second commit

defaults

@@ -0,0 +1,6 @@
+{   
+    "starfusion_database_dir":"oss://pgx-reference-data/reference/starfusion/ctat_genome_lib_build_dir",
+    "starfusion_docker":"registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/trinityctat/starfusion:1.10.0",
+    "starfusion_cluster":"OnDemand bcs.a2.large img-ubuntu-vpc",
+    "disk_size":"200"
+}

inputs

@@ -0,0 +1,9 @@
+{
+	"{{ project_name }}.sample_id": "{{ sample_id }}",
+	"{{ project_name }}.fastq1": "{{ fastq1 }}",
+	"{{ project_name }}.fastq2": "{{ fastq2 }}",
+	"{{ project_name }}.starfusion_database_dir": "{{ starfusion_database_dir }}",
+	"{{ project_name }}.starfusion_docker": "{{ starfusion_docker }}",
+	"{{ project_name }}.starfusion_cluster": "{{ starfusion_cluster }}",
+	"{{ project_name }}.disk_size": "{{ disk_size }}"
+}

tasks/starfusion.wdl

@@ -0,0 +1,38 @@
+task starfusion{
+	String sample_id
+	File fastq1
+	File fastq2
+	File database_dir
+	
+	String docker
+	String cluster
+	String disk_size
+
+	command <<<
+	
+	set -o pipefail
+	set -e
+
+	mkdir -p ${sample_id}/output
+
+	STAR-Fusion --genome_lib_dir ${database_dir} \
+        --left_fq ${fastq1} \
+        --right_fq ${fastq2} \
+        --CPU 4 \
+        --output_dir  ${sample_id}/output
+	>>>
+	
+	runtime {
+	docker :  docker
+	cluster: cluster
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+	Array[File] starfusion_result=glob("${sample_id}/output/*")
+	}
+
+}
+
+

test_input_output/star-fusion.fusion_predictions.tsv

@@ -0,0 +1,17 @@
+#FusionName	JunctionReadCount	SpanningFragCount	est_J	est_S	SpliceType	LeftGene	LeftBreakpoint	RightGene	RightBreakpoint	JunctionReads	SpanningFrags	LargeAnchorSupport	FFPM	LeftBreakDinuc	LeftBreakEntropy	RightBreakDinuc	RightBreakEntropy	annots
+FGFR3--TACC3	264	522	264.00	522.00	INCL_NON_REF_SPLICE	FGFR3^ENSG00000068078.20	chr4:1806934:+	TACC3^ENSG00000013810.20	chr4:1727977:+	