diff --git a/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint-samples.json b/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint-samples.json
index 92146c1..de8f2c7 100644
--- a/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint-samples.json
+++ b/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint-samples.json
@@ -7,7 +7,9 @@
         [
             "polyx"
         ],
-        []
+        [
+            "polyx"
+        ]
     ],
     "config__algorithm__align_split_size": [
         null,
@@ -24,7 +26,7 @@
     "config__algorithm__coverage": [
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/automated/coverage_transcripts-bam.bed"
+            "path": "../../testdata/automated/coverage_transcripts-bam.bed"
         },
         null
     ],
@@ -105,25 +107,25 @@
     "config__algorithm__validate": [
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/reference_material/7_100326_FC6107FAAXX-grade.vcf"
+            "path": "../../testdata/reference_material/7_100326_FC6107FAAXX-grade.vcf"
         },
         null
     ],
     "config__algorithm__validate_regions": [
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
+            "path": "../../testdata/automated/variant_regions-bam.bed"
         },
         null
     ],
     "config__algorithm__variant_regions": [
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
+            "path": "../../testdata/automated/variant_regions-bam.bed"
         },
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/automated/variant_regions-bam.bed"
+            "path": "../../testdata/automated/variant_regions-bam.bed"
         }
     ],
     "config__algorithm__variantcaller": [
@@ -140,21 +142,21 @@
         [
             {
                 "class": "File",
-                "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.conf"
+                "path": "../../testdata/genomes/hg19/config/vcfanno/gemini.conf"
             },
             {
                 "class": "File",
-                "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.lua"
+                "path": "../../testdata/genomes/hg19/config/vcfanno/gemini.lua"
             }
         ],
         [
             {
                 "class": "File",
-                "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.conf"
+                "path": "../../testdata/genomes/hg19/config/vcfanno/gemini.conf"
             },
             {
                 "class": "File",
-                "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/config/vcfanno/gemini.lua"
+                "path": "../../testdata/genomes/hg19/config/vcfanno/gemini.lua"
             }
         ]
     ],
@@ -166,11 +168,11 @@
         [
             {
                 "class": "File",
-                "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam",
+                "path": "../../testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam",
                 "secondaryFiles": [
                     {
                         "class": "File",
-                        "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam.bai"
+                        "path": "../../testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam.bai"
                     }
                 ]
             }
@@ -178,7 +180,7 @@
         [
             {
                 "class": "File",
-                "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/100326_FC6107FAAXX/6_100326_FC6107FAAXX.bam"
+                "path": "../../testdata/100326_FC6107FAAXX/6_100326_FC6107FAAXX.bam"
             }
         ]
     ],
@@ -201,31 +203,31 @@
     "genome_resources__rnaseq__gene_bed": [
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
+            "path": "../../testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
         },
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
+            "path": "../../testdata/genomes/hg19/rnaseq/ref-transcripts.bed"
         }
     ],
     "genome_resources__variation__1000g": [
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
+            "path": "../../testdata/genomes/hg19/variation/1000g.vcf.gz",
             "secondaryFiles": [
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
+                    "path": "../../testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
                 }
             ]
         },
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz",
+            "path": "../../testdata/genomes/hg19/variation/1000g.vcf.gz",
             "secondaryFiles": [
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
+                    "path": "../../testdata/genomes/hg19/variation/1000g.vcf.gz.tbi"
                 }
             ]
         }
@@ -233,21 +235,21 @@
     "genome_resources__variation__clinvar": [
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
+            "path": "../../testdata/genomes/hg19/variation/clinvar.vcf.gz",
             "secondaryFiles": [
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
+                    "path": "../../testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
                 }
             ]
         },
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz",
+            "path": "../../testdata/genomes/hg19/variation/clinvar.vcf.gz",
             "secondaryFiles": [
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
