[WIP] superenhancer-final

test/superenhancer-job.json

@@ -1,19 +1,15 @@
 {
     "genome": {
         "class": "File",
-        "path": "test-files/hg18_refseq.ucsc"
+        "path": "./hg18_refseq.ucsc"
     },
     "inputgff": {
         "class": "File",
-        "path": "test-files/F750DD5E-CF29-1720-F2A9-CA655F726017.gff"
+        "path": "./ROSE_DATA/data/HG18_MM1S_MED1.gff"
     },
     "inputbam": {
         "class": "File",
-        "path": "test-files/F750DD5E-CF29-1720-F2A9-CA655F726017.sorted.bam"
+        "path": "./ROSE_DATA/data/MM1S_MED1.hg18.bwt.sorted.bam"
     },
-    "inputbai": {
-        "class": "File",
-        "path": "test-files/F750DD5E-CF29-1720-F2A9-CA655F726017.sorted.bai"
-    },
-    "output_name": ""
-}
+    "output_name": "output"
+}

test/superenhancer-test.yaml

@@ -2,14 +2,14 @@
     "python",
     "/usr/local/bin/ROSE_main.py",
     "-g",
-    "./test-files/hg18_refseq.ucsc",
+    "./hg18_refseq.ucsc",
     "-r",
-    "./test-files/F750DD5E-CF29-1720-F2A9-CA655F726017.sorted.bam",
+    "./ROSE_DATA/data/MM1S_MED1.hg18.bwt.sorted.bam",
     "-i",
-    "./test-files/F750DD5E-CF29-1720-F2A9-CA655F726017.gff",
+    "./ROSE_DATA/data/HG18_MM1S_MED1.gff",
     "-o",
-    ""
+    "output"
   ]
   job:  superenhancer-job.json
-  tool: ../tools/superenhancer.cwl
-  doc: General test of command line generation
+  tool: superenhancer.yml
+  doc: General test of command line generation

tools/alea-createGenome.cwl

@@ -1,12 +1,15 @@
 #!/usr/bin/env cwl-runner
 
-cwlVersion: "cwl:draft-3"
+cwlVersion: v1.0
 
 class: CommandLineTool
 
+baseCommand: ["alea", "createGenome"]
+
 requirements:
-- $import: envvar-global.yml
 - $import: alea-docker.yml
+- $import: envvar-global.yml
+- class: InlineJavascriptRequirement
 - class: EnvVarRequirement
   envDef:
   - envName: "AL_USE_CONCATENATED_GENOME"
@@ -15,101 +18,100 @@ requirements:
     envValue: "-k 0 -n 0 -t 4"
   - envName: "AL_DIR_TOOLS"
     envValue: "/usr/local/bin/"
-- class: InlineJavascriptRequirement
 
 inputs:
-- id: "reference"
+ reference:
   type: File
-  description: |
+  doc: |
     the reference genome fasta file
   inputBinding:
     position: 2
   secondaryFiles:
   - ".fai"
 
-- id: "phased"
+ phased:
   type: File
-  description: |
+  doc: |
     the phased variants vcf file (including SNPs and Indels)
     or the phased SNPs (should be specified first)
   inputBinding:
     position: 3
   secondaryFiles:
   - ".tbi"
 
-- id: "phasedindels"
-  type: ["null", File]
-  description: |
+ phasedindels:
+  type: File?
+  doc: |
     the phased Indels (should be specified second)
   inputBinding:
     position: 4
   secondaryFiles:
   - ".tbi"
 
