V1.14rc

.circleci/config.yml

@@ -141,6 +141,7 @@ variables:
         cp $ORIG/workflows/rnaseq/run_downstream_test.sh $DEPLOY/workflows/rnaseq/run_downstream_test.sh
         cp $ORIG/workflows/references/run_test.sh $DEPLOY/workflows/references/run_test.sh
         # cp $ORIG/workflows/colocalization/run_test.sh $DEPLOY/workflows/colocalization/run_test.sh
+        cp $ORIG/workflows/variant-calling/run_test.sh $DEPLOY/workflows/variant-calling/run_test.sh
 
         mkdir $DEPLOY/ci
         mkdir $DEPLOY/test
@@ -170,7 +171,7 @@ variables:
         test/lcdb-wf-test unit_tests --ensure-docs
 
         # find all URLs in reference configs and make sure they exist
-        test/lcdb-wf-test unit_tests --url-check
+        # test/lcdb-wf-test unit_tests --url-check
 
         # run R package unit tests using the R env
         test/lcdb-wf-test unit_tests --r-test
@@ -230,6 +231,11 @@ variables:
           conda activate $LCDBWF_ENV
           $DEPLOY/test/lcdb-wf-test references --run-workflow --configfile=config/config.yaml -j2 -p -k --orig $ORIG
 
+          # Variant-calling references
+          $DEPLOY/test/lcdb-wf-test references --run-workflow --configfile=$ORIG/test/test_configs/variant-calling.yaml -j2 -p -k --orig $ORIG
+
+
+
   # --------------------------------------------------------------------------
   # Standard RNA-seq workflow
   rnaseq-step: &rnaseq-step
@@ -292,6 +298,21 @@ variables:
   #         conda activate $LCDBWF_ENV
   #         $DEPLOY/test/lcdb-wf-test colocalization --run-workflow -k -p -j2 --use-conda --orig $ORIG
 
+
+  # --------------------------------------------------------------------------
+  # Variant-calling workflow
+  variantcalling-step: &variantcalling-step
+      run:
+        name: variantcalling workflow
+        command: |
+          cd $DEPLOY
+          source /opt/miniforge/etc/profile.d/conda.sh
+          conda activate $LCDBWF_ENV
+          $DEPLOY/test/lcdb-wf-test variantcalling --run-workflow -n
+          $DEPLOY/test/lcdb-wf-test variantcalling --run-workflow --use-conda -j2
+
+          tar -zcf /tmp/variantcalling.tar.gz workflows/variant-calling/results
+
 # --------------------------------------------------------------------------
 # Syntax note: All of the steps above, with their "&step-name" labels, can be
 # referred to by a corresponding "*step-name" below. The "<<: *defaults"
@@ -390,8 +411,22 @@ jobs:
           destination: gene-patterns.html
 
 
+  variantcalling:
+    <<: *defaults
+    resource_class: large
+    steps:
+      - checkout
+      - *restore_cache
+      - *set-path
+      - *get-data
+      - *variantcalling-step
+      - store_artifacts:
+          path: /tmp/variantcalling.tar.gz
+          destination: variantcalling.tar.gz
+
   rnaseq-misc:
     <<: *defaults
+    resource_class: large
     steps:
       - checkout
       - *restore_cache
@@ -497,6 +532,10 @@ workflows:
       #     requires:
       #       - initial-setup
       #       - pytest
+      - variantcalling:
+         requires:
+           - initial-setup
+           - pytest
       - build-docs:
           requires:
             - initial-setup
@@ -508,3 +547,4 @@ workflows:
             - chipseq-misc
             - references
             # - colocalization
+            - variantcalling

.gitignore

@@ -66,3 +66,6 @@ workflows/rnaseq/downstream/rnaseq.html
 ._*
 Rplots.pdf
 /lib/include/*
+WORKLOG.rst
+workflows/variant-calling/references/
+workflows/variant-calling/results/

deploy.py

@@ -108,13 +108,21 @@ def write_include_file(source, flavor="all"):
             "recursive-include workflows/figures *",
             "recursive-include workflows/external *",
         ],
+
+        "variant-calling": [
+            "include workflows/variant-calling/Snakefile",
+            "recursive-include workflows/variant-calling/config *",
+        ],
+
     }
 
     patterns = []
     if flavor in ("full", "rnaseq"):
         patterns.extend(PATTERN_DICT["rnaseq"])
     if flavor in ("full", "chipseq"):
         patterns.extend(PATTERN_DICT["chipseq"])
+    if flavor in ("full", "variant-calling"):
+        patterns.extend(PATTERN_DICT["variant-calling"])
     if flavor == "full":
         patterns.extend(PATTERN_DICT["full"])
     patterns.extend(PATTERN_DICT["all"])
@@ -348,7 +356,7 @@ def build_envs(dest, additional_main=None, additional_r=None, conda_frontend="co
         "--flavor",
         default="full",
         help="""Options are {0}. Default is full.""".format(
-            ["full", "rnaseq", "chipseq"]
+            ["full", "rnaseq", "chipseq", "variant-calling"]
         ),
     )
     ap.add_argument(

docs/toc.rst

@@ -13,6 +13,7 @@ Table of Contents
    rnaseq
    downstream-rnaseq
    chipseq
+   variant-calling
    integrative
    conda
    tests