variant calling workflow + testing

.circleci/config.yml

@@ -152,6 +152,7 @@ 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
@@ -239,8 +240,14 @@ variables:
         command: |
           source /opt/mambaforge/etc/profile.d/conda.sh
           conda activate $LCDBWF_ENV
+          # RNA-seq/ChIP-seq references
           $DEPLOY/test/lcdb-wf-test references --run-workflow --configfile=config/config.yaml -j2 -p -r -k --orig $ORIG
 
+          # Variant-calling references
+          $DEPLOY/test/lcdb-wf-test references --run-workflow --configfile=$ORIG/test/test_configs/variant-calling.yaml -j2 -p -r -k --orig $ORIG
+
+
+
   # --------------------------------------------------------------------------
   # Standard RNA-seq workflow
   rnaseq-step: &rnaseq-step
@@ -303,6 +310,21 @@ variables:
           conda activate $LCDBWF_ENV
           $DEPLOY/test/lcdb-wf-test colocalization --run-workflow -k -r -p -j2 --use-conda --orig $ORIG
 
+
+  # --------------------------------------------------------------------------
+  # Variant-calling workflow
+  variantcalling-step: &variantcalling-step
+      run:
+        name: variantcalling workflow
+        command: |
+          cd $DEPLOY
+          source /opt/mambaforge/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"
@@ -401,6 +423,18 @@ jobs:
           destination: gene-patterns.html
 
 
+  variantcalling:
+    <<: *defaults
+    steps:
+      - checkout
+      - *restore_cache
+      - *set-path
+      - *get-data
+      - *variantcalling-step
+      - store_artifacts:
+          path: /tmp/variantcalling.tar.gz
+          destination: variantcalling.tar.gz
+
   rnaseq-misc:
     <<: *defaults
     steps:
@@ -501,13 +535,16 @@ workflows:
             - initial-setup
             - pytest
       - references:
-          requires:
-            - initial-setup
-            - pytest
+         requires:
+           - initial-setup
+           - pytest
       - colocalization:
           requires:
             - initial-setup
             - pytest
+      - variantcalling:
+         requires:
+           - initial-setup
       - build-docs:
           requires:
             - initial-setup
@@ -517,5 +554,6 @@ workflows:
             - rnaseq-misc
             - chipseq
             - chipseq-misc
-            - references
+          # - references
             - colocalization
+            - variantcalling

deploy.py

@@ -93,6 +93,10 @@ def write_include_file(source, flavor='all'):
             'recursive-include workflows/chipseq/config *',
             'include workflows/chipseq/chipseq_trackhub.py',
         ],
+        'variant-calling': [
+            'include workflows/variant-calling/Snakefile',
+            'recursive-include workflows/variant-calling/config *',
+        ],
         'all': [
             'recursive-include wrappers *',
             'recursive-include include *',
@@ -110,13 +114,16 @@ def write_include_file(source, flavor='all'):
             'recursive-include workflows/external *',
         ]
 
+
     }
 
     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'])
@@ -328,7 +335,7 @@ def build_envs(dest, conda_frontend="mamba"):
     ap.add_argument(
         "--flavor",
         default="full",
-        help="""Options are {0}. Default is full.""".format(['full', 'rnaseq', 'chipseq']),
+        help="""Options are {0}. Default is full.""".format(['full', 'rnaseq', 'chipseq', 'variant-calling']),
     )
     ap.add_argument(
         "--dest", help="""Destination directory in which to copy files""", required=True

docs/toc.rst

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