-- id: "strain1"
+ strain1:
   type: string
-  description: |
+  doc: |
     name of strain1 exactly as specified in the vcf file (e.g. hap1)
     mouse:
-        129P2_OlaHsd	(129P2/OlaHsd)	F	52
-        129S1_SvImJ	(129S1/SvImJ)	F	68
-        129S5SvEvBrd	(129S5SvEvBrd)	F	22
-        A_J	(A/J)	F	52
-        AKR_J	(AKR/J)	F	57
-        BALB_cJ	(BALB/cJ)	F	62
-        BTBR_T+_Itpr3tf_J	(BTBR T+ Itpr3tf/J)	M	85
-        BUB_BnJ	(BUB/BnJ)	M	49
-        C3H_HeH	(C3H/HeH)	F	14
-        C3H_HeJ	(C3H/HeJ)	F	63
-        C57BL_10J	(C57BL/10J)	M	37
-        C57BL_6NJ	(C57BL/6NJ)	F	61
-        C57BR_cdJ	(C57BR/cdJ)	M	51
-        C57L_J	(C57L/J)	M	64
-        C58_J	(C58/J)	M	55
-        CAST_EiJ	(CAST/EiJ)	F	53
-        CBA_J	(CBA/J)	F	56
-        DBA_1J	(DBA/1J)	M	49
-        DBA_2J	(DBA/2J)	F	56
-        FVB_NJ	(FVB/NJ)	F	73
-        I_LnJ	(I/LnJ)	M	45
-        KK_HiJ	(KK/HiJ)	M	55
-        LEWES_EiJ	(LEWES/EiJ)	F	19
-        LP_J	(LP/J)	F	54
-        MOLF_EiJ	(MOLF/EiJ)	M	40
-        NOD_ShiLtJ	(NOD/ShiLtJ)	F	66
-        NZB_B1NJ	(NZB/B1NJ)	M	47
-        NZO_HlLtJ	(NZO/HlLtJ)	F	72
-        NZW_LacJ	(NZW/LacJ)	M	58
-        PWK_PhJ	(PWK/PhJ)	F	53
-        RF_J	(RF/J)	M	54
-        SEA_GnJ	(SEA/GnJ)	M	49
-        SPRET_EiJ	(SPRET/EiJ)	F	67
-        ST_bJ	(ST/bJ)	M	81
-        WSB_EiJ	(WSB/EiJ)	F	51
-        ZALENDE_EiJ	(ZALENDE/EiJ)	M	19
+        129P2_OlaHsd  (129P2/OlaHsd)  F 52
+        129S1_SvImJ (129S1/SvImJ) F 68
+        129S5SvEvBrd  (129S5SvEvBrd)  F 22
+        A_J (A/J) F 52
+        AKR_J (AKR/J) F 57
+        BALB_cJ (BALB/cJ) F 62
+        BTBR_T+_Itpr3tf_J (BTBR T+ Itpr3tf/J) M 85
+        BUB_BnJ (BUB/BnJ) M 49
+        C3H_HeH (C3H/HeH) F 14
+        C3H_HeJ (C3H/HeJ) F 63
+        C57BL_10J (C57BL/10J) M 37
+        C57BL_6NJ (C57BL/6NJ) F 61
+        C57BR_cdJ (C57BR/cdJ) M 51
+        C57L_J  (C57L/J)  M 64
+        C58_J (C58/J) M 55
+        CAST_EiJ  (CAST/EiJ)  F 53
+        CBA_J (CBA/J) F 56
+        DBA_1J  (DBA/1J)  M 49
+        DBA_2J  (DBA/2J)  F 56
+        FVB_NJ  (FVB/NJ)  F 73
+        I_LnJ (I/LnJ) M 45
+        KK_HiJ  (KK/HiJ)  M 55
+        LEWES_EiJ (LEWES/EiJ) F 19
+        LP_J  (LP/J)  F 54
+        MOLF_EiJ  (MOLF/EiJ)  M 40
+        NOD_ShiLtJ  (NOD/ShiLtJ)  F 66
+        NZB_B1NJ  (NZB/B1NJ)  M 47
+        NZO_HlLtJ (NZO/HlLtJ) F 72
+        NZW_LacJ  (NZW/LacJ)  M 58
+        PWK_PhJ (PWK/PhJ) F 53
+        RF_J  (RF/J)  M 54
+        SEA_GnJ (SEA/GnJ) M 49
+        SPRET_EiJ (SPRET/EiJ) F 67
+        ST_bJ (ST/bJ) M 81
+        WSB_EiJ (WSB/EiJ) F 51
+        ZALENDE_EiJ (ZALENDE/EiJ) M 19
   inputBinding:
     position: 5
 
-- id: "strain2"
+ strain2:
   type: string
-  description: |
+  doc: |
     name of strain2 exactly as specified in the vcf file (e.g. hap2)
   inputBinding:
     position: 6
 
-- id: "outputDir"
+ outputDir:
   type: string
-  description: |
+  doc: |
     location of the output directory
   inputBinding:
     position: 7
 
-- id: "CONCATENATED_GENOME"
+ CONCATENATED_GENOME:
   type: boolean
   default: false
 
 outputs:
-- id: "strain1_indices"
+ strain1_indices:
   type: File
   outputBinding:
     glob: $(inputs.outputDir+"/"+inputs.strain1+".fasta")
@@ -121,7 +123,8 @@ outputs:
   - ".pac"
   - ".refmap"
   - ".sa"
-- id: "strain2_indices"
+
+ strain2_indices:
   type: File
   outputBinding:
     glob: $(inputs.outputDir+"/"+inputs.strain1+".fasta")
@@ -133,8 +136,9 @@ outputs:
   - ".pac"
   - ".refmap"
   - ".sa"
-- id: "strain12_indices"
-  type: ["null",File]
+
+ strain12_indices:
+  type: File?
   outputBinding:
     glob: $(inputs.CONCATENATED_GENOME?inputs.outputDir+"/"+inputs.strain1+"_"+inputs.strain2+".fasta":[])
   secondaryFiles:
@@ -145,8 +149,6 @@ outputs:
   - ".pac"
   - ".sa"
 
-baseCommand: ["alea", "createGenome"]
-
 arguments:
   - valueFrom: $(inputs.phasedindels?"-snps-indels-separately":[])
     position: 1
@@ -180,5 +182,4 @@ s:author:
     s:location: "3333 Burnet Ave, Cincinnati, OH 45229-3026"
     s:department:
     - class: s:Organization
-      s:name: "Barski Lab"
-
+      s:name: "Barski Lab"