Merge pull request #135 from pdimens/metasssembly

log changes and fixes

.deprecated/align-minimap.smk

@@ -54,7 +54,7 @@ def get_fq(wildcards):
     r = re.compile(fr".*/({re.escape(wildcards.sample)}){bn_r}", flags = re.IGNORECASE)
     return sorted(list(filter(r.match, fqlist))[:2])
 
-rule setup_genome:
+rule process_genome:
     input:
         genomefile
     output: 
@@ -73,7 +73,7 @@ rule setup_genome:
         fi
         """
 
-rule faidx_genome:
+rule index_genome:
     input: 
         f"Genome/{bn}"
     output: 

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -14,17 +14,23 @@ body:
     id: version
     attributes:
       label: Harpy Version
-      description: Please include the version of harpy that is causing this issue. The version number is provided by running `harpy --version`.
-      placeholder: |
-        x.x.x
+      description: Please include the version of harpy that is causing this issue.
+      placeholder: use `harpy --version` to find the version number
     validations:
       required: true
 
+  - type: checkboxes
+    id: checklist
+    attributes:
+      options:
+        - label: this is the latest version of Harpy
+          required: true
+
   - type: textarea
     id: error-file
     attributes:
       label: File that triggers the error (if applicable)
-      description: Please drag and drop (and upload to the GitHub issue) an input file that can be used to replicate the error. You may also copy-and-paste it as a code block. If the file type is not allowed, please compress into a `.zip` or `.gz` file.
+      description: Please drag and drop (and upload to the GitHub issue) an input file that can be used to replicate the error. You may also copy-and-paste it as a code block. If the file type is not allowed, please compress into a `.zip` or `.gz` file. Alternatively, a snakemake log file would be helpful here too.
       placeholder: |
         [ Copy and paste or drag and drop an example file here to upload ]
 
@@ -47,16 +53,3 @@ body:
         test/bam/sample2.bam test/bam_phased/sample2.bam
         test/bam/sample1.bam test/bam_phased/sample1.bam
 
-  - type: checkboxes
-    id: checklist
-    attributes:
-      label: Before submitting
-      description: >-
-        Please ensure your bug report fulfills all of the following requirements.
-      options:
-        - label: >-
-            I have read the [relevant documentation](https://pdimens.github.io/harpy/).
-          required: true
-        - label: >-
-            I am using the latest release of Harpy.
-          required: true

.github/filters.yml

@@ -152,6 +152,7 @@ simreads: &simreads
 other: &other
   - 'harpy/stitchparams.py'
   - 'harpy/popgroup.py'
+  - 'harpy/hpc.py'
 modules:
   - *common
   - *demux

.github/workflows/tests.yml

@@ -780,4 +780,11 @@ jobs:
         run: harpy stitchparams -o params.file
       - name: harpy popgroup
         shell: micromamba-shell {0}
-        run: harpy popgroup test/fastq
+        run: harpy popgroup test/fastq
+      - name: harpy hpc
+        shell: micromamba-shell {0}
+        run: |
+          harpy hpc slurm
+          harpy hpc googlebatch
+          harpy hpc lsf
+          harpy hpc htcondor

.gitignore

@@ -15,6 +15,7 @@ Simulate/
 Impute/
 Preflight/
 Phase/
+Metassembly/
 samples.populations
 *.fasta
 *.bcf

harpy/__main__.py

@@ -2,18 +2,19 @@
 
 import rich_click as click
 from . import align
+from . import deconvolve
 from . import demultiplex
+from . import container
+from . import hpc
 from . import impute
+from . import metassembly
+from . import qc
 from . import phase
 from . import preflight
-from . import qc
+from . import resume
 from . import simulate
 from . import snp
 from . import sv
-from . import container
-from . import hpc
-from . import resume
-from . import deconvolve
 from .popgroups import popgroup
 from .stitchparams import stitchparams
 
@@ -24,9 +25,7 @@
 click.rich_click.MAX_WIDTH = 75
 click.rich_click.REQUIRED_SHORT_STRING = ""
 click.rich_click.ERRORS_SUGGESTION = "Try the '--help' flag for more information."
-click.rich_click.ERRORS_EPILOGUE = """
-See the documentation: [link=https://pdimens.github.io/harpy/]https://pdimens.github.io/harpy/[/link]
-"""
+click.rich_click.ERRORS_EPILOGUE = "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("0.0.0", prog_name="harpy")
@@ -57,14 +56,15 @@ def cli():
 cli.add_command(hpc.hpc)
 cli.add_command(resume.resume)
 cli.add_command(deconvolve.deconvolve)
+cli.add_command(metassembly.metassembly)
 
 ## the modules ##
 click.rich_click.COMMAND_GROUPS = {
     "harpy":
         [
             {
                 "name": "Modules",
-                "commands": ["demultiplex","qc", "align","snp","sv","impute","phase", "simulate"],
+                "commands": ["demultiplex", "metassembly","qc", "align","snp","sv","impute","phase", "simulate"],
             },
             {
                 "name": "Other Commands",
@@ -73,5 +73,5 @@ def cli():
         ],
  } | simulate.commandstring | hpc.docstring
 
-for i in [align, deconvolve, demultiplex, impute, phase, preflight, qc, simulate, snp, sv]:
+for i in [align, deconvolve, demultiplex, impute, phase, preflight, qc, simulate, snp, sv, metassembly]:
     click.rich_click.OPTION_GROUPS |= i.docstring

harpy/_conda.py

@@ -2,7 +2,7 @@
 
 import os
 
-def generate_conda_deps():
+def create_conda_recipes():
     """Create the YAML files of the workflow conda dependencies"""
     condachannels = ["bioconda","conda-forge","defaults"]
     environ = {
@@ -17,6 +17,12 @@ def generate_conda_deps():
             "conda-forge::libzlib",
             "conda-forge::xz"
             ],
+        "metassembly" : [
+            "bioconda::spades=4.0"
+        ],
+        "athena": [
+            "bioconda::athena_meta"
+        ],
         "phase" : [
             "bioconda::hapcut2",
             "bioconda::whatshap"
@@ -52,16 +58,14 @@ def generate_conda_deps():
             "conda-forge::numpy",
             "conda-forge::perl"
             ],
-        "snp": [
+        "variants": [
             "bioconda::bcftools=1.20",
-            "bioconda::freebayes=1.3.6"
+            "bioconda::freebayes=1.3.6",
+            "bioconda::leviathan",
+            "bioconda::naibr-plus"
             ],
         "stitch" : [
             "bioconda::r-stitch=1.6.10"
-            ],
-        "sv": [
-            "bioconda::leviathan",
-            "bioconda::naibr-plus"
             ]
     }