+                    "path": "../../testdata/genomes/hg19/variation/clinvar.vcf.gz.tbi"
                 }
             ]
         }
@@ -255,21 +257,21 @@
     "genome_resources__variation__cosmic": [
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
+            "path": "../../testdata/genomes/hg19/variation/cosmic.vcf.gz",
             "secondaryFiles": [
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
+                    "path": "../../testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
                 }
             ]
         },
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz",
+            "path": "../../testdata/genomes/hg19/variation/cosmic.vcf.gz",
             "secondaryFiles": [
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
+                    "path": "../../testdata/genomes/hg19/variation/cosmic.vcf.gz.tbi"
                 }
             ]
         }
@@ -277,21 +279,21 @@
     "genome_resources__variation__dbsnp": [
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
+            "path": "../../testdata/genomes/hg19/variation/dbsnp.vcf.gz",
             "secondaryFiles": [
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
+                    "path": "../../testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
                 }
             ]
         },
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz",
+            "path": "../../testdata/genomes/hg19/variation/dbsnp.vcf.gz",
             "secondaryFiles": [
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
+                    "path": "../../testdata/genomes/hg19/variation/dbsnp.vcf.gz.tbi"
                 }
             ]
         }
@@ -303,21 +305,21 @@
     "genome_resources__variation__esp": [
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
+            "path": "../../testdata/genomes/hg19/variation/esp.vcf.gz",
             "secondaryFiles": [
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
+                    "path": "../../testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
                 }
             ]
         },
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz",
+            "path": "../../testdata/genomes/hg19/variation/esp.vcf.gz",
             "secondaryFiles": [
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
+                    "path": "../../testdata/genomes/hg19/variation/esp.vcf.gz.tbi"
                 }
             ]
         }
@@ -325,21 +327,21 @@
     "genome_resources__variation__exac": [
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
+            "path": "../../testdata/genomes/hg19/variation/exac.vcf.gz",
             "secondaryFiles": [
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
+                    "path": "../../testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
                 }
             ]
         },
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz",
+            "path": "../../testdata/genomes/hg19/variation/exac.vcf.gz",
             "secondaryFiles": [
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
+                    "path": "../../testdata/genomes/hg19/variation/exac.vcf.gz.tbi"
                 }
             ]
         }
@@ -347,21 +349,21 @@
     "genome_resources__variation__gnomad_exome": [
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
+            "path": "../../testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
             "secondaryFiles": [
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
+                    "path": "../../testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
                 }
             ]
         },
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
+            "path": "../../testdata/genomes/hg19/variation/gnomad_exome.vcf.gz",
             "secondaryFiles": [
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
+                    "path": "../../testdata/genomes/hg19/variation/gnomad_exome.vcf.gz.tbi"
                 }
             ]
         }
@@ -377,21 +379,21 @@
     "genome_resources__variation__train_hapmap": [
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
+            "path": "../../testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
             "secondaryFiles": [
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
+                    "path": "../../testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
                 }
             ]
         },
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
+            "path": "../../testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz",
             "secondaryFiles": [
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
+                    "path": "../../testdata/genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi"
                 }
             ]
         }
@@ -399,21 +401,21 @@
     "genome_resources__variation__train_indels": [
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
+            "path": "../../testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
             "secondaryFiles": [
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
+                    "path": "../../testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
                 }
             ]
         },
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
+            "path": "../../testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz",
             "secondaryFiles": [