98W,8KR,8MA,8JW,8MX,8IK,8KL,8JP,8M8,8NZ,90F,8JO,8YX,8L7,8JG,8OT,8MN,8JS,8MK,8IE,9BD,8LQ,8UC,8P1,90A,8K8,8LK,94Z,8HW,8ME,8LF,90Q,8NL,9BY,8MZ,8V1,8II,8MG,8I2,8ID,8IH,8UY,8JN,8JI,93E,9AT,8OJ,8ZB,8OD,8J3,8NJ,8KI,8I5,8KV,8JL,8NK,8KQ,8O8,8TL,928,8M2,8KY,8MI,8L9,9A8,8K9,8J0,8JY,8KW,977,94W,8KE,9B8,8KM,8LD,936,8J5,9B4,8O6,8O1,8IO,8JM,8JZ,8JE,8JA,8ND,8I3,8L0,8QY,8J9,935,8MF,920,8X0,8MU,8I8,8MY,8K6,8MR,8L8,8ZR,94A,8M7,8K0,8LU,8IL,8MV,9AN,92H,8L2,8MS,8KZ,8M9,8NB,8JB,90D,9AB,8I0,8HT,8IS,8M0,8IX,8IT,8MD,8K1,8J7,8LO,8MH,8JV,8IQ,8OZ,8MB,8HU,8LN,96I,97J,8T9,8HZ,8J8,9AF,8JR,8KT,8MO,8LV,8NV,8HV,8JX,8K5,8J2,8KK,8K4,8UL,912,93S,8N1,8LJ,8KX,9A7,8IJ,8OE,9C7,8I7,8NR,8L6,8LT,8KD,8I6,8KG,8HX,8K2,8R2,8IU,8KJ,8PP,8LE,8HY,8LI,98J,8K3,9BO,8UA,8LG,8IB,8LA,8VS,8RW,8KS,8IG,9AX,8LP,8ML,8XI,8JF,8KP,8IW,8LZ,8KF,8I9,8OY,8M5,9A6,8ON,8MJ,8JU,8LC,8IY,8MC,8L4,8LB,908,8L1,97O,8IR,8IP,8JK,8VK,8JQ,8OG,8LY,8IZ,8MP,8LL,8JT,8IN,8JH,8QU,8M1,8I1,8KN,8J6,9AJ,8LH,8MQ,8O0,93C,8I4,8OR,8J1,8IA,8MT,9AG,8IV,8NT,8TX,91M,8K7,92F,919,8LM,8RM,8L3,90U,9BE,8IC,8M3,8KO,8OL,96R,8JJ,8JD,9AQ,8KU,8KA,8LX	96E,8WO,8ZC,8YH,8V0,8TA,8VM,90P,92D,94K,8WW,8WZ,8S6,8X4,94C,8UP,8RY,98M,98K,8RV,8YQ,8RJ,98R,952,8QD,96J,97R,8Y7,8PY,9B5,95K,8TF,9AI,92S,94M,8UR,8VY,92O,973,96Z,92I,9BL,93J,96Q,8PB,96Y,8R1,95A,8V4,8TB,8XG,8Z7,8ZM,92C,92P,8NS,8Q9,8X6,8PE,8R4,90W,8SF,8VP,8VR,914,91Y,97M,91V,92U,8U9,8Y6,8P5,8QO,9BV,8TU,8YV,8SQ,8SY,8XA,92X,8ZY,8W0,8ZV,982,933,971,8U6,96T,8VH,95S,8XO,96L,8YI,966,92G,975,921,96V,8ZI,8S8,8Z4,92W,8RC,8YP,93D,95X,8TP,93X,90N,8YB,8SL,92T,8PH,8SI,94P,8YG,8QB,93W,956,8VQ,8X5,91Z,8PA,8P9,8WA,8SE,90M,8Q5,93O,8UJ,8YO,8R3,8WR,91F,95P,8X3,90E,8QX,964,94H,8YA,8UD,8VC,932,91X,94L,98B,91I,97L,91D,97T,8YE,8PQ,910,8QG,8VN,97K,8S9,8YU,906,90C,92A,8XK,95E,8QE,8V5,8RF,937,96X,929,8ZA,91P,91T,8S0,93F,9A5,8RI,8Y4,8VT,8T0,8U2,8Z5,8TD,8WY,92L,8T6,96H,8PL,986,8UZ,8OI,95I,94G,8ZK,95Q,8SZ,97A,8VU,954,98P,98I,949,8V9,90S,90V,8QQ,8WB,8TW,948,91W,8T4,8QH,8ZZ,8W6,9BB,8PX,8RT,8RQ,946,8XZ,92K,8W8,8TG,8NX,8RS,8Z0,96M,905,98S,8UM,8UT,8PU,8XY,8V2,96O,8S5,8T1,940,8S1,8T2,8OO,92V,8O5,95Z,8XL,8T8,9AC,8QR,8UE,8Z2,902,98T,98U,961,8SS,8PV,8QJ,8YW,8WN,8UB,8Y2,98F,8SP,8YN,8NW,8X8,8TQ,94S,907,8SJ,8XD,97X,8RE,8Y8,8R6,91S,8SC,90L,8U7,8R9,96K,95F,8Q4,8W7,95O,98H,8R5,93G,93Z,95M,976,8XV,8RA,8QL,8ZF,8ZO,91Q,91U,93A,8XC,96B,9AL,96S,8VF,8XS,96G,8ZE,8S7,8WM,93T,8SW,8YS,8RR,91R,8ZX,8QZ,8SK,8Z1,979,9B9,8WG,955,8TK,8VB,8OF,94X,925,8WD,95Y,8RP,8Z9,8Y0,941,8XM,9BG,8XE,972,96D,8YT,8YM,8U8,930,9B2,8RX,8VA,8VL,8RL,90T,8P6,926,8P4,8X2,9BC