update

defaults

@@ -0,0 +1,6 @@
+{   
+    "fusioncatcher_database_dir":"/data/minio/reference-data/reference/fusioncatcher/human_v102",
+    "fusioncatcher_docker":"registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fusioncatcher:v1.33_2",
+    "fusioncatcher_cluster":"OnDemand bcs.ps.r.xlarge img-ubuntu-vpc",
+    "disk_size":"200"
+}

inputs

@@ -0,0 +1,9 @@
+{
+	"{{ project_name }}.fastq1": "{{ fastq1 }}",
+	"{{ project_name }}.fastq2": "{{ fastq2 }}",
+	"{{ project_name }}.sample_id": "{{ sample_id }}",
+	"{{ project_name }}.fusioncatcher_docker": "{{ fusioncatcher_docker }}",
+	"{{ project_name }}.fusioncatcher_database_dir": "{{ fusioncatcher_database_dir }}",
+	"{{ project_name }}.fusioncatcher_cluster": "{{ fusioncatcher_cluster }}",
+	"{{ project_name }}.disk_size": "{{ disk_size }}"
+}

schema.json

@@ -0,0 +1,68 @@
+{
+  "formMode":"batch",
+  "fields":[
+    {
+      "tmplType":"sample_id",
+      "type":"number",
+      "label":"Sample ID",
+      "name":"sample_id",
+      "question":"How many samples? For auto generating sample id.",
+      "placeholder":"How many samples? For auto generating sample id.",
+      "model":"sample_id",
+      "disabled":false,
+      "min":1,
+      "max":10,
+      "config":{
+        "rules":[{"type":"number","required":true,"message":"Please input a number."}]
+      }
+    },
+    {
+      "tmplType":"file",
+      "label":"Read1 Files",
+      "model":"read1",
+      "readOnly":false,
+      "multiple":true,
+      "filterType":"fastq|fastq.gz|fq|fq.gz",
+      "placeholder":"Select files for read1.",
+      "config":{
+        "rules":[
+          {
+            "type":"array",
+            "required":true,
+            "message":"Please select files for read1."
+          }
+        ]
+      }
+    },
+    {
+      "tmplType":"file",
+      "label":"Read2 Files",
+      "model":"read2",
+      "readOnly":false,
+      "multiple":true,
+      "filterType":"fastq|fastq.gz|fq|fq.gz",
+      "placeholder":"Select files for read2.",
+      "config":{
+        "rules":[
+          {
+            "type":"array",
+            "required":true,
+            "message":"Please select files for read2."
+          }
+        ]
+      }
+    },
+    {
+      "tmplType":"actions",
+      "buttons":[
+        {"type":"cancel","buttonType":"default","buttonLabel":"Previous Step"},
+        {
+          "type":"submit",
+          "buttonType":"primary",
+          "buttonLabel":"Next Step",
+          "validate":true
+        }
+      ]
+    }
+  ]
+}

tasks/fusioncatcher.wdl

@@ -0,0 +1,42 @@
+task fusioncatcher{
+    String sample_id
+    File fastq1
+    File fastq2
+    File database_dir
+	
+    String docker
+    String cluster
+    String disk_size
+
+    command <<<
+	
+        set -o pipefail
+        set -e
+
+        mkdir ./output/
+
+        /software/fusioncatcher/bin/fusioncatcher \
+            -d ${database_dir} \
+            -p 4 \
+            -i ${fastq1},${fastq2} \
+            --output ./output
+
+    >>>
+	
+    runtime {
+        docker : docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        Array[File] fusioncatcher_result=glob("./output/*.txt")
+        Array[File] fusioncatcher_zip=glob("./output/*.zip")
+        Array[File] fusioncatcher_log=glob("./output/*.log")
+        Array[File] fusioncatcher_vcf=glob("./output/*.vcf")
+    }
+
+}
+
+