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
+                    "path": "../../testdata/genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi"
                 }
             ]
         }
@@ -429,45 +431,45 @@
     "reference__bwa__indexes": [
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.amb",
+            "path": "../../testdata/genomes/hg19/bwa/hg19.fa.amb",
             "secondaryFiles": [
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.ann"
+                    "path": "../../testdata/genomes/hg19/bwa/hg19.fa.ann"
                 },
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.bwt"
+                    "path": "../../testdata/genomes/hg19/bwa/hg19.fa.bwt"
                 },
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.pac"
+                    "path": "../../testdata/genomes/hg19/bwa/hg19.fa.pac"
                 },
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.sa"
+                    "path": "../../testdata/genomes/hg19/bwa/hg19.fa.sa"
                 }
             ]
         },
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.amb",
+            "path": "../../testdata/genomes/hg19/bwa/hg19.fa.amb",
             "secondaryFiles": [
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.ann"
+                    "path": "../../testdata/genomes/hg19/bwa/hg19.fa.ann"
                 },
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.bwt"
+                    "path": "../../testdata/genomes/hg19/bwa/hg19.fa.bwt"
                 },
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.pac"
+                    "path": "../../testdata/genomes/hg19/bwa/hg19.fa.pac"
                 },
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/bwa/hg19.fa.sa"
+                    "path": "../../testdata/genomes/hg19/bwa/hg19.fa.sa"
                 }
             ]
         }
@@ -475,29 +477,29 @@
     "reference__fasta__base": [
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
+            "path": "../../testdata/genomes/hg19/seq/hg19.fa",
             "secondaryFiles": [
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
+                    "path": "../../testdata/genomes/hg19/seq/hg19.fa.fai"
                 },
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
+                    "path": "../../testdata/genomes/hg19/seq/hg19.dict"
                 }
             ]
         },
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa",
+            "path": "../../testdata/genomes/hg19/seq/hg19.fa",
             "secondaryFiles": [
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.fa.fai"
+                    "path": "../../testdata/genomes/hg19/seq/hg19.fa.fai"
                 },
                 {
                     "class": "File",
-                    "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/seq/hg19.dict"
+                    "path": "../../testdata/genomes/hg19/seq/hg19.dict"
                 }
             ]
         }
@@ -506,21 +508,21 @@
         [
             {
                 "class": "File",
-                "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
+                "path": "../../testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
                 "secondaryFiles": [
                     {
                         "class": "File",
-                        "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
+                        "path": "../../testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
                     }
                 ]
             },
             {
                 "class": "File",
-                "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
+                "path": "../../testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
                 "secondaryFiles": [
                     {
                         "class": "File",
-                        "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
+                        "path": "../../testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
                     }
                 ]
             }
@@ -528,21 +530,21 @@
         [
             {
                 "class": "File",
-                "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
+                "path": "../../testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz",
                 "secondaryFiles": [
                     {
                         "class": "File",
-                        "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
+                        "path": "../../testdata/genomes/hg19/coverage/problem_regions/GA4GH/test.bed.gz.tbi"
                     }
                 ]
             },
             {
                 "class": "File",
-                "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
+                "path": "../../testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz",
                 "secondaryFiles": [
                     {
                         "class": "File",
-                        "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
+                        "path": "../../testdata/genomes/hg19/coverage/problem_regions/GA4GH/test2.bed.gz.tbi"
                     }
                 ]
             }
@@ -551,31 +553,31 @@
     "reference__rtg": [
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
