 2.7.2 | +| Tool | Previous version | New version | +| --------- | ---------------- | ----------- | +| GTDB-Tk | 2.5.2 | 2.7.2 | +| nf-schema | 2.5.1 | 2.7.2 | ### `Deprecated` From 5f8ec6c4145bd965218c452ece4bcb472c064c43 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 24 Jun 2026 08:24:32 +0200 Subject: [PATCH 5/8] Update nextflow.config Co-authored-by: Diego Alvarez S. --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 857e2bcf1..710a08bd5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -110,8 +110,8 @@ params { gtdbtk_pplacer_useram = false gtdbtk_use_full_tree = false gtdbtk_place_species = false - gtdbtk_skip_aniscreen = false // DEPRECATED: use gtdbtk_place_species instead + gtdbtk_skip_aniscreen = false gtdbtk_single_job = false // long read preprocessing options From 11ae462151f86570f709d10b7e2899d69d8a27d4 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 25 Jun 2026 08:37:51 +0200 Subject: [PATCH 6/8] Apply suggestions from code review Co-authored-by: Daniel Lundin --- docs/usage/resource_guidance.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/usage/resource_guidance.md b/docs/usage/resource_guidance.md index 84bb3211d..8d8fd4f29 100644 --- a/docs/usage/resource_guidance.md +++ b/docs/usage/resource_guidance.md @@ -18,7 +18,7 @@ There are a few exceptions to this. In the following cases, depending on the options you set in the pipeline, you may see some steps running as a single job with multiple samples. - Multiple samples processed in one job: - - If `--coassemble_group`: all reads across all samples will be pooled into one assembly job (e.g. MEGAHIT, metaSPAdes) + - If `--coassemble_group`: all reads across all samples in a group will be pooled into one assembly job (e.g. MEGAHIT, metaSPAdes) - If `--gtdbtk_single_job`: all bins across all samples will be pooled into a single GTDBTk classification job ## Default resource requests @@ -30,7 +30,7 @@ To customise these resource requests, see the central [nf-core instructions](htt Please also note the following: -- Not all modules in this table will run in every pipeline run, nor that the tool will necessarily actually _use_ the requested amount. +- Not all modules in this table will run in every pipeline run, nor will the tool necessarily _use_ the requested amount. - On certain module execution failures (such as out of memory), Nextflow will try and resubmit with increased resources with the equation ` * task.attempt`, up to a certain number of retries. See `conf/base.conf` for more information. - Some modules have a dedicate flag to fix the number of CPUs for reproducibility reasons (e.g. `--megahit_fix_cpu_1`). See the [parameters page](https://nf-co.re/mag/dev/parameters). From e60aa7d36f7fc7eb32fb4a8eaaa03a9cec43174c Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 25 Jun 2026 08:38:11 +0200 Subject: [PATCH 7/8] Update docs/usage/resource_guidance.md --- docs/usage/resource_guidance.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/usage/resource_guidance.md b/docs/usage/resource_guidance.md index 8d8fd4f29..49109827d 100644 --- a/docs/usage/resource_guidance.md +++ b/docs/usage/resource_guidance.md @@ -1,9 +1,7 @@ # Resource usage guidance **nf-core/mag** is a bioinformatics best-practice analysis pipeline for the assembly, binning, and annotation of metagenomes. - Due to the nature of metagenomic samples, nf-core/mag can in some cases require large amounts of computational resources to execute. - In this page we provide information and guidance on how nf-core/mag works by default, and in some cases how to optimise computational resource usage. ## Multi-sample or bin executing modules From 66fa29b7eb352c63f732ee34729997a8368ff1d3 Mon Sep 17 00:00:00 2001 From: "Diego Alvarez S." Date: Mon, 13 Jul 2026 22:46:47 -0300 Subject: [PATCH 8/8] chore: update resources --- docs/usage/resource_guidance.md | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/docs/usage/resource_guidance.md b/docs/usage/resource_guidance.md index 49109827d..f2064ce08 100644 --- a/docs/usage/resource_guidance.md +++ b/docs/usage/resource_guidance.md @@ -31,8 +31,10 @@ Please also note the following: - Not all modules in this table will run in every pipeline run, nor will the tool necessarily _use_ the requested amount. - On certain module execution failures (such as out of memory), Nextflow will try and resubmit with increased resources with the equation ` * task.attempt`, up to a certain number of retries. See `conf/base.conf` for more information. - Some modules have a dedicate flag to fix the number of CPUs for reproducibility reasons (e.g. `--megahit_fix_cpu_1`). See the [parameters page](https://nf-co.re/mag/dev/parameters). +- `METASPADES`, `METASPADESHYBRID`, `FILTLONG`, `METAMDBG_ASM` and `FLYE` grow memory and time exponentially with each retry (` * 2 ** (task.attempt - 1)`); the table shows the first-attempt request. +- `ALE` requests 18.GB by default, but 30.GB when `--coassemble_group` is set. -The table is ordered first by 'memory', then 'Source' of defaults by specificity of definition, and then 'Module name' by alphabetical order. +The table is ordered first by 'Source' of defaults by specificity of definition, then by 'memory', and then 'Module name' by alphabetical order. | Module Name | CPU | Memory | Time | Source | | ------------------------------------ | --- | ------ | ---- | --------------------- | @@ -41,26 +43,30 @@ The table is ordered first by 'memory', then 'Source' of defaults by specificity | FLYE | 12 | 72.GB | 24.h | Named customisation | | METAMDBG_ASM | 12 | 72.GB | 24.h | Named customisation | | FILTLONG | 8 | 64.GB | 24.h | Named customisation | +| METASPADES | 10 | 64.GB | 24.h | Named customisation | +| METASPADESHYBRID | 10 | 64.GB | 24.h | Named customisation | +| PORECHOP_ABI | 4 | 64.GB | 8.h | Named customisation | | CATPACK_CONTIGS | 6 | 60.GB | 8.h | Named customisation | | CHECKM_LINEAGEWF | 6 | 42.GB | 8.h | Named customisation | | MEGAHIT | 8 | 40.GB | 16.h | Named customisation | -| METASPADES | 10 | 40.GB | 16.h | Named customisation | -| METASPADESHYBRID | 10 | 40.GB | 16.h | Named customisation | | PORECHOP_PORECHOP | 4 | 30.GB | 4.h | Named customisation | | BOWTIE2_HOST_REMOVAL_BUILD | 10 | 20.GB | 4.h | Named customisation | | METABAT2_METABAT2 | 8 | 20.GB | 8.h | Named customisation | +| ALE | 1 | 18.GB | 4.h | Named customisation | | MAG_DEPTHS | 1 | 16.GB | 4.h | Named customisation | | BUSCO_BUSCO | 10 | 12.GB | 8.h | Named customisation | | BOWTIE2_HOST_REMOVAL_ALIGN | 10 | 10.GB | 6.h | Named customisation | | NANOLYSE | 2 | 10.GB | 3.h | Named customisation | | BOWTIE2_ASSEMBLY_ALIGN | 2 | 8.GB | 8.h | Named customisation | -| BOWTIE2_PHIX_REMOVAL_ALIGN | 4 | 8.GB | 6.h | Named customisation | -| BOWTIE2_ASSEMBLY_BUILD | 1 | 7.GB | 4.h | Named customisation | +| BOWTIE2_PHIX_REMOVAL_ALIGN | 4 | 4.GB | 6.h | Named customisation | | CONCAT_BUSCO_TSV | 1 | 1.GB | 4.h | Named customisation | | CONCAT_CHECKM_TSV | 1 | 1.GB | 4.h | Named customisation | | CONCAT_CHECKM2_TSV | 1 | 1.GB | 4.h | Named customisation | | CONCAT_GUNC_CHECKM_TSV | 1 | 1.GB | 4.h | Named customisation | | CONCAT_GUNC_TSV | 1 | 1.GB | 4.h | Named customisation | +| RENAME_POSTDASTOOL | 1 | 1.GB | 4.h | Named customisation | +| RENAME_PREDASTOOL | 1 | 1.GB | 4.h | Named customisation | +| SEQKIT_STATS | 1 | 1.GB | 4.h | Named customisation | | COMEBIN_RUNCOMEBIN | 12 | 72.GB | 16.h | Label: process_high | | CONCOCT_CONCOCT | 12 | 72.GB | 16.h | Label: process_high | | GENOMAD_ENDTOEND | 12 | 72.GB | 16.h | Label: process_high | @@ -80,7 +86,6 @@ The table is ordered first by 'memory', then 'Source' of defaults by specificity | METABINNER_METABINNER | 6 | 36.GB | 8.h | Label: process_medium | | METAEUK_EASYPREDICT | 6 | 36.GB | 8.h | Label: process_medium | | MMSEQS_DATABASES | 6 | 36.GB | 8.h | Label: process_medium | -| PORECHOP_ABI | 6 | 36.GB | 8.h | Label: process_medium | | PYDAMAGE_ANALYZE | 6 | 36.GB | 8.h | Label: process_medium | | SEMIBIN_SINGLEEASYBIN | 6 | 36.GB | 8.h | Label: process_medium | | TIARA_TIARA | 6 | 36.GB | 8.h | Label: process_medium | @@ -98,14 +103,10 @@ The table is ordered first by 'memory', then 'Source' of defaults by specificity | NANOQ | 2 | 12.GB | 4.h | Label: process_low | | PROKKA | 2 | 12.GB | 4.h | Label: process_low | | PYPOLCA_RUN | 2 | 12.GB | 4.h | Label: process_low | -| RENAME_POSTDASTOOL | 2 | 12.GB | 4.h | Label: process_low | -| RENAME_PREDASTOOL | 2 | 12.GB | 4.h | Label: process_low | | SAMTOOLS_INDEX | 2 | 12.GB | 4.h | Label: process_low | | SAMTOOLS_UNMAPPED | 2 | 12.GB | 4.h | Label: process_low | -| SEQKIT_STATS | 2 | 12.GB | 4.h | Label: process_low | | SPLIT_FASTA | 2 | 12.GB | 4.h | Label: process_low | | SUMMARISE_PYDAMAGEBINS | 2 | 12.GB | 4.h | Label: process_low | -| ALE | 1 | 6.GB | 4.h | Label: process_single | | CAT_FASTQ | 1 | 6.GB | 4.h | Label: process_single | | CATPACK_ADDNAMES | 1 | 6.GB | 4.h | Label: process_single | | CATPACK_DOWNLOAD | 1 | 6.GB | 4.h | Label: process_single | @@ -131,6 +132,7 @@ The table is ordered first by 'memory', then 'Source' of defaults by specificity | TIARA_CLASSIFY | 1 | 6.GB | 4.h | Label: process_single | | UNTAR | 1 | 6.GB | 4.h | Label: process_single | | BIN_SUMMARY | 1 | 7.GB | 4.h | Default | +| BOWTIE2_ASSEMBLY_BUILD | 1 | 7.GB | 4.h | Default | | BOWTIE2_PHIX_REMOVAL_BUILD | 1 | 7.GB | 4.h | Default | | CONVERT_DEPTHS | 1 | 7.GB | 4.h | Default | | GTDBTK_DB_PREPARATION | 1 | 7.GB | 4.h | Default |