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Merge pull request #337 from cokelaer/dev
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- Fix benchmark plot
- add fast52pod5
- fix go into goalign/gotree in the different methods based on goalign/gotree
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@cokelaer
cokelaer committed Jul 17, 2023
2 parents 87342d4 + 8636823 commit fef2abc
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1 change: 0 additions & 1 deletion .github/workflows/abi2fasta.yml
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/abi2fastq.yml
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/abi2qual.yml
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mawk
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bam2bedgraph.yml
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bam2bigwig.yml
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bam2cov.yml
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mawk
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bam2cram.yml
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bam2fasta.yml
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mawk
xlrd
# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bam2fastq.yml
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mawk
xlrd
# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bam2json.yml
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mawk
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bam2sam.yml
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mawk
xlrd
# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bam2tsv.yml
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mawk
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bam2wiggle.yml
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mawk
xlrd
# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bcf2vcf.yml
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bcf2wiggle.yml
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mawk
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bed2wiggle.yml
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bedgraph2bigwig.yml
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bedgraph2cov.yml
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bedgraph2wiggle.yml
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bigbed2bed.yml
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bigbed2wiggle.yml
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bigwig2bedgraph.yml
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bigwig2wiggle.yml
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mawk
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bplink2plink.yml
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bplink2vcf.yml
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/bz22gz.yml
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/clustal2fasta.yml
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mawk
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/clustal2nexus.yml
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/clustal2phylip.yml
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/clustal2stockholm.yml
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/cram2bam.yml
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/cram2fasta.yml
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mawk
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/cram2fastq.yml
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mawk
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/cram2sam.yml
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mawk
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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3 changes: 1 addition & 2 deletions .github/workflows/create_wk.py
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mawk
xlrd
# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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"""


for x in ['abi2fasta','abi2fastq','abi2qual','bam2bedgraph','bam2bigwig','bam2cov','bam2cram','bam2fasta','bam2fastq','bam2json','bam2sam','bam2tsv','bam2wiggle','bcf2vcf','bcf2wiggle','bed2wiggle','bedgraph2bigwig','bedgraph2cov','bedgraph2wiggle','bigbed2bed','bigbed2wiggle','bigwig2bedgraph','bigwig2wiggle','bplink2plink','bplink2vcf','bz22gz','clustal2fasta','clustal2nexus','clustal2phylip','clustal2stockholm','cram2bam','cram2fasta','cram2fastq','cram2sam','csv2tsv','csv2xls','dsrc2gz','embl2fasta','embl2genbank','fasta2clustal','fasta2faa','fasta2fasta_agp','fasta2fastq','fasta2genbank','fasta2nexus','fasta2phylip','fasta2twobit','fasta_qual2fastq','fastq2fasta_qual','fastq2fasta','fastq2qual','genbank2embl','genbank2fasta','genbank2gff3','gfa2fasta','gff22gff3','gff32gff2','gff32gtf', 'gz2bz2','gz2dsrc','json2yaml','maf2sam','newick2nexus','newick2phyloxml','nexus2clustal','nexus2fasta','nexus2newick','nexus2phylip','nexus2phyloxml','ods2csv','pdb2faa', 'phylip2clustal','phylip2fasta','phylip2nexus','phylip2stockholm','phylip2xmfa','phyloxml2newick','phyloxml2nexus','plink2bplink','plink2vcf','sam2bam','sam2cram','sam2paf','scf2fasta','scf2fastq','sra2fastq','stockholm2clustal','stockholm2phylip','tsv2csv','twobit2fasta','vcf2bcf','vcf2bed','vcf2bplink','vcf2plink','vcf2wiggle','wig2bed','xls2csv','xlsx2csv','xmfa2phylip','yaml2json']:
for x in ['abi2fasta','abi2fastq','abi2qual','bam2bedgraph','bam2bigwig','bam2cov','bam2cram','bam2fasta','bam2fastq','bam2json','bam2sam','bam2tsv','bam2wiggle','bcf2vcf','bcf2wiggle','bed2wiggle','bedgraph2bigwig','bedgraph2cov','bedgraph2wiggle','bigbed2bed','bigbed2wiggle','bigwig2bedgraph','bigwig2wiggle','bplink2plink','bplink2vcf','bz22gz','clustal2fasta','clustal2nexus','clustal2phylip','clustal2stockholm','cram2bam','cram2fasta','cram2fastq','cram2sam','csv2tsv','csv2xls','dsrc2gz','embl2fasta','embl2genbank','fasta52pod5', 'fasta2clustal','fasta2faa','fasta2fasta_agp','fasta2fastq','fasta2genbank','fasta2nexus','fasta2phylip','fasta2twobit','fasta_qual2fastq','fastq2fasta_qual','fastq2fasta','fastq2qual','genbank2embl','genbank2fasta','genbank2gff3','gfa2fasta','gff22gff3','gff32gff2','gff32gtf', 'gz2bz2','gz2dsrc','json2yaml','maf2sam','newick2nexus','newick2phyloxml','nexus2clustal','nexus2fasta','nexus2newick','nexus2phylip','nexus2phyloxml','ods2csv','pdb2faa', 'phylip2clustal','phylip2fasta','phylip2nexus','phylip2stockholm','phylip2xmfa','phyloxml2newick','phyloxml2nexus','plink2bplink','plink2vcf','sam2bam','sam2cram','sam2paf','scf2fasta','scf2fastq','sra2fastq','stockholm2clustal','stockholm2phylip','tsv2csv','twobit2fasta','vcf2bcf','vcf2bed','vcf2bplink','vcf2plink','vcf2wiggle','wig2bed','xls2csv','xlsx2csv','xmfa2phylip','yaml2json']:
with open(f"{x}.yml", "w") as fout:
fout.write(TEMPLATE.replace("__NAME__", x))

1 change: 0 additions & 1 deletion .github/workflows/csv2tsv.yml
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mawk
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/csv2xls.yml
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mawk
xlrd
# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/dsrc2gz.yml
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mawk
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/embl2fasta.yml
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mawk
xlrd
# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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1 change: 0 additions & 1 deletion .github/workflows/embl2genbank.yml
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mawk
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# mamba install -c conda-forge -c bioconda --quiet -y samtools bedtools bamtools mosdepth pbzip2 pigz dsrc sambamba squizz
- name: Install with pip
shell: bash -l {0}
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