add CITATION.cff

Author: sreichl

CITATION.cff

@@ -0,0 +1,34 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: >-
+  Workflow to Fetch Public Sequencing Data and Metadata
+  Using iSeq
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Stephan
+    family-names: Reichl
+    orcid: 'https://orcid.org/0000-0001-8555-7198'
+    affiliation: CeMM Research Center for Molecular Medicine
+  - given-names: Christoph
+    family-names: Bock
+    orcid: 'https://orcid.org/0000-0001-6091-3088'
+    affiliation: CeMM Research Center for Molecular Medicine
+repository-code: 'https://github.com/epigen/fetch_ngs'
+url: 'https://epigen.github.io/fetch_ngs/'
+abstract: >-
+  A Snakemake workflow to fetch (download) and process
+  public sequencing data and metadata from GSA, SRA, ENA,
+  GEO and DDBJ databases using iSeq.
+keywords:
+  - Bioinformatics
+  - Workflow
+  - Databases
+  - Metadata
+  - NGS
+  - Snakemake
+license: MIT

README.md

@@ -1,12 +1,12 @@
 [![MrBiomics](https://img.shields.io/badge/MrBiomics-red)](https://github.com/epigen/MrBiomics/)
 [![](https://tokei.rs/b1/github/epigen/fetch_ngs?category=code)]() 
 [![](https://tokei.rs/b1/github/epigen/fetch_ngs?category=files)]()
-[![GitHub license](https://img.shields.io/github/license/epigen/fetch_ngs)](https://github.com/epigen/fetch_ngs/blob/master/LICENSE)
+[![GitHub license](https://img.shields.io/github/license/epigen/fetch_ngs)](https://github.com/epigen/fetch_ngs/blob/main/LICENSE)
 ![GitHub Release](https://img.shields.io/github/v/release/epigen/fetch_ngs)
 [![Snakemake](https://img.shields.io/badge/Snakemake->=8.20.1-green)](https://snakemake.readthedocs.io/en/stable/)
 
-# Retrieval Workflow for Public Sequencing Data Using iSeq
-A [Snakemake 8](https://snakemake.readthedocs.io/en/stable/) workflow for downloading and processing public sequencing data and metadata from **[GSA](https://ngdc.cncb.ac.cn/gsa/)**, **[SRA](https://www.ncbi.nlm.nih.gov/sra/)**, **[ENA](https://www.ebi.ac.uk/ena/)**, and **[DDBJ](https://www.ddbj.nig.ac.jp/)** databases using [iSeq](https://github.com/BioOmics/iSeq).
+# Workflow to Fetch Public Sequencing Data and Metadata Using iSeq
+A [Snakemake 8](https://snakemake.readthedocs.io/en/stable/) workflow to fetch (download) and process public sequencing data and metadata from **[GSA](https://ngdc.cncb.ac.cn/gsa/)**, **[SRA](https://www.ncbi.nlm.nih.gov/sra/)**, **[ENA](https://www.ebi.ac.uk/ena/)**, **[GEO](https://www.ncbi.nlm.nih.gov/geo/)** and **[DDBJ](https://www.ddbj.nig.ac.jp/)** databases using [iSeq](https://github.com/BioOmics/iSeq).
 
 > [!NOTE]  
 > This workflow adheres to the module specifications of [MrBiomics](https://github.com/epigen/MrBiomics), an effort to augment research by modularizing (biomedical) data science. For more details, instructions, and modules check out the project's repository.

workflow/Snakefile

@@ -33,6 +33,8 @@ ruleorder: fastq_to_bam>fetch_file>iseq_download
 rule all:
     input:
         os.path.join(result_path,"metadata.csv"),
+    params:
+        metadata_only = config["metadata_only"],
     resources:
         mem_mb=config.get("mem", "4000"),
     threads: 1