diff --git a/CITATION.cff b/CITATION.cff index 13f06d5..9dd74aa 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,6 +1,7 @@ cff-version: 1.2.0 message: "If you use this software, please cite it as below." title: "Seq-N-Slide" +abstract: "Automated workflows for common genomic sequencing-based protocols. Documentation is available at https://igordot.github.io/sns" type: software authors: - orcid: "https://orcid.org/0000-0003-4451-126X" diff --git a/README.md b/README.md index 81d8c04..183f481 100644 --- a/README.md +++ b/README.md @@ -4,42 +4,4 @@ Automated workflows for common sequencing-based (Illumina) protocols, such as RNA-seq, ChIP-seq, ATAC-seq, WGBS/RRBS methylation, whole genome/exome/targeted variant detection, and contaminant screening. -## Brief usage overview - -Download the code. - -``` -git clone --depth 1 https://github.com/igordot/sns -``` - -Generate a sample sheet based on a directory of FASTQ files. - -``` -sns/gather-fastqs -``` - -Specify the reference genome. - -``` -sns/generate-settings -``` - -Run the analysis using a specific route. - -``` -sns/run -``` - -Check if the jobs are submitted and running. - -``` -squeue -u $USER -``` - -Check for problems. - -``` -grep "ERROR:" logs-sbatch/* -``` - -For more details, check the full documentation at: https://igordot.github.io/sns +For more information, see the full documentation at https://igordot.github.io/sns