test_input_output/final-list_candidate-fusion-genes.txt

@@ -0,0 +1,23 @@
+Gene_1_symbol(5end_fusion_partner)	Gene_2_symbol(3end_fusion_partner)	Fusion_description	Counts_of_common_mapping_reads	Spanning_pairs	Spanning_unique_reads	Longest_anchor_found	Fusion_finding_method	Fusion_point_for_gene_1(5end_fusion_partner)	Fusion_point_for_gene_2(3end_fusion_partner)	Gene_1_id(5end_fusion_partner)	Gene_2_id(3end_fusion_partner)	Exon_1_id(5end_fusion_partner)	Exon_2_id(3end_fusion_partner)	Fusion_sequence	Predicted_effect
+FGFR3	TACC3	known,adjacent,oncogene,cosmic,ticdb,tcga,ccle2,18cancers,gliomas,chimer4kb,chimer4pub,chimer4seq,cancer,tcga-cancer,tcga2,oncokb,mitelman,pcawg,ccle,tcga3,t37,tcga-oesophagus,10K<gap<100K	0	857	77	42	BOWTIE+BLAT;BOWTIE+STAR	4:1806934:+	4:1727977:+	ENSG00000068078	ENSG00000013810			AGCAGCTGGTGGAGGACCTGGACCGTGTCCTTACCGTGACGTCCACCGAC*ACAGAAGAGTGACACCCGCCTCTGAGACCCTAGAAGACCCTTGCAGGACA	in-frame
+FGFR3	TACC3	known,adjacent,oncogene,cosmic,ticdb,tcga,ccle2,18cancers,gliomas,chimer4kb,chimer4pub,chimer4seq,cancer,tcga-cancer,tcga2,oncokb,mitelman,pcawg,ccle,tcga3,t37,tcga-oesophagus,10K<gap<100K	0	857	10	42	BOWTIE+BLAT;BOWTIE+STAR	4:1807033:+	4:1727832:+	ENSG00000068078	ENSG00000013810			CCGTCCCCGGCCATCCTGCCCCCCAGAGTGCTGAGGTGTGGGGCGGGCCT*TCTGGCCCAGGTGCCCTGGCTGACCTGGACTGCTCAAGCTCTTCCCAGAG	intronic/CDS(truncated)
+FIP1L1	PDGFRA	known,oncogene,chimer2,cgp,ticdb,cacg,tcga,chimer4kb,chimer4pub,chimer4seq,cancer,tumor,tcga2,oncokb,mitelman,t71	0	118	49	47	BOWTIE+BLAT;BOWTIE+STAR	4:53425965:+	4:54274925:+	ENSG00000145216	ENSG00000134853			TCAGCCGAGTAGAAGGCAGGCGACGGGCAAATGAGAACAGCAACATACAG*CTGCCTTATGACTCAAGATGGGAGTTTCCAAGAGATGGACTAGTGCTTGG	in-frame
+GOPC	ROS1	known,oncogene,cosmic,chimer2,cgp,ticdb,cacg,chimer4kb,chimer4pub,cancer,tumor,oncokb,mitelman,ccle,100K<gap<200K,exon-exon	0	73	20	29	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	6:117566854:-	6:117321394:-	ENSG00000047932	ENSG00000047936	ENSE00003526662	ENSE00000442460	GCTAGTTGCAAAGACACAAGTGGGGAAATCAAAGTATTACAAG*TCTGGCATAGAAGATTAAAGAATCAAAAAAGTGCCAAGGAAGG	in-frame
+GOPC	ROS1	known,oncogene,cosmic,chimer2,cgp,ticdb,cacg,chimer4kb,chimer4pub,cancer,tumor,oncokb,mitelman,ccle,100K<gap<200K,exon-exon	0	73	2	26	BOWTIE	6:117566854:-	6:117320030:-	ENSG00000047932	ENSG00000047936	ENSE00003526662	ENSE00003478828	GCTAGTTGCAAAGACACAAGTGGGGAAATCAAAGTATTACAAG*TACTCTTCCAACCCAAGAGGAGATTGAAAATCTTCCTGCCTTC	out-of-frame
+IGH@	CRLF2	known,oncogene,cancer,oncokb,mitelman	0	32	10	95	BOWTIE+SPOTLIGHT	14:105863258:+	X:105799296:-	ENSG09000000014	ENSG00000205755			CGACGGGGAATTCTCACAGGAGACGAGGGGGAAAAGGGTTGGGGCGGATGCACTCCCTGAGGAGACGGTGACCGTGGTCCCTTTGCCCCAGACGTCCATGTAGTAGTAGTAGTATCA*GGGGCCCGGGGAATAGAAGCTGTGAGCTGGGGAGAGGATATATAAGAACTTTCTGTACTTTCTGCAAATTTTGCTCTCAA	---/intergenic
+IGH@	CRLF2	known,oncogene,cancer,oncokb,mitelman	0	32	5	32	BOWTIE+STAR	14:105863262:+	X:1228687:-	ENSG09000000014	ENSG00000205755			CGTGGTCCCTTTGCCCCAGACGTCCATGTAGTAGTAGTAGTAGTAATCA*NNNNNNNNNNNNNNNNNNNNNGAAGCTGTGAGCTGGGGAGAGGATATATAAGAACTTTCTGTACTTTCTG	---/intergenic
