From f4e9d11b71aa72261d1e64007e3b2b3d4e22f306 Mon Sep 17 00:00:00 2001
From: Katherine Eaton <ktmeaton@gmail.com>
Date: Mon, 21 Sep 2020 14:32:03 -0400
Subject: [PATCH] test new pipeline workflow after updating docs

---
 .github/workflows/pipeline.yaml | 68 +++++++++++++++++++++++++++++++++
 .gitignore                      |  1 +
 workflow/Snakefile              | 34 +++++++++++++++--
 workflow/envs/iqtree.yaml       |  5 +++
 workflow/rules/phylogeny.smk    |  8 +++-
 5 files changed, 110 insertions(+), 6 deletions(-)
 create mode 100644 .github/workflows/pipeline.yaml
 create mode 100644 workflow/envs/iqtree.yaml

diff --git a/.github/workflows/pipeline.yaml b/.github/workflows/pipeline.yaml
new file mode 100644
index 000000000..14e2c952e
--- /dev/null
+++ b/.github/workflows/pipeline.yaml
@@ -0,0 +1,68 @@
+#------------------------------------------------------------------------------#
+name: Pipeline
+#------------------------------------------------------------------------------#
+# Global workflow environment variables
+env:
+    CONDA_ENVS_PATH: "/home/runner/miniconda/envs:/usr/share/miniconda/envs"
+    CONDA_PKGS_DIRS: "/home/runner/miniconda/pkgs"
+#------------------------------------------------------------------------------#
+# Workflow conditions
+on:
+  push:
+    branches:
+      - '*'
+    paths:
+      - '.github/workflows/pipeline.yaml'
+      - 'workflow/Snakefile'
+      - 'workflow/rules/*.smk'
+      - 'workflow/envs/*.yaml'
+  pull_request:
+    branches:
+      - '*'
+  release:
+    types: [published]
+#------------------------------------------------------------------------------#
+jobs:
+  #----------------------------------------------------------------------------#
+  # Install dependencies
+  install :
+    runs-on: ubuntu-latest
+    steps:
+      #------------------------------------------------------------------------#
+      # Checkout Repository
+      - name: checkout repo
+        uses: actions/checkout@v2
+      #------------------------------------------------------------------------#
+      # Setup conda with mamba
+      - name: setup conda
+        uses: goanpeca/setup-miniconda@v1
+        with:
+          auto-update-conda: true
+          mamba-version: "*"
+          channels: conda-forge
+      #------------------------------------------------------------------------#
+      #  Restore (cache) conda environments
+      - name: cache default env
+        id: cache-default
+        uses: actions/cache@v2
+        with:
+          path: /home/runner/miniconda/envs/default
+          key: snakemake-default-${{ runner.os }}-${{ hashFiles('workflow/envs/default.yaml') }}
+      # Check conda environments
+      - name: check cache
+        run: |
+          conda info --envs
+      # Create environment (if not cached)
+      - name: create default environment
+        if: steps.cache-default.outputs.cache-hit != 'true'
+        shell: bash -l {0}
+        run:
+          mamba env create -f workflow/envs/default.yaml
+      #------------------------------------------------------------------------#
+      #  Test pipeline
+      - name: test pipeline
+        shell: bash -l {0}
+        run:
+          conda activate default;
+          snakemake all --use-conda --profile profiles/gh-actions;
+          conda deactivate;
diff --git a/.gitignore b/.gitignore
index 28bf39b73..ddaee5fec 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
 results/*
 test/*
 sra/*
+workflow/logs/*
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 35c112a85..42580ab22 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -44,6 +44,9 @@ report: "report/workflow.rst"
 # -----------------------------------------------------------------------------#
 
 rule all:
+    """
+    The default pipeline target.
+    """
     input:
         "results/iqtree/iqtree.treefile"
 
@@ -57,9 +60,32 @@ rule help:
   """
   run:
     for rule in workflow.rules:
+      print("-" * 80)
       print("rule: ", rule.name )
       print(rule.docstring )
-      if rule._input: print("input: ", rule._input)
-      if rule._output: print("output: ", rule._output)
-      if rule._params: print("params: ", rule._params)
-      print("")
+      # Rule Inputs
+      if rule._input:
+          print("\tinput:")
+          for in_file in rule.input:
+              print("\t\t" + in_file)
+          for in_file in rule.input.keys():
+              print("\t\t" + in_file + ": " + str(rule.input[in_file]))
+      if rule._output:
+          print("\toutput:")
+          for out_file in rule.output:
+              print("\t\t" + out_file)
+          for out_file in rule.output.keys():
+              print("\t\t" + out_file + ": " + str(rule.output[out_file]))
+      if rule._params:
+          print("\tparams:")
+          for param in rule.params.keys():
+              print("\t\t" + param + ": " + str(rule.params[param]))
+      if rule.resources:
+          print("\tresources:")
+          for resource in rule.resources.keys():
+              print("\t\t" + resource.strip("_") + ": " + str(rule.resources[resource]))
+      if rule.conda_env:
+          print("\t\tconda: ", rule.conda_env)
+      if rule._log:
+          print("\t\tlog: ", rule._log)
+      #print(rule.conda_env)
diff --git a/workflow/envs/iqtree.yaml b/workflow/envs/iqtree.yaml
new file mode 100644
index 000000000..b95d6090c
--- /dev/null
+++ b/workflow/envs/iqtree.yaml
@@ -0,0 +1,5 @@
+channels:
+  - bioconda
+  - defaults
+dependencies:
+  - iqtree=2.0.3
diff --git a/workflow/rules/phylogeny.smk b/workflow/rules/phylogeny.smk
index 9bec42a97..573104df7 100644
--- a/workflow/rules/phylogeny.smk
+++ b/workflow/rules/phylogeny.smk
@@ -9,5 +9,9 @@ rule iqtree:
         snp_aln = "results/snippy_multi/snippy-core.full.aln"
     output:
         tree = "results/iqtree/iqtree.treefile"
-    run:
-        shell("touch {output.tree}")
+    threads:
+        workflow.cores,
+    conda:
+        os.path.join(envs_dir,"iqtree.yaml")
+    shell:
+        "touch {output.tree}"