github.com/nf-core/mag

Assembly, binning and annotation of metagenomes ========================================= nf-core/mag v ========================================= Usage: The typical command for running the pipeline is as follows: nextflow run nf-core/mag --reads '*_R{1,2}.fastq.gz' -profile docker Mandatory arguments: --reads Path to input data (must be surrounded with quotes) -profile Configuration profile to use. Can use multiple (comma separated) Available: standard, conda, docker, singularity, awsbatch, test Options: -name Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic. --singleEnd Specifies that the input is single end reads --outdir The output directory where the results will be saved --email Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits Trimming options: --adapter_forward Sequence of 3' adapter to remove in the forward reads --adapter_reverse Sequence of 3' adapter to remove in the reverse reads --mean_quality Mean qualified quality value for keeping read (default: 15) --trimming_quality Trimming quality value for the sliding window (default: 15) Binning options: --refinem Enable bin refinement with refinem. --refinem_db Path to refinem database --no_checkm Disable bin QC and merging with checkm --min_contig_size Minimum contig size to be considered for binning (default: 1500) --delta_cont Maximum increase in contamination to merge compatible bins (default: 5) --merged_cont Maximum total contamination to merge compatible bins (default: 15) --delta_compl Minimum increase in completion to merge compatible bins (default: 10) --abs_delta_cov Minimum coverage ratio to merge compatible bins (default: 0.75) --delta_gc Maximum %GC difference to merge compatible bins (default: 3) --ssu_evalue Evalue threshold to filter incongruent 16S (default 1e-6) AWSBatch options: --awsqueue The AWSBatch JobQueue that needs to be set when running on AWSBatch --awsregion The AWS Region for your AWS Batch job to run on