Update README.md

README.md

@@ -45,39 +45,23 @@ snakemake --cores 6 --config input_bam_location=.tests/data output_location=.tes
 
 6. Generate report on example data
 ```
-<<<<<<< HEAD
 snakemake --cores 6 --config input_bam_location=.tests/data output_location=.tests/output chromosomes="[chr21]" reference=.tests/external_data/chr21.fna snv_sites_to_genotype=.tests/external_data/1000G_chr21.vcf.gz --use-conda --use-singularity --singularity-args "-B /<disk>:/<disk>" --latency-wait 60 --report <REPORT.zip>
-=======
-snakemake --cores 12 --config mode=mosaiclassifier plot=True input_bam_location=.tests/data/ output_location=.tests/output/ chromosomes="[chr21]" snv_sites_to_genotype=.tests/external_data/1000G_chr21.vcf.gz reference=.tests/external_data/chr21.fna containerized=True --use-conda --use-singularity --singularity-args "-B /<disk>:/<disk>" --latency-wait 60 
->>>>>>> master
 ```
 
 7. Download reference data for running your own analysis
 
 ```
-<<<<<<< HEAD
 snakemake --cores 1 --config mode=download_data dl_external_files=True
-=======
-snakemake --cores 12 --config mode=mosaiclassifier plot=True input_bam_location=.tests/data/ output_location=.tests/output/ chromosomes="[chr21]" snv_sites_to_genotype=.tests/external_data/1000G_chr21.vcf.gz reference=.tests/external_data/chr21.fna containerized=True --use-conda --use-singularity --singularity-args "-B /<disk>:/<disk>" --latency-wait 60 --report <REPORT.zip>
->>>>>>> master
 ```
 
 8. Start running your own analysis
 ```
-<<<<<<< HEAD
 snakemake --cores 12 --config input_bam_location=<INPUT_DATA_FOLDER> output_location=<OUTPUT_DATA_FOLDER> --use-conda --use-singularity --singularity-args "-B /<disk>:/<disk>" --latency-wait 60 
-=======
-snakemake --cores 12 --config mode=mosaiclassifier plot=True input_bam_location=<INPUT_DATA_FOLDER> output_location=<OUTPUT_DATA_FOLDER> containerized=True --use-conda --use-singularity --singularity-args "-B /<disk>:/<disk>" --latency-wait 60 
->>>>>>> master
 
 ```
 9. Generate report 
 ```
-<<<<<<< HEAD
 snakemake --cores 12 --config input_bam_location=<INPUT_DATA_FOLDER> output_location=<OUTPUT_DATA_FOLDER> --use-conda --use-singularity --singularity-args "-B /<disk>:/<disk>" --latency-wait 60 --report <REPORT.zip>
-=======
-snakemake --cores 12 --config mode=mosaiclassifier plot=True input_bam_location=<INPUT_DATA_FOLDER> output_location=<OUTPUT_DATA_FOLDER> containerized=True --use-conda --use-singularity --singularity-args "-B /<disk>:/<disk>" --latency-wait 60 --report <REPORT.zip>
->>>>>>> master
 ```
 
 
@@ -87,11 +71,7 @@ snakemake --cores 12 --config mode=mosaiclassifier plot=True input_bam_location=
 
 * [Usage](docs/usage.md)
 * [Parameters & input](docs/parameters.md)
-<<<<<<< HEAD
-* [Output](docs/output.md) (#TODO)
-=======
 * [Output](docs/output.md)
->>>>>>> master