+IGH@	CRLF2	known,oncogene,cancer,oncokb,mitelman	0	32	3	96	BOWTIE+SPOTLIGHT	14:105863343:+	X:105812546:-	ENSG09000000014	ENSG00000205755			TGCTGATGTCAGAGTTGTTCTTGTATTTCCAGGAGAAAGTGATGGAGTCGGGAAGGAAGTCCTGTGCGAGGCAGCCAACGGCCACGCTGCTCGTATCCGACGGGGAATTCTCACAGGAGACGAGGGGGAAAAGGGTTGGGGCGGATGCACTCCCTGAGGAGACGGTGACCGTGGTCCCTTTGCCCCAGACGTCCATGTAGTAGTAGTAGTATCAGGGGCCCGGGGAATAGAAG*CTGTGAGGGTTAATCCAATCTTCCTGCTGTCAAGCAAAAGAACACCTAAAATTCTTCCGTCACGTACTG	---/intergenic
+HOOK3	RET	known,oncogene,cosmic,cgp,ticdb,chimer4kb,chimer4pub,chimer4seq,cancer,tumor,mitelman,t3,exon-exon	0	13	10	29	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	8:42968214:+	10:43116584:+	ENSG00000168172	ENSG00000165731	ENSE00003485179	ENSE00001095944	GGCCAACGCAGCGCGAAGTCAACTTGAAACCTACAAGAGACAG*GAGGATCCAAAGTGGGAATTCCCTCGGAAGAACTTGGTTCTTG	in-frame
+AKAP9	BRAF	known,oncogene,cosmic,chimer2,cgp,ticdb,chimer4kb,chimer4pub,chimer4seq,cancer,tumor,oncokb,mitelman,t2,exon-exon	0	12	13	30	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	7:92003235:+	7:140787584:-	ENSG00000127914	ENSG00000157764	ENSE00003484877	ENSE00003680515	TGATAAACTTCAGAAAGAACTCAATGTACTTAAATCAGAACAG*GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAA	in-frame
+EWSR1	ATF1	known,oncogene,cosmic,cgp,ticdb,chimer4kb,chimer4pub,chimer4seq,cancer,tumor,m5,oncokb,mitelman,t1,exon-exon	0	11	10	30	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	22:29287134:+	12:50814280:+	ENSG00000182944	ENSG00000123268	ENSE00003570564	ENSE00003675908	CCAAGTCAATATAGCCAACAGAGCAGCAGCTACGGGCAGCAGA*CTGCATCAGGAGATATGCAAACATATCAGATCCGAACTACACC	in-frame
+TMPRSS2	ETV1	known,oncogene,cosmic,chimer2,cgp,ticdb,chimer4kb,chimer4pub,chimer4seq,cancer,tumor,tcga-cancer,oncokb,mitelman,t3	0	10	11	37	BOWTIE+STAR	21:41494381:-	7:13935844:-	ENSG00000184012	ENSG00000006468			GGGTCCTGACGCAGGCTTCCAACCCCGTCGTCTGCACGCAGCCCAAATCC*CCATCCAGCACGCCAGTGTCCCCACTGCATCATGCATCTCCAAACTCAAC	in-frame
+EWSR1	FLI1	known,oncogene,cosmic,cgp,ticdb,ccle2,chimer4kb,chimer4pub,chimer4seq,cancer,tumor,m6,oncokb,mitelman,ccle,exon-exon	0	9	12	29	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	22:29287134:+	11:128807180:+	ENSG00000182944	ENSG00000151702	ENSE00003570564	ENSE00003702967	CCAAGTCAATATAGCCAACAGAGCAGCAGCTACGGGCAGCAGA*GTCCTCCCCTTGGAGGGGCACAAACGATCAGTAAGAATACAGA	in-frame
+ETV6	NTRK3	known,oncogene,cosmic,chimer2,cgp,ticdb,tcga,ccle2,18cancers,chimer4kb,chimer4pub,chimer4seq,cancer,tumor,tcga-cancer,tcga2,oncokb,mitelman,pcawg,tcga3,t1,exon-exon	0	7	9	29	BOWTIE	12:11869969:+	15:87940753:-	ENSG00000139083	ENSG00000140538	ENSE00001788162	ENSE00001134154	TCCCCGCCTGAAGAGCACGCCATGCCCATTGGGAGAATAGCAG*ATGTGCAGCACATTAAGAGGAGAGACATCGTGCTGAAGCGAGA	in-frame
+BRD4	NUTM1	known,oncogene,cosmic,chimer2,cgp,ticdb,ccle2,chimer4kb,chimer4pub,chimer4seq,cancer,oncokb,mitelman,ccle,t1,exon-exon	0	6	9	29	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	19:15254152:-	15:34347969:+	ENSG00000141867	ENSG00000184507	ENSE00001187704	ENSE00001367212	TCCAGTGAGTCCAGCTCCTCTGACAGCGAAGACTCCGAAACAG*CATCTGCATTGCCGGGACCGGATATGAGCATGAAACCTAGTGC	in-frame
