Update README.md

README.md

@@ -11,7 +11,7 @@
 
 ## Overview
 
-The align-DNA nextflow pipeline, aligns paired-end data utilizing [BWA-MEM2](https://github.com/bwa-mem2/bwa-mem2) and/or [HISAT2](http://daehwankimlab.github.io/hisat2/main), [Picard](https://github.com/broadinstitute/picard) Tools and [SAMtools](https://github.com/samtools/samtools). The pipeline has been engineered to run in a 4 layer stack in a cloud-based scalable environment of CycleCloud, Slurm, Nextflow and Docker. Additionally, it has been validated with the SMC-HET dataset and reference GRCh38, where paired-end fastq’s were created with BAM Surgeon.
+The align-DNA Nextflow pipeline, aligns paired-end data utilizing [BWA-MEM2](https://github.com/bwa-mem2/bwa-mem2) and/or [HISAT2](http://daehwankimlab.github.io/hisat2/main), [Picard](https://github.com/broadinstitute/picard) Tools and [SAMtools](https://github.com/samtools/samtools). The pipeline has been engineered to run in a 4 layer stack in a cloud-based scalable environment of CycleCloud, Slurm, Nextflow and Docker. Additionally, it has been validated with the SMC-HET dataset and reference GRCh38, where paired-end fastq’s were created with BAM Surgeon.
 
 The pipeline should be run **WITH A SINGLE SAMPLE AT A TIME**. Otherwise resource allocation and Nextflow errors could cause the pipeline to fail.
 
@@ -69,7 +69,7 @@ python path/to/submit_nextflow_pipeline.py \
 ```
 
 <b><i> BWA-MEM2 Genome Index </i></b>
-The reference genome index must be generated by BWA-MEM2 with the correct version. Genome index generated by old BWA-MEM2 versions or the original BWA is not accepted. The reference genome index can be generated using the [`generate-genme-index.nf`](module/generate-genome-index.nf) nextflow pipeline. To run this pipeline, you need to create a config file using this [template](config/index.config) to specify the path of `reference_fasta` and the `temp_dir`. The `temp_dir` is used to store intermediate files of nextflow. The genome index files are saved to the same directory of the input reference FASTA by the pipeline. Use the command below to run this generate genome index pipeline:
+The reference genome index must be generated by BWA-MEM2 with the correct version. Genome index generated by old BWA-MEM2 versions or the original BWA is not accepted. The reference genome index can be generated using the [`generate-genome-index.nf`](module/generate-genome-index.nf) nextflow pipeline. To run this pipeline, you need to create a config file using this [template](config/index.config) to specify the path of `reference_fasta` and the `temp_dir`. The `temp_dir` is used to store intermediate files of Nextflow. The genome index files are saved to the same directory of the input reference FASTA by the pipeline. Use the command below to run this generate genome index pipeline:
 
 ```bash
 nextflow run path/to/generate-genome-index.nf -config path/to/genome-specific.config
@@ -207,7 +207,7 @@ After marking duplicated reads in BAM files, the BAM files are then indexed by u
 | `.bam.bai` | Index file for each BAM file | align-DNA-*DATE*/*ALIGNER* |
 | `.bam` files and metrics files | Intermediate outputs for each scientific tool (OPTIONAL) | align-DNA-*DATE*/*ALIGNER* |
 | `report.html`, `timeline.html` and `trace.txt` | A Nextflowreport, timeline and trace files | align-DNA-*DATE*/log |
-| `log.command.*` | Process specific logging files created by nextflow. | align-DNA-*DATE* |
+| `log.command.*` | Process specific logging files created by Nextflow. | align-DNA-*DATE* |
 
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