metapi 0.7.0

a pipeline to construct a genome catalogue from metagenomics data

#+TITLE: metapi

• Install #+BEGIN_SRC bash conda install metapi #+END_SRC

• Run ** help #+BEGIN_SRC bash $ metapi --help

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Omics for All, Open Source for All

A pipeline to construct a genome catalogue from metagenomics data

optional arguments: -h, --help show this help message and exit -v, --version print software version and exit

available subcommands:

init init project denovo_wf denovo_wf pipeline #+END_SRC ** init #+BEGIN_SRC bash $ metapi init --help

usage: metapi init [-h] [-d WORKDIR] [-s SAMPLES] [-b {simulate,trimmingrmhost,assembly}]

arguments: -h, --help show this help message and exit -d WORKDIR, --workdir WORKDIR project workdir -s SAMPLES, --samples SAMPLES samples list, tsv format required if begin from trimming, rmhost, or assembly: if it is fastq: the header is [id, fq1, fq2], else it is sra: the header is [id, sra] else begin from simulate: the header is [id, genome, abundance, reads_num, model] -b {simulate,trimming,rmhost,assembly}, --begin {simulate,trimming,rmhost,assembly} pipeline starting point #+END_SRC

** denovo_wf #+BEGIN_SRC bash $ metapi denovo_wf --help

usage: metapi denovo_wf [-h] [-d WORKDIR] [--cores CORES] [--jobs JOBS] [--list] [--run] [--debug] [--dry_run] [--qsub] [--wait WAIT] [--snake [SNAKEMAKEARGS]] [TASK]

positional arguments: TASK pipeline end point. Allowed values are simulate_all, prepare_reads_all, raw_fastqc_all, rmhost_bwa_all, rmhost_bowtie2_all, rmhost_all, assebmly_megahit_all, assembly_idba_ud_all, assembly_metaspades_all, assembly_spades_all, assembly_metaquast_all, assembly_report_all, assembly_all, alignment_base_depth_all, alignment_all, binning_metabat2_all, binning_maxbin2_all, binning_all, predcit_scafitgs_gene_all, predict_bins_gene_all, predcit_all, checkm_link_bins, checkm_all, dereplicate_drep_all, dereplicate_all, classify_short_reads_kraken2_all, classify_hmq_bins_gtdbtk_all, classify_all, profiling_metaphlan2_all, profiling_jgi_all, profiling_humann2_all, profiling_all, upload_sequencing_all, upload_assembly_all, upload_all, all

arguments: -h, --help show this help message and exit -d WORKDIR, --workdir WORKDIR project workdir, default: ./ --cores CORES CPU cores --jobs JOBS qsub job numbers --list list pipeline rules --run run pipeline --debug debug pipeline --dry_run dry run pipeline --qsub qsub pipeline --wait WAIT wait given seconds --snake [SNAKEMAKEARGS] other snakemake command options, if want --touch, just --snake touch #+END_SRC

** input requirements Please supply samples.tsv format like below: | id | fq1 | fq2 | |----+---------------+---------------| | s1 | s1.1.fq.gz | s1.2.fq.gz | | s2 | s2.1.fq.gz | s2.2.fq.gz | | s2 | s21.1.fq.gz | s21.2.fq.g | | s3 | hello.1.fq.gz | hello.2.fq.gz | The header must be: id fq1 fq2. If id is same, the fq1 and fq2 belong to one sample, and will be merged to process.

• License

• Omics for all, Open Source for all.
• GPLv3+