,98N,9BI,8P2,970,8VE,8SA,8RN,91H,8QC,8V6,8Q3,8WX,8P8,94J,91E,8RK,97S,8ZN,93K,8U4,918,8PZ,960,92N,8O3,94Q,8ZG,98C,8Q1,92B,901,8SB,95W,913,981,8QF,8ZT,8X9,94F,93Y,98A,8TM,8UG,8V8,8OP,9BK,8Y5,95U,8T5,924,8TY,9BT,98G,967,97D,8YK,8O9,8X7,8UW,93V,8P7,8TT,93H,962,8XJ,96F,8QA,9BU,917,8U3,911,8TR,94I,95C,8UU,9B6,8PD,8ZD,8X1,8YZ,8S4,8R8,8R7,8OU,939,8QS,92J,93B,8YY,8SD,8OV,8VV,980,8VD,8WU,8TZ,91J,958,90J,8XT,8UQ,8UK,968,943,8QW,8XR,8PJ,915,8XH,97E,96N,9AW,8OH,8WT,8Y3,974,8PM,8PG,8NC,9C5,98O,8YF,95G,95J,94U,95L,8RU,8PF,9A3,8XQ,8S3,8U0,97P,8SG,96A,8XU,8Y1,8TS,8VG,8W1,9BW,8WH,97B,94Y,945,97G,8YC,98Q,90O,8QM,90Z,8QK,97F,931,92R,8SR,927,8PN,8ZW,8XP,8UN,91N,95R,923,8TE,94O,8P3,8ZQ,93M	YES_LDAS	62649.4501	GT	1.8892	AG	1.7465	["ChimerKB","ChimerSeq","TCGA_StarF2019","CCLE_StarF2019","YOSHIHARA_TCGA","Klijn_CellLines","DEEPEST2019","GUO2018CR_TCGA","ChimerPub","TumorFusionsNAR2018","Cosmic","INTRACHROMOSOMAL[chr4:0.05Mb]","LOCAL_REARRANGEMENT:+:[48122]"]
+FIP1L1--PDGFRA	130	17	130.00	17.00	INCL_NON_REF_SPLICE	FIP1L1^ENSG00000145216.16	chr4:53425965:+	PDGFRA^ENSG00000134853.12	chr4:54274925:+	9DI,9D4,9ET,9EB,9CE,9CP,9CG,9GM,9GI,9CJ,9CF,9EL,9GC,9G3,9DZ,9D3,9D5,9GQ,9DR,9EK,9EP,9DC,9DK,9CM,9E2,9CA,9EV,9EN,9EA,9DS,9FC,9DX,9EH,9FP,9DB,9F0,9G4,9FQ,9FJ,9DJ,9ED,9FS,9CI,9E0,9HH,9DY,9FX,9DP,9DE,9EC,9FY,9FH,9CY,9DG,9FL,9DN,9EQ,9D0,9ES,9CR,9FF,9DQ,9E1,9FI,9DL,9CU,9E7,9FZ,9CK,9CW,9GH,9CQ,9DV,9D9,9FD,9G1,9CL,9DT,9DA,9DH,9D7,9CN,9E6,9GB,9D2,9FN,9FG,9EI,9CS,9EF,9FT,9E8,9GF,9EO,9EY,9DD,9GN,9DM,9CB,9EM,9G8,9FU,9EG,9FO,9E5,9D1,9D8,9EJ,9FW,9E4,9FR,9DO,9FV,9EU,9CZ,9EE,9D6,9DF,9FM,9DU,9G0,9H4,9G6,9CH,9G2,9FE,9CC,9HA,9CT,9ER	9GW,9GJ,9H0,9GY,9GS,9HK,9GV,9GL,9H7,9GZ,9H5,9GK,9H1,9H2,9H9,9GT,9GX	YES_LDAS	11716.8819	GT	1.6402	AG	1.9086	["Mitelman","ChimerKB","chimerdb_pubmed","ConjoinG","ChimerSeq","INTRACHROMOSOMAL[chr4:0.77Mb]"]
+GOPC--ROS1	52	40	52.00	40.00	ONLY_REF_SPLICE	GOPC^ENSG00000047932.14	chr6:117566854:-	ROS1^ENSG00000047936.11	chr6:117321394:-	9I7,9IU,9IY,9J0,9LK,9JD,9IX,9JB,9JE,9HT,9J7,9J1,9IF,9IQ,9IG,9JW,9JF,9I3,9IZ,9HV,9HX,9IT,9J6,9I5,9IC,9HL,9J8,9ID,9I8,9J4,9IJ,9JC,9HQ,9HN,9HZ,9JT,9I6,9IB,9IS,9I4,9IK,9IP,9J9,9JA,9J3,9HP,9HS,9II,9IO,9JS,9I0,9HM	9JH,9LV,9JG,9KQ,9LM,9L6,9LR,9LN,9KZ,9LD,9KW,9LA,9L2,9LL,9KA,9KM,9LU,9KO,9LJ,9KJ,9LC,9LE,9KT,9LZ,9L9,9LI,9KV,9L4,9KI,9LY,9LQ,9KB,9KN,9K7,9LB,9LH,9L0,9LG,9KL,9L3	YES_LDAS	7333.0145	GT	1.7968	AG	1.9329	["Mitelman","ChimerKB","chimerdb_pubmed","ChimerPub","Cosmic","CCLE_StarF2019","INTRACHROMOSOMAL[chr6:0.13Mb]"]