+CD74	ROS1	known,oncogene,cosmic,chimer2,cgp,ticdb,tcga,ccle2,18cancers,chimer4kb,chimer4pub,chimer4seq,cancer,tumor,tcga-cancer,tcga2,oncokb,mitelman,pcawg,t3,exon-exon	0	6	7	30	BOWTIE;BOWTIE+BLAT;BOWTIE+STAR	5:150404680:-	6:117324415:-	ENSG00000019582	ENSG00000047936	ENSE00000841201	ENSE00000762702	AGGCACTCCTTGGAGCAAAAGCCCACTGACGCTCCACCGAAAG*ATGATTTTTGGATACCAGAAACAAGTTTCATACTTACTATTAT	in-frame
+CIC	DUX4	known,cosmic,chimer2,cgp,ticdb,chimer4kb,chimer4pub,cancer,oncokb,mitelman,ccle	0	5	5	34	BOWTIE+STAR	19:42295047:+	4:190174446:+	ENSG00000079432	ENSG00000260596			CTGCCCCTGCCCCCACTCCCAGCCCCGCAGGGGGCCCTGACCCCACCTCA*CCGGCAGAGGGGATCTCCCAACCTGCCCCGGCGCGCGGGGATTTCGCCTA	in-frame
+DUX4	IGH@	known,cancer,mitelman	0	5	5	84	BOWTIE+SPOTLIGHT	4:190174997:+	14:190287409:+	ENSG00000260596	ENSG09000000014			CGCAACCTCTCCTAGAAACGGAGGCCCCGGGGGAGCTGGAGGCCTCGGAAGAGGCCGCCTCGCTG*CGATCCCTCAGGGTTGGCTGTAGTCACCGTATGGGGGAAGCCTGTGTCATCATTTATTTACCCAACCTGGGTTAATGTCTTTGCTATTATGAATAGTGCTGG	CDS(truncated)/---
+EML4	ALK	known,oncogene,cosmic,chimer2,cgp,ticdb,tcga,ccle2,18cancers,chimer4kb,chimer4pub,chimer4seq,cancer,tumor,tcga-cancer,tcga2,oncokb,mitelman,pcawg,ccle,ccle3,tcga3,t1	0	5	4	33	BOWTIE+STAR	2:42301391:+	2:29223587:-	ENSG00000143924	ENSG00000171094			AGAAAAATAATTCTGTGGGATCATGATCTGAATCCTGAAAGAGAAATAGA*GTGTAGTGCTTCAAGGGCCAGGCTGCCAGGCCATGTTGCAGCTGACCACC	CDS(truncated)/UTR
+DUX4	IGH@	known,cancer,mitelman	0	4	8	37	BOWTIE+BLAT;BOWTIE+STAR	4:190175284:+	14:106638525:-	ENSG00000260596	ENSG09000001017			TTCTTTCCTGGGCATCCCGGGGATCCCAGAGCCGGCCCAGGTACCAGCAG*GCAGAGAAGAGGCCATGTGGAGACATAGTGCACTAGAAGGTGGCCCAGTG	UTR/---
+MALT1	IGH@	known,oncogene,chimer2,cancer,oncokb,mitelman	0	3	3	34	BOWTIE+STAR	18:58669909:+	14:105888559:+	ENSG00000172175	ENSG09000000014			AGCTATATTGGCTAAGAGTAAATAACACTGGCACCCATTTAACTCGTATG*AGTCACCACCACAATATGCTCACAGTGACACGAACCCCCACAAAATCCTC	intergenic/---
+NPM1	ALK	known,oncogene,cosmic,chimer2,cgp,ticdb,ccle2,chimer4kb,chimer4pub,chimer4seq,cancer,tumor,oncokb,mitelman,ccle,ccle3,exon-exon	0	3	3	30	BOWTIE	5:171391799:+	2:29223528:-	ENSG00000181163	ENSG00000171094	ENSE00003625205	ENSE00001154407	TGTGGTTCAGGGCCAGTGCATATTAGTGGACAGCACTTAGTAG*TGTACCGCCGGAAGCACCAGGAGCTGCAAGCCATGCAGATGGA	in-frame

workflow.wdl

@@ -0,0 +1,26 @@
+import "./tasks/fusioncatcher.wdl" as fusioncatcher
+
+workflow {{ project_name }} {
+    String sample_id
+    File fastq1
+    File fastq2
+    File fusioncatcher_database_dir
+
+    String fusioncatcher_docker
+    String fusioncatcher_cluster
+    String disk_size
+
+        call fusioncatcher.fusioncatcher as fusioncatcher {
+                input:	
+                sample_id=sample_id,
+                fastq1=fastq1,
+                fastq2=fastq2,
+                database_dir=fusioncatcher_database_dir,
+                docker=fusioncatcher_docker,
+                cluster=fusioncatcher_cluster,
+                disk_size=disk_size
+        }
+
+
+}	
+