Resolve "Enhance type strictness and parsing"

Closes #4 (closed) Most of the modifications are done in workflow_job.py A lot of changes across all the yaml files to conform to the new standard.

chipathlon/jobs/modules/peak_call.yaml

@@ -51,35 +51,6 @@ peak_call:
         outputs:
           - results_sorted.narrowPeak:
               type: file
-  - jamm[tool]:
-    - jamm_prep:
-        inputs:
-          - exp.bed:
-              type: file
-          - control.bed:
-              type: file
-          - jamm_dir:
-              type: string
-        additional_inputs: null
-        outputs:
-          - jamm_exp.bed:
-              type: file
-          - jamm_control.bed:
-              type: file
-    - jamm_callpeak:
-        inputs:
-          - chrom.sizes:
-              type: file
-          - jamm_dir:
-              type: string
-        additional_inputs:
-          - jamm_exp.bed:
-              type: file
-          - jamm_control.bed:
-              type: file
-        outputs:
-          - results_sorted.narrowPeak:
-              type: file
   - gem[tool]:
     - gem_callpeak:
         inputs:
@@ -100,7 +71,7 @@ peak_call:
           - results_sorted.narrowPeak:
               type: file
   - spp[tool]:
-    - cp_bed_tagalign_exp:
+    - cp_bed_tagalign:
         inputs:
           - exp.bed:
               type: file
@@ -108,7 +79,7 @@ peak_call:
         outputs:
           - exp.tagAlign:
               type: file
-    - cp_bed_tagalign_control:
+    - cp_bed_tagalign:
         inputs:
           - control.bed:
               type: file