+DUX4--IGH@-ext	18	0	18.00	0.00	INCL_NON_REF_SPLICE	DUX4^ENSG00000260596.5	chr4:190175284:+	IGH@-ext^IGH.g@-ext	chr14:106638525:-	9NE,9NP,9NA,9NM,9ND,9NK,9NN,9NJ,9NI,9NB,9NQ,9NO,9N9,9NG,9NC,9NH,9NL,9NF	.	YES_LDAS	1434.7202	GT	1.8062	AG	1.5219	["INTERCHROMOSOMAL[chr4--chr14]"]
+HOOK3--RET	11	2	11.00	2.00	ONLY_REF_SPLICE	HOOK3^ENSG00000168172.9	chr8:42968214:+	RET^ENSG00000165731.20	chr10:43116584:+	5YM,7AL,36K,1BJ,6FY,02M,1MP,734,50Q,77F,3U0	84R,676	YES_LDAS	1036.1869	GT	1.7465	AG	1.8323	["ChimerKB","HaasMedCancer","Cosmic","ChimerSeq","INTERCHROMOSOMAL[chr8--chr10]"]
+TMPRSS2--ETV1	11	3	11.00	3.00	INCL_NON_REF_SPLICE	TMPRSS2^ENSG00000184012.14	chr21:41494375:-	ETV1^ENSG00000006468.14	chr7:13935838:-	486,16O,3JO,0IR,303,1YC,14G,2TC,52H,0GZ,0TV	75B,6ME,6EE	YES_LDAS	1115.8935	GG	1.3383	CC	1.8892	["ChimerKB","ChimerSeq","TCGA_StarF2019","DEEPEST2019","chimerdb_pubmed","ChimerPub","TumorFusionsNAR2018","Cosmic","INTERCHROMOSOMAL[chr21--chr7]"]
+EWSR1--ATF1	10	3	10.00	3.00	ONLY_REF_SPLICE	EWSR1^ENSG00000182944.18	chr22:29287134:+	ATF1^ENSG00000123268.9	chr12:50814280:+	1CY,2U2,06O,66A,407,0DH,2EO,3V6,5VR,1GL	5DS,1GP,89R	YES_LDAS	1036.1868	GT	1.8062	AG	1.9656	["Mitelman","ChimerKB","ChimerPub","Cosmic","ChimerSeq","INTERCHROMOSOMAL[chr22--chr12]"]
+ETV6--NTRK3	10	4	10.00	4.00	ONLY_REF_SPLICE	ETV6^ENSG00000139083.11	chr12:11869969:+	NTRK3^ENSG00000140538.16	chr15:87940753:-	6MX,63S,37X,3VA,6QT,4OA,2H7,6XD,3L1,09A	4SW,5TV,60G,568	YES_LDAS	1115.8935	GT	1.7819	AG	1.9656	["ChimerKB","Larsson_TCGA","ChimerSeq","TCGA_StarF2019","YOSHIHARA_TCGA","HaasMedCancer","chimerdb_pubmed","chimerdb_omim","DEEPEST2019","GUO2018CR_TCGA","ChimerPub","TumorFusionsNAR2018","Cosmic","INTERCHROMOSOMAL[chr12--chr15]"]
+AKAP9--BRAF	9	4	9.00	4.00	ONLY_REF_SPLICE	AKAP9^ENSG00000127914.19	chr7:92003235:+	BRAF^ENSG00000157764.14	chr7:140787584:-	5YQ,2WW,0ZW,77O,4O5,185,1XG,22F,48H	5I5,0CG,6JD,77B	YES_LDAS	1036.1868	GT	1.8295	AG	1.9329	["ChimerKB","HaasMedCancer","chimerdb_pubmed","ChimerPub","Cosmic","ChimerSeq","INTRACHROMOSOMAL[chr7:48.61Mb]"]
