Merge pull request #101 from pdimens/100-impute-create-separate-conda…

…-env-for-stitch 100 impute create separate conda env for stitch
pdimens · Jul 3, 2024 · d22bc3a · d22bc3a
2 parents 0844aac + bb1867f
commit d22bc3a
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Showing 6 changed files with 14 additions and 8 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "harpy"
-version = "1.1.0"
+version = "1.1.1"
 authors = [
     {name = "Pavel Dimens"}
 ]

diff --git a/src/harpy/__main__.py b/src/harpy/__main__.py
@@ -41,7 +41,7 @@
 click.rich_click.ERRORS_EPILOGUE = "See the documentation: [link=https://pdimens.github.io/harpy/]https://pdimens.github.io/harpy/[/link]"
 
 @click.group(options_metavar='', context_settings={"help_option_names" : ["-h", "--help"]})
-@click.version_option("1.1.0", prog_name="Harpy")
+@click.version_option("1.1.1", prog_name="Harpy")
 def cli():
     """
     An automated workflow for haplotagging linked-read data

diff --git a/src/harpy/conda_deps.py b/src/harpy/conda_deps.py
@@ -6,13 +6,14 @@ def generate_conda_deps():
     """Create the YAML files of the workflow conda dependencies"""
     condachannels = ["bioconda","conda-forge","defaults"]
     environ = {
-        "qc" : ["bioconda::falco", "bioconda::fastp", "bioconda::multiqc=1.22", "bioconda::pysam=0.22"],
+        "qc" : ["bioconda::quickdeconvolution", "bioconda::falco", "bioconda::fastp", "bioconda::multiqc=1.22", "bioconda::pysam=0.22"],
         "align": ["bioconda::bwa", "bioconda::ema","bioconda::strobealign", "conda-forge::icu","conda-forge::libzlib", "bioconda::samtools=1.20", "bioconda::seqtk", "bioconda::tabix", "conda-forge::xz"],
         "snp": ["bioconda::bcftools=1.20", "bioconda::freebayes=1.3.6"],
         "sv": ["bioconda::leviathan", "bioconda::naibr-plus"],
         "phase" : ["bioconda::hapcut2", "bioconda::whatshap"],
         "simulations" : ["conda-forge::perl", "bioconda::perl-math-random", "bioconda::perl-inline-c", "bioconda::perl-parse-recdescent", "conda-forge::numpy", "bioconda::dwgsim", "alienzj::msort"],
-        "r" : ["conda-forge::r-xml2", "conda-forge::r-highcharter", "conda-forge::r-circlize", "r::r-biocircos", "conda-forge::r-dt", "conda-forge::r-flexdashboard", "conda-forge::r-ggplot2", "conda-forge::r-ggridges", "conda-forge::r-plotly", "conda-forge::r-tidyr", "bioconda::r-stitch"]
+        "r" : ["conda-forge::r-xml2", "conda-forge::r-highcharter", "conda-forge::r-circlize", "r::r-biocircos", "conda-forge::r-dt", "conda-forge::r-flexdashboard", "conda-forge::r-ggplot2", "conda-forge::r-ggridges", "conda-forge::r-plotly", "conda-forge::r-tidyr"],
+        "stitch" : ["bioconda::r-stitch=1.6.10"]
     }
     os.makedirs(".harpy_envs", exist_ok = True)
     # overwrites existing

diff --git a/src/harpy/snakefiles/containerize.smk b/src/harpy/snakefiles/containerize.smk
@@ -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"
@@ -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"

diff --git a/src/harpy/snakefiles/impute.smk b/src/harpy/snakefiles/impute.smk
@@ -129,7 +129,7 @@ rule impute:
         parameters = paramspace.instance,
         extra = config.get("extra", "")
     conda:
-        f"{envdir}/r.yaml"
+        f"{envdir}/stitch.yaml"
     benchmark:
         f".Benchmark/{outdir}/stitch.{paramspace.wildcard_pattern}" + ".{part}.txt"
     threads:

diff --git a/src/harpy/validations.py b/src/harpy/validations.py
@@ -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"]
+    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)