change sims prefix to be universal and simpler

Author: pdimens

.github/workflows/tests.yml

@@ -688,25 +688,25 @@ jobs:
         shell: micromamba-shell {0}
         run: |
           harpy simulate snpindel --quiet --snp-count 10 --indel-count 10 -z 0.5  test/genome/genome.fasta.gz
-          harpy simulate snpindel --quiet --prefix Simulate/snpvcf --snp-vcf Simulate/snpindel/diploid/sim.snpindel.snp.hap1.vcf --indel-vcf Simulate/snpindel/diploid/sim.snpindel.indel.hap1.vcf  test/genome/genome.fasta.gz
+          harpy simulate snpindel --quiet --prefix Simulate/snpvcf --snp-vcf Simulate/snpindel/diploid/sim.snp.hap1.vcf --indel-vcf Simulate/snpindel/diploid/sim.indel.hap1.vcf  test/genome/genome.fasta.gz
       - name: simulate inversions
         shell: micromamba-shell {0}
         if: always()
         run: |
           harpy simulate inversion --quiet --count 10 -z 0.5 test/genome/genome.fasta.gz
-          harpy simulate inversion --quiet --prefix Simulate/invvcf --vcf Simulate/inversion/diploid/sim.inversion.inversion.hap1.vcf  test/genome/genome.fasta.gz
+          harpy simulate inversion --quiet --prefix Simulate/invvcf --vcf Simulate/inversion/diploid/sim.inversion.hap1.vcf  test/genome/genome.fasta.gz
       - name: simulate cnv
         shell: micromamba-shell {0}
         if: always()
         run: |
           harpy simulate cnv --quiet --count 10 -z 0.5 test/genome/genome.fasta.gz
-          harpy simulate cnv --quiet --prefix Simulate/cnvvcf --vcf Simulate/cnv/diploid/sim.cnv.cnv.hap1.vcf  test/genome/genome.fasta.gz
+          harpy simulate cnv --quiet --prefix Simulate/cnvvcf --vcf Simulate/cnv/diploid/sim.cnv.hap1.vcf  test/genome/genome.fasta.gz
       - name: simulate translocations
         shell: micromamba-shell {0}
         if: always()
         run: |
           harpy simulate translocation --quiet --count 10 -z 0.5 test/genome/genome.fasta.gz
-          harpy simulate translocation --quiet --prefix Simulate/transvcf --vcf Simulate/translocation/diploid/sim.translocation.translocation.hap1.vcf  test/genome/genome.fasta.gz
+          harpy simulate translocation --quiet --prefix Simulate/transvcf --vcf Simulate/translocation/diploid/sim.translocation.hap1.vcf  test/genome/genome.fasta.gz
 
   simulate_linkedreads:
     needs: [changes, pkgbuild]

harpy/simulate.py

@@ -219,7 +219,7 @@ def linkedreads(genome_hap1, genome_hap2, output_dir, outer_distance, mutation_r
 @click.option('--only-vcf',  is_flag = True, default = False, help = 'If setting heterozygosity, only create the vcf rather than the fasta files')
 @click.option('-e', '--exclude-chr', type = click.Path(exists=True, dir_okay=False, readable=True), help = "Text file of chromosomes to avoid")
 @click.option('-o', '--output-dir', type = click.Path(exists = False), default = "Simulate/snpindel", show_default=True,  help = 'Output directory name')
-@click.option('-p', '--prefix', type = str, default= "sim.snpindel", show_default=True, help = "Naming prefix for output files")
+@click.option('-p', '--prefix', type = str, default= "sim", show_default=True, help = "Naming prefix for output files")
 @click.option('--conda',  is_flag = True, default = False, help = 'Use conda/mamba instead of container')
 @click.option('--setup-only',  is_flag = True, hidden = True, show_default = True, default = False, help = 'Setup the workflow and exit')
 @click.option('--hpc',  type = click.Path(exists = True, file_okay = False, readable=True), help = 'Directory with HPC submission `config.yaml` file')
@@ -340,7 +340,7 @@ def snpindel(genome, snp_vcf, indel_vcf, only_vcf, output_dir, prefix, snp_count
 @click.option('-g', '--genes', type = click.Path(exists=True, dir_okay=False, readable=True), help = "GFF3 file of genes to avoid when simulating")
 @click.option('-z', '--heterozygosity', type = click.FloatRange(0,1), default = 0, show_default=True, help = 'heterozygosity to simulate diploid variants')
 @click.option('-e', '--exclude-chr', type = click.Path(exists=True, dir_okay=False, readable=True), help = "Text file of chromosomes to avoid")
-@click.option('-p', '--prefix', type = str, default= "sim.inversion", show_default=True, help = "Naming prefix for output files")
+@click.option('-p', '--prefix', type = str, default= "sim", show_default=True, help = "Naming prefix for output files")
 @click.option('--only-vcf',  is_flag = True, default = False, help = 'If setting heterozygosity, only create the vcf rather than the fasta files')
 @click.option('-o', '--output-dir', type = click.Path(exists = False), default = "Simulate/inversion", show_default=True,  help = 'Output directory name')
 @click.option('--conda',  is_flag = True, default = False, help = 'Use conda/mamba instead of container')
@@ -450,7 +450,7 @@ def inversion(genome, vcf, only_vcf, prefix, output_dir, count, min_size, max_si
 @click.option('--only-vcf',  is_flag = True, default = False, help = 'If setting heterozygosity, only create the vcf rather than the fasta files')
 @click.option('-e', '--exclude-chr', type = click.Path(exists=True, dir_okay=False, readable=True), help = "Text file of chromosomes to avoid")
 @click.option('-o', '--output-dir', type = click.Path(exists = False), default = "Simulate/cnv", show_default=True,  help = 'Output directory name')
-@click.option('-p', '--prefix', type = str, default= "sim.cnv", show_default=True, help = "Naming prefix for output files")
+@click.option('-p', '--prefix', type = str, default= "sim", show_default=True, help = "Naming prefix for output files")
 @click.option('--conda',  is_flag = True, default = False, help = 'Use conda/mamba instead of container')
 @click.option('--setup-only',  is_flag = True, hidden = True, show_default = True, default = False, help = 'Setup the workflow and exit')
 @click.option('--hpc',  type = click.Path(exists = True, file_okay = False, readable=True), help = 'Directory with HPC submission `config.yaml` file')
@@ -561,7 +561,7 @@ def cnv(genome, output_dir, vcf, only_vcf, prefix, count, min_size, max_size, du
 @click.option('--only-vcf',  is_flag = True, default = False, help = 'If setting heterozygosity, only create the vcf rather than the fasta files')
 @click.option('-e', '--exclude-chr', type = click.Path(exists=True, dir_okay=False, readable=True), help = "Text file of chromosomes to avoid")
 @click.option('-o', '--output-dir', type = click.Path(exists = False), default = "Simulate/translocation", show_default=True,  help = 'Output directory name')
-@click.option('-p', '--prefix', type = str, default= "sim.translocation", show_default=True, help = "Naming prefix for output files")
+@click.option('-p', '--prefix', type = str, default= "sim", show_default=True, help = "Naming prefix for output files")
 @click.option('--conda',  is_flag = True, default = False, help = 'Use conda/mamba instead of container')
 @click.option('--setup-only',  is_flag = True, hidden = True, show_default = True, default = False, help = 'Setup the workflow and exit')
 @click.option('--hpc',  type = click.Path(exists = True, file_okay = False, readable=True), help = 'Directory with HPC submission `config.yaml` file')