diff --git a/README.md b/README.md index 2f63706..a4d4c6a 100644 --- a/README.md +++ b/README.md @@ -35,14 +35,14 @@ conda activate masterenv ## Quick Start ```console -nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file] --organism [mm10|mm9|hg19|hg38] +nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file] --organism [mm10|mm9|hg19|hg38] --gtf_annotation [GTF-file] ``` ### Demo run There are files provided inside ./demo/ for a demo run. Go to the main directory and run following command: ``` -nextflow run pipeline.nf --bigwig ./demo/buenrostro50k_chr1_fp.bw --bed ./demo/buenrostro50k_chr1_peaks.bed --genome_fasta ./demo/hg38_chr1.fa --motif_db ./demo/jaspar_vertebrates.meme --out ./demo/buenrostro50k_chr1_out/ --organism hg38 +nextflow run pipeline.nf --bigwig ./demo/buenrostro50k_chr1_fp.bw --bed ./demo/buenrostro50k_chr1_peaks.bed --genome_fasta ./demo/hg38_chr1.fa --motif_db ./demo/jaspar_vertebrates.meme --out ./demo/buenrostro50k_chr1_out/ --organism hg38 --gtf_annotation ./demo\homo_sapiens.94.mainChr.gtf ``` ## Parameters diff --git a/demo/homo_sapiens.94.mainChr.gtf b/demo/homo_sapiens.94.mainChr.gtf new file mode 100644 index 0000000..e4bed46 Binary files /dev/null and b/demo/homo_sapiens.94.mainChr.gtf differ