+            "path": "../../testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
         },
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
+            "path": "../../testdata/genomes/hg19/rtg--hg19.sdf-wf.tar.gz"
         }
     ],
     "reference__snpeff__hg19": [
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
+            "path": "../../testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
         },
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
+            "path": "../../testdata/genomes/hg19/snpeff--hg19-wf.tar.gz"
         }
     ],
     "reference__versions": [
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
+            "path": "../../testdata/genomes/hg19/versions.csv"
         },
         {
             "class": "File",
-            "path": "/home/chapmanb/drive/work/cwl/test_bcbio_cwl/testdata/genomes/hg19/versions.csv"
+            "path": "../../testdata/genomes/hg19/versions.csv"
         }
     ],
     "resources": [
diff --git a/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint.cwl b/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint.cwl
index 69c805f..a798100 100644
--- a/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint.cwl
+++ b/gvcf_joint/gvcf-joint-workflow/main-gvcf-joint.cwl
@@ -51,10 +51,7 @@ inputs:
 - id: config__algorithm__adapters
   type:
     items:
-    - 'null'
-    - items:
-      - 'null'
-      - string
+      items: string
       type: array
     type: array
 - id: genome_resources__variation__1000g
diff --git a/gvcf_joint/gvcf-joint-workflow/steps/alignment_to_rec.cwl b/gvcf_joint/gvcf-joint-workflow/steps/alignment_to_rec.cwl
index aee319f..b0a18eb 100644
--- a/gvcf_joint/gvcf-joint-workflow/steps/alignment_to_rec.cwl
+++ b/gvcf_joint/gvcf-joint-workflow/steps/alignment_to_rec.cwl
@@ -98,10 +98,7 @@ inputs:
 - id: config__algorithm__adapters
   type:
     items:
-    - 'null'
-    - items:
-      - 'null'
-      - string
+      items: string
       type: array
     type: array
 - id: config__algorithm__bam_clean
@@ -156,10 +153,7 @@ outputs:
         type: File
       - name: config__algorithm__adapters
         type:
-        - 'null'
-        - items:
-          - 'null'
-          - string
+          items: string
           type: array
       - name: rgnames__lb
         type:
diff --git a/gvcf_joint/gvcf-joint-workflow/steps/merge_split_alignments.cwl b/gvcf_joint/gvcf-joint-workflow/steps/merge_split_alignments.cwl
index 6680b2c..2bed715 100644
--- a/gvcf_joint/gvcf-joint-workflow/steps/merge_split_alignments.cwl
+++ b/gvcf_joint/gvcf-joint-workflow/steps/merge_split_alignments.cwl
@@ -61,10 +61,7 @@ inputs:
       type: File
     - name: config__algorithm__adapters
       type:
-      - 'null'
-      - items:
-        - 'null'
-        - string
+        items: string
         type: array
     - name: rgnames__lb
       type:
diff --git a/gvcf_joint/gvcf-joint-workflow/steps/prep_align_inputs.cwl b/gvcf_joint/gvcf-joint-workflow/steps/prep_align_inputs.cwl
index 00f3447..2280f27 100644
--- a/gvcf_joint/gvcf-joint-workflow/steps/prep_align_inputs.cwl
+++ b/gvcf_joint/gvcf-joint-workflow/steps/prep_align_inputs.cwl
@@ -77,10 +77,7 @@ inputs:
       type: File
     - name: config__algorithm__adapters
       type:
-      - 'null'
-      - items:
-        - 'null'
-        - string
+        items: string
         type: array
     - name: rgnames__lb
       type:
diff --git a/gvcf_joint/gvcf-joint-workflow/steps/process_alignment.cwl b/gvcf_joint/gvcf-joint-workflow/steps/process_alignment.cwl
index c846a48..47fde41 100644
--- a/gvcf_joint/gvcf-joint-workflow/steps/process_alignment.cwl
+++ b/gvcf_joint/gvcf-joint-workflow/steps/process_alignment.cwl
@@ -106,10 +106,7 @@ inputs:
       type: File
     - name: config__algorithm__adapters
       type:
-      - 'null'
-      - items:
-        - 'null'
-        - string
+        items: string
         type: array
     - name: rgnames__lb
       type:
diff --git a/gvcf_joint/gvcf-joint-workflow/wf-alignment.cwl b/gvcf_joint/gvcf-joint-workflow/wf-alignment.cwl
index 1cb0144..27c76c7 100644
--- a/gvcf_joint/gvcf-joint-workflow/wf-alignment.cwl
+++ b/gvcf_joint/gvcf-joint-workflow/wf-alignment.cwl
@@ -26,10 +26,7 @@ inputs:
       type: File
     - name: config__algorithm__adapters
       type:
-      - 'null'
-      - items:
-        - 'null'
-        - string
+        items: string
         type: array
     - name: rgnames__lb
       type:
diff --git a/gvcf_joint/gvcf-joint.yaml b/gvcf_joint/gvcf-joint.yaml
index 981d8ea..1db5c02 100644
--- a/gvcf_joint/gvcf-joint.yaml
+++ b/gvcf_joint/gvcf-joint.yaml
@@ -20,6 +20,7 @@ details:
    files: ../testdata/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam
  - algorithm:
      aligner: bwa
+     adapters: polyx
      recalibrate: true
      variantcaller: [gatk-haplotype, strelka2]
      tools_on: [gvcf]
diff --git a/gvcf_joint/run_generate_cwl.sh b/gvcf_joint/run_generate_cwl.sh
index 05b0550..ad28954 100644
--- a/gvcf_joint/run_generate_cwl.sh
+++ b/gvcf_joint/run_generate_cwl.sh
@@ -6,5 +6,5 @@ PNAME=gvcf-joint
 rm -rf $PNAME-workflow
 bcbio_vm.py cwl --systemconfig=../bcbio_system.yaml gvcf-joint.yaml
 
-#BASEDIR=`cd .. && pwd`
-#sed -i.bak "s#$BASEDIR/testdata#../../testdata#" $PNAME-workflow/main-$PNAME-samples.json
+BASEDIR=`cd .. && pwd`
+sed -i.bak "s#$BASEDIR/testdata#../../testdata#" $PNAME-workflow/main-$PNAME-samples.json