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Expand resource usage guidance in documentation
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| # Resource usage guidance | ||
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| **nf-core/mag** is a bioinformatics best-practice analysis pipeline for the assembly, binning, and annotation of metagenomes. | ||
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| Due to the nature of metagenomic samples, nf-core/mag can in some cases require large amounts of computational resources to execute. | ||
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| 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. | ||
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| ## Multi-sample or bin executing modules | ||
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| 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. | ||
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| 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. | ||
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| 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. | ||
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| - 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) | ||
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| - If `--gtdbtk_single_job`: all bins across all samples will be pooled into a single GTDBTk classification job | ||
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| ## Default resource requests | ||
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| 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`. | ||
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| 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). | ||
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| Please also note the following: | ||
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| - Not all modules in this table will run in every pipeline run, nor that the tool will necessarily actually _use_ the requested amount. | ||
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| - On certain module execution failures (such as out of memory), Nextflow will try and resubmit with increased resources with the equation `<resource value> * 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). | ||
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| The table is ordered first by 'memory', then 'Source' of defaults by specificity of definition, and then 'Module name' by alphabetical order. | ||
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| | 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 | | ||
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| _Table generated for nf-core/mag v5.5, using Claude Haiku 4.5, and corrected for accuracy by a human._ | ||
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| <!-- TODO mag: update when new modules added/defaults changed, if using an LLM, careful to tell it to follow module import aliases --> | ||
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The long table might become a maintenance headache, but it will be useful I believe. In a better world, this would be generated by nf-core/tools by inspection of module code perhaps?
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Yes, I've made an issue proposing this: nf-core/tools#4345, if you want to add support to it :)