Fix/load bai key (#113)

* fixed bug with calculation of upload key

* same bug was present in load_bam and load_sqlite steps

* fixed bug in main wf

Author: tzuni

gdc-dnaseq-aln-cwl/gdc_dnaseq.bamfastq_align.workflow.cwl

@@ -137,7 +137,8 @@ steps:
       input: transform/output_bam
       upload-bucket: bioclient_load_bucket
       upload-key:
-        valueFrom: $(inputs.job_uuid)/$(inputs.input.basename)
+        source: job_uuid
+        valueFrom: $(self)/$(inputs.input.basename)
     out: [ output ]
 
   load_bai:
@@ -149,7 +150,8 @@ steps:
         valueFrom: $(self.secondaryFiles[0])
       upload-bucket: bioclient_load_bucket
       upload-key:
-        valueFrom: $(inputs.job_uuid)/$(inputs.input.nameroot).bai
+        source: job_uuid
+        valueFrom: $(self)/$(inputs.input.nameroot).bai
     out: [ output ]
 
   load_sqlite:
@@ -159,7 +161,8 @@ steps:
       input: transform/sqlite
       upload-bucket: bioclient_load_bucket
       upload-key:
-        valueFrom: $(inputs.job_uuid)/$(inputs.input.basename)
+        source: job_uuid
+        valueFrom: $(self)/$(inputs.input.basename)
     out: [ output ]
 
   emit_bam_uuid:

gdc-dnaseq-prealn-cwl/gdc_dnaseq.aligned_reads.workflow.cwl

@@ -133,7 +133,8 @@ steps:
       input: transform/output_bam
       upload-bucket: bioclient_load_bucket
       upload-key:
-        valueFrom: $(inputs.job_uuid)/$(inputs.input.basename)
+        source: job_uuid
+        valueFrom: $(self)/$(inputs.input.basename)
     out: [ output ]
 
   load_bai:
@@ -145,7 +146,8 @@ steps:
         valueFrom: $(self.secondaryFiles[0])
       upload-bucket: bioclient_load_bucket
       upload-key:
-        valueFrom: $(inputs.job_uuid)/$(inputs.input.nameroot).bai
+        source: job_uuid
+        valueFrom: $(self)/$(inputs.input.basename)
     out: [ output ]
 
   load_sqlite:
@@ -155,7 +157,8 @@ steps:
       input: transform/sqlite
       upload-bucket: bioclient_load_bucket
       upload-key:
-        valueFrom: $(inputs.job_uuid)/$(inputs.input.basename)
+        source: job_uuid
+        valueFrom: $(self)/$(inputs.input.basename)
     out: [ output ]
 
   emit_bam_uuid:

tools/emit_json_value.cwl

@@ -9,7 +9,6 @@ inputs:
     type: File
     inputBinding:
       loadContents: true
-      # valueFrom: $(null)
 
   key:
     type: string