+CD74--ROS1	8	0	8.00	0.00	ONLY_REF_SPLICE	CD74^ENSG00000019582.16	chr5:150404680:-	ROS1^ENSG00000047936.11	chr6:117324415:-	20K,0HO,4G4,4UC,2TX,1QX,33N,2B9	.	YES_LDAS	637.6534	GT	1.7819	AG	1.7465	["ChimerKB","ChimerSeq","TCGA_StarF2019","Klijn_CellLines","chimerdb_pubmed","DEEPEST2019","GUO2018CR_TCGA","ChimerPub","TumorFusionsNAR2018","Cosmic","INTERCHROMOSOMAL[chr5--chr6]"]
+BRD4--NUTM1	6	2	6.00	2.00	ONLY_REF_SPLICE	BRD4^ENSG00000141867.19	chr19:15254152:-	NUTM1^ENSG00000184507.16	chr15:34347969:+	6C6,1XJ,0BK,5SY,0ZN,0YN	1Z3,4TU	YES_LDAS	637.6535	GT	1.7465	AG	1.9329	["ChimerKB","HaasMedCancer","Cosmic","ChimerSeq","CCLE_StarF2019","INTERCHROMOSOMAL[chr19--chr15]"]
+NPM1--ALK	5	2	5.00	2.00	ONLY_REF_SPLICE	NPM1^ENSG00000181163.14	chr5:171391799:+	ALK^ENSG00000171094.18	chr2:29223528:-	9O2,9O0,9NY,9NZ,9O1	9NX,9NW	YES_LDAS	557.9468	GT	1.9656	AG	1.9086	["Mitelman","ChimerKB","ChimerSeq","CCLE_StarF2019","Klijn_CellLines","chimerdb_omim","chimerdb_pubmed","ChimerPub","Cosmic","INTERCHROMOSOMAL[chr5--chr2]"]
+EWSR1--FLI1	5	3	5.00	3.00	ONLY_REF_SPLICE	EWSR1^ENSG00000182944.18	chr22:29287134:+	FLI1^ENSG00000151702.17	chr11:128807180:+	67A,3N8,345,0IO,1FV	2DA,7DK,1L0	YES_LDAS	637.6534	GT	1.8062	AG	1.8062	["Mitelman","ChimerKB","Klijn_CellLines","ChimerPub","Cosmic","ChimerSeq","CCLE_StarF2019","INTERCHROMOSOMAL[chr22--chr11]"]
+EML4--ALK	5	4	5.00	4.00	INCL_NON_REF_SPLICE	EML4^ENSG00000143924.19	chr2:42301394:+	ALK^ENSG00000171094.18	chr2:29223584:-	26T,7A8,2GO,6Q8,2YK	3UT,2ZL,883,0DV	YES_LDAS	717.3601	AA	1.3996	TG	1.9656	["ChimerKB","ChimerSeq","TCGA_StarF2019","CCLE_StarF2019","YOSHIHARA_TCGA","HaasMedCancer","Klijn_CellLines","chimerdb_pubmed","DEEPEST2019","GUO2018CR_TCGA","ChimerPub","TumorFusionsNAR2018","Cosmic","INTRACHROMOSOMAL[chr2:12.25Mb]"]
+CIC--DUX4	4	4	4.00	4.00	INCL_NON_REF_SPLICE	CIC^ENSG00000079432.8	chr19:42295049:+	DUX4^ENSG00000260596.5	chr4:190174448:+	9O3,9O5,9O4,9O7	9OA,9OB,9O9,9OC	YES_LDAS	637.6534	CA	1.5546	CC	1.8295	["Mitelman","ChimerKB","chimerdb_pubmed","CCLE_StarF2019","INTERