From 6d73d6b3adc9dbabb4cec79244bb4791f32c9623 Mon Sep 17 00:00:00 2001
From: aknecht2 <aknecht2@unl.edu>
Date: Thu, 3 Mar 2016 10:55:02 -0600
Subject: [PATCH] Updated yaml files.  Added bowtie2 yaml files.

---
 chipathlon/jobs/modules/align.yaml            | 38 +++++++++++++++++--
 .../jobs/params/bowtie2_align_paired.yaml     | 36 ++++++++++++++++++
 .../jobs/params/bowtie2_align_single.yaml     | 31 +++++++++++++++
 chipathlon/jobs/params/bwa_align_paired.yaml  | 10 ++---
 chipathlon/jobs/params/bwa_align_single.yaml  | 10 ++---
 chipathlon/test/run/run.yaml                  | 20 +++++++---
 chipathlon/workflow_module.py                 | 10 +++++
 7 files changed, 135 insertions(+), 20 deletions(-)
 create mode 100644 chipathlon/jobs/params/bowtie2_align_paired.yaml
 create mode 100644 chipathlon/jobs/params/bowtie2_align_single.yaml
 create mode 100644 chipathlon/workflow_module.py

diff --git a/chipathlon/jobs/modules/align.yaml b/chipathlon/jobs/modules/align.yaml
index b418a90..78da92d 100644
--- a/chipathlon/jobs/modules/align.yaml
+++ b/chipathlon/jobs/modules/align.yaml
@@ -24,7 +24,7 @@ align:
       paired:
         - bwa_align_paired:
             inputs:
-              - ref_genome.fa
+              - ref_genome
               - download_1.fastq
               - download_2.fastq
             additional_inputs:
@@ -43,7 +43,37 @@ align:
           - align.bam
   bowtie2:
     - single:
-        - bowtie2_align_single
+        - bowtie2_align_single:
+            inputs:
+              - ref_genome
+              - download_1.fastq
+            additional_inputs:
+                - ref_genome.1.bt2
+                - ref_genome.2.bt2
+                - ref_genome.3.bt2
+                - ref_genome.4.bt2
+                - ref_genome.rev.1.bt2
+                - ref_genome.rev.2.bt2
+            outputs:
+              - align.sam
       paired:
-        - bowtie2_align_paired
-    - samtools_sam_to_bam
+        - bowtie2_align_paired:
+            inputs:
+              - ref_genome
+              - download_1.fastq
+              - download_2.fastq
+            additional_inputs:
+              - ref_genome.1.bt2
+              - ref_genome.2.bt2
+              - ref_genome.3.bt2
+              - ref_genome.4.bt2
+              - ref_genome.rev.1.bt2
+              - ref_genome.rev.2.bt2
+            outputs:
+              - align.sam
+    - samtools_sam_to_bam:
+        inputs:
+          - align.sam
+        additional_inputs: null
+        outputs:
+          - align.bam
diff --git a/chipathlon/jobs/params/bowtie2_align_paired.yaml b/chipathlon/jobs/params/bowtie2_align_paired.yaml
new file mode 100644
index 0000000..20ec2cf
--- /dev/null
+++ b/chipathlon/jobs/params/bowtie2_align_paired.yaml
@@ -0,0 +1,36 @@
+bwa_align_paired:
+  inputs:
+    -
+      - fna
+      - fa
+    - fastq
+    - fastq
+  additional_inputs:
+    - .1.bt2
+    - .2.bt2
+    - .3.bt2
+    - .4.bt2
+    - .rev.1.bt2
+    - .rev.2.bt2
+  outputs:
+    - sam
+  command: bowtie2
+  arguments:
+    - "-x":
+        changeable: false
+        required: true
+        value: $inputs.0
+    - "-1":
+        changeable: false
+        required: true
+        value: $inputs.1
+    - "-2":
+        changeable: false
+        required: true
+        value: $inputs.2
+    - "-S":
+        changeable: false
+        required: true
+        value: $outputs.0
+  walltime: 2000
+  memory: 2000
diff --git a/chipathlon/jobs/params/bowtie2_align_single.yaml b/chipathlon/jobs/params/bowtie2_align_single.yaml
new file mode 100644
index 0000000..f6a13c1
--- /dev/null
+++ b/chipathlon/jobs/params/bowtie2_align_single.yaml
@@ -0,0 +1,31 @@
+bwa_align_single:
+  inputs:
+    -
+      - fna
+      - fa
+    - fastq
+  additional_inputs:
+    - .1.bt2
+    - .2.bt2
+    - .3.bt2
+    - .4.bt2
+    - .rev.1.bt2
+    - .rev.2.bt2
+  outputs:
+    - sam
+  command: bowtie2
+  arguments:
+    - "-x":
+        changeable: false
+        required: true
+        value: $inputs.0
+    - "-U":
+        changeable: false
+        required: true
+        value: $inputs.1
+    - "-S":
+        changeable: false
+        required: true
+        value: $outputs.0
+  walltime: 2000
+  memory: 2000
diff --git a/chipathlon/jobs/params/bwa_align_paired.yaml b/chipathlon/jobs/params/bwa_align_paired.yaml
index da1cdd6..65d7ebb 100644
--- a/chipathlon/jobs/params/bwa_align_paired.yaml
+++ b/chipathlon/jobs/params/bwa_align_paired.yaml
@@ -6,11 +6,11 @@ bwa_align_paired:
     - fastq
     - fastq
   additional_inputs:
-    - fa.amb
-    - fa.ann
-    - fa.bwt
-    - fa.pac
-    - fa.sa
+    - .amb
+    - .ann
+    - .bwt
+    - .pac
+    - .sa
   outputs:
     - sam
   command: bwa
diff --git a/chipathlon/jobs/params/bwa_align_single.yaml b/chipathlon/jobs/params/bwa_align_single.yaml
index 368ad02..fe898c9 100644
--- a/chipathlon/jobs/params/bwa_align_single.yaml
+++ b/chipathlon/jobs/params/bwa_align_single.yaml
@@ -5,11 +5,11 @@ bwa_align_single:
       - fa
     - fastq
   additional_inputs:
-    - fa.amb
-    - fa.ann
-    - fa.bwt
-    - fa.pac
-    - fa.sa
+    - .amb
+    - .ann
+    - .bwt
+    - .pac
+    - .sa
   outputs:
     - sai
   command: bwa
diff --git a/chipathlon/test/run/run.yaml b/chipathlon/test/run/run.yaml
index 6234c7b..d704d81 100644
--- a/chipathlon/test/run/run.yaml
+++ b/chipathlon/test/run/run.yaml
@@ -1,6 +1,14 @@
-- experiment: "ENCSR000BSE"
-  align: bwa
-  peak: spp
-- experiment: "ENCSR000BSE"
-  align: bowtie2
-  peak: spp
+runs:
+  - experiment: "ENCSR000BSE"
+    align: bwa
+    peak: spp
+  - experiment: "ENCSR000BSE"
+    align: bowtie2
+    peak: spp
+genomes:
+  bwa:
+    hg19: "/path/to/genome/base"
+    mm9: "/path/to/genome/base"
+  bowtie2:
+    hg19: "/path/to/genome/base"
+    mm9: "/path/to/genome/base"
diff --git a/chipathlon/workflow_module.py b/chipathlon/workflow_module.py
new file mode 100644
index 0000000..d27b977
--- /dev/null
+++ b/chipathlon/workflow_module.py
@@ -0,0 +1,10 @@
+
+
+
+
+
+class WorkflowModule(Workflow):
+
+    def __init__(self):
+
+        return
-- 
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