Updated yaml files. Added bowtie2 yaml files.

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

chipathlon/jobs/params/bowtie2_align_paired.yaml

+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

chipathlon/jobs/params/bowtie2_align_single.yaml

+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

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

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

chipathlon/test/run/run.yaml

+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"

chipathlon/workflow_module.py

+
+
+
+
+
+class WorkflowModule(Workflow):
+
+    def __init__(self):
+
+        return