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move --output-dir to other options
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@pdimens
pdimens committed Mar 21, 2024
1 parent 211ff6f commit a0fdff2
Showing 1 changed file with 22 additions and 22 deletions.
44 changes: 22 additions & 22 deletions src/harpy/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -169,113 +169,113 @@ def preflight():
},
{
"name": "Other Options",
"options": ["--threads", "--snakemake", "--quiet", "--help"],
"options": ["--output-dir", "--threads", "--snakemake", "--quiet", "--help"],
},
],
"harpy preflight fastq": [
{
"name": "Other Options",
"options": ["--threads", "--snakemake", "--quiet", "--help"],
"options": ["--output-dir", "--threads", "--snakemake", "--quiet", "--help"],
},
],
"harpy demultiplex gen1": [
{
"name": "Configuration",
"options": ["--output-dir", "--samplesheet"],
"options": ["--samplesheet"],
},
{
"name": "Other Options",
"options": ["--threads", "--skipreports", "--snakemake", "--quiet", "--help"],
"options": ["--output-dir", "--threads", "--skipreports", "--snakemake", "--quiet", "--help"],
},
],
"harpy qc": [
{
"name": "Configuration",
"options": ["--output-dir", "--max-length", "--ignore-adapters", "--extra-params"],
"options": ["--max-length", "--ignore-adapters", "--extra-params"],
},
{
"name": "Other Options",
"options": ["--threads", "--skipreports", "--snakemake", "--quiet", "--help"],
"options": ["--output-dir", "--threads", "--skipreports", "--snakemake", "--quiet", "--help"],
},
],
"harpy align bwa": [
{
"name": "Configuration",
"options": ["--output-dir", "--genome", "--quality-filter", "--molecule-distance", "--extra-params"],
"options": ["--genome", "--quality-filter", "--molecule-distance", "--extra-params"],
},
{
"name": "Other Options",
"options": ["--threads", "--skipreports", "--snakemake", "--quiet", "--help"],
"options": ["--output-dir", "--threads", "--skipreports", "--snakemake", "--quiet", "--help"],
},
],
"harpy align ema": [
{
"name": "Configuration",
"options": ["--output-dir", "--platform", "--whitelist", "--genome", "--quality-filter", "--ema-bins", "--extra-params"],
"options": ["--platform", "--whitelist", "--genome", "--quality-filter", "--ema-bins", "--extra-params"],
},
{
"name": "Other Options",
"options": ["--threads", "--skipreports", "--snakemake", "--quiet", "--help"],
"options": ["--output-dir", "--threads", "--skipreports", "--snakemake", "--quiet", "--help"],
},
],
"harpy snp mpileup": [
{
"name": "Configuration",
"options": ["--output-dir", "--genome", "--populations", "--ploidy", "--windowsize", "--extra-params"],
"options": ["--genome", "--populations", "--ploidy", "--windowsize", "--extra-params"],
},
{
"name": "Other Options",
"options": ["--threads", "--skipreports", "--snakemake", "--quiet", "--help"],
"options": ["--output-dir", "--threads", "--skipreports", "--snakemake", "--quiet", "--help"],
},
],
"harpy snp freebayes": [
{
"name": "Configuration",
"options": ["--output-dir", "--genome", "--populations", "--ploidy", "--windowsize", "--extra-params"],
"options": ["--genome", "--populations", "--ploidy", "--windowsize", "--extra-params"],
},
{
"name": "Other Options",
"options": ["--threads", "--skipreports", "--snakemake", "--quiet", "--help"],
"options": ["--output-dir", "--threads", "--skipreports", "--snakemake", "--quiet", "--help"],
},
],
"harpy sv leviathan": [
{
"name": "Configuration",
"options": ["--output-dir", "--genome", "--populations", "--extra-params"],
"options": ["--genome", "--populations", "--extra-params"],
},
{
"name": "Other Options",
"options": ["--threads", "--skipreports", "--snakemake", "--quiet", "--help"],
"options": ["--output-dir", "--threads", "--skipreports", "--snakemake", "--quiet", "--help"],
},
],
"harpy sv naibr": [
{
"name": "Configuration",
"options": ["--output-dir", "--genome", "--vcf", "--molecule-distance", "--populations", "--extra-params"],
"options": ["--genome", "--vcf", "--molecule-distance", "--populations", "--extra-params"],
},
{
"name": "Other Options",
"options": ["--threads", "--skipreports", "--snakemake", "--quiet", "--help"],
"options": ["--output-dir", "--threads", "--skipreports", "--snakemake", "--quiet", "--help"],
},
],
"harpy impute": [
{
"name": "Configuration",
"options": ["--output-dir", "--vcf", "--parameters", "--extra-params", "--vcf-samples"],
"options": ["--vcf", "--parameters", "--extra-params", "--vcf-samples"],
},
{
"name": "Other Options",
"options": ["--threads", "--skipreports", "--snakemake", "--quiet", "--help"],
"options": ["--output-dir", "--threads", "--skipreports", "--snakemake", "--quiet", "--help"],
},
],
"harpy phase": [
{
"name": "Configuration",
"options": ["--output-dir", "--vcf", "--molecule-distance", "--genome", "--prune-threshold", "--ignore-bx", "--extra-params", "--vcf-samples"],
"options": ["--vcf", "--molecule-distance", "--genome", "--prune-threshold", "--ignore-bx", "--extra-params", "--vcf-samples"],
},
{
"name": "Other Options",
"options": ["--threads", "--skipreports", "--snakemake", "--quiet", "--help"],
"options": ["--output-dir", "--threads", "--skipreports", "--snakemake", "--quiet", "--help"],
},
]
}
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