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Merge branch 'main' into deconvolute
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pdimens authored Jul 4, 2024
2 parents aba12c9 + d22bc3a commit 2f9f94c
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Showing 3 changed files with 9 additions and 3 deletions.
1 change: 1 addition & 0 deletions src/harpy/__main__.py
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Expand Up @@ -30,6 +30,7 @@

@click.group(options_metavar='', context_settings={"help_option_names" : ["-h", "--help"]})
@click.version_option("0.0.0", prog_name="harpy")

def cli():
"""
An automated workflow for haplotagging linked-read data
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9 changes: 7 additions & 2 deletions src/harpy/snakefiles/containerize.smk
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Expand Up @@ -6,7 +6,7 @@ onsuccess:

rule all:
input:
collect("{conda}.env", conda = ["qc","align","snp","sv","phase","r","simulations"])
collect("{conda}.env", conda = ["align", "phase", "qc", "r", "simulations", "snp", "stitch", "sv"])

rule qc:
output: "qc.env"
Expand All @@ -33,11 +33,16 @@ rule phase:
conda: os.getcwd() + "/.harpy_envs/phase.yaml"
shell: "touch {output}"

rule r_env:
rule r:
output: "r.env"
conda: os.getcwd() + "/.harpy_envs/r.yaml"
shell: "touch {output}"

rule stitch:
output: "stitch.env"
conda: os.getcwd() + "/.harpy_envs/stitch.yaml"
shell: "touch {output}"

rule simulations:
output: "simulations.env"
conda: os.getcwd() + "/.harpy_envs/simulations.yaml"
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2 changes: 1 addition & 1 deletion src/harpy/validations.py
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Expand Up @@ -18,7 +18,7 @@ def check_envdir(dirpath):
print_error("This working directory does not contain the expected directory of conda environment definitions ([blue bold].harpy_envs/[/blue bold])\n - use [green bold]--conda[/green bold] to recreate it")
sys.exit(1)
envlist = os.listdir(dirpath)
envs = ["qc", "align", "snp", "sv", "phase", "simulations", "r", "stitch"]
envs = ["align", "phase", "qc", "r", "simulations", "snp", "stitch", "sv"]
errcount = 0
errtable = Table(show_footer=True, box=box.SIMPLE)
errtable.add_column("File", justify="left", style="blue", no_wrap=True)
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