update README.md and version

README.md

@@ -1,6 +1,21 @@
-# Microbiome profiling pipeline (WIP)
+[![bioconda-badge](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io)
+[![ohmeta-badge](https://img.shields.io/badge/install%20with-ohmeta-brightgreen.svg?style=flat)](http://anaconda.org/ohmeta)
+[![PyPI version](https://badge.fury.io/py/quantpi.svg)](https://badge.fury.io/py/quantpi)
+[![Anaconda-Server Badge](https://anaconda.org/bioconda/quantpi/badges/downloads.svg)](https://anaconda.org/bioconda/quantpi)
 
+# Microbiome profiling pipeline
 
+## Overview
+<div align=center><img width="800" height="120" src="docs/workflow.svg"></div>
+
+## Installation
+```
+mamba install quantpi=0.2.0
+# or
+pip install quantpi=0.2.0
+```
+
+## Run
 ```
 ➤ quantpi --help
 
@@ -25,4 +40,109 @@ available subcommands:
     profiling_wf
                  metagenome-profiling pipeline
     sync         quantpi sync project
-```
+```
+
+## Workflow list
+```
+➤ quantpi profiling_wf --list
+
+Running quantpi profiling_wf:
+snakemake --snakefile /home/jiezhu/toolkit/quantpi/quantpi/snakefiles/profiling_wf.smk --configfile ./config.yaml --cores 240 --rerun-incomplete --keep-going --printshellcmds --re
+ason --until all --list
+
+simulate_all
+prepare_short_reads
+prepare_short_reads_all
+prepare_long_reads_all
+prepare_reads_all
+raw_fastqc_all
+raw_report
+raw_report_merge
+raw_report_all
+raw_all
+trimming_oas1_all
+trimming_sickle_all
+trimming_fastp
+trimming_fastp_multiqc
+trimming_fastp_all
+trimming_report
+trimming_report_merge
+trimming_report_all
+trimming_all
+rmhost_soap_all
+rmhost_bowtie2_index
+rmhost_bowtie2
+rmhost_kraken2_all
+rmhost_kneaddata_all
+rmhost_alignment_report
+rmhost_bwa_all
+rmhost_bowtie2_all
+rmhost_minimap2_all
+rmhost_report
+rmhost_report_merge
+rmhost_report_all
+rmhost_all
+qcreport_summary
+qcreport_plot
+qcreport_all
+profiling_kraken2
+profiling_kraken2_krona_report
+profiling_kraken2_combine_kreport
+profiling_kraken2_combine_kreport_mpa
+profiling_kraken2_all
+profiling_bracken
+profiling_bracken_merge
+profiling_bracken_all
+profiling_kmcp_search
+profiling_kmcp_search_merge
+profiling_kmcp_profile
+profiling_kmcp_profile_merge
+profiling_kmcp_all
+profiling_metaphlan2_all
+profiling_metaphlan3
+profiling_metaphlan3_merge
+profiling_metaphlan3_all
+profiling_alignment_bowtie2
+profiling_alignment_bam_postprocess
+profiling_genomecov_gen_bed
+profiling_genomecov_gen_cov
+profiling_genomecov_gen_cov_merge
+profiling_genomecov_all
+profiling_genome_coverm
+profiling_genome_coverm_merge
+profiling_genome_coverm_all
+profiling_custom_bgi_soap_all
+profiling_custom_bowtie2_all
+profiling_custom_jgi_all
+profiling_humann2_all
+profiling_humann3_config
+profiling_humann3
+profiling_humann3_postprocess
+profiling_humann3_join
+profiling_humann3_split_stratified
+profiling_humann3_all
+profiling_all
+all
+```
+
+## Workflow
+### profiling_kraken2_all
+<div align=center><img width="800" height="500" src="docs/workflow_kraken2.svg"></div>
+
+### profiling_bracken_all
+<div align=center><img width="800" height="500" src="docs/workflow_bracken.svg"></div>
+
+### profiling_kmcp_all
+<div align=center><img width="800" height="500" src="docs/workflow_kmcp.svg"></div>
+
+### profiling_genomecov_all
+<div align=center><img width="800" height="500" src="docs/workflow_genomecov.svg"></div>
+
+### profiling_genome_coverm_all
+<div align=center><img width="800" height="500" src="docs/workflow_coverm.svg"></div>
+
+### profiling_metaphlan3_all
+<div align=center><img width="800" height="500" src="docs/workflow_metaphlan3.svg"></div>
+
+### profiling_humann3_all
+<div align=center><img width="800" height="500" src="docs/workflow_humann3.svg"></div>

quantpi/__about__.py

@@ -1,4 +1,4 @@
 #!/usr/bin/env python3
 
-__version__ = '0.1.0'
+__version__ = '0.2.0'
 __author__ = "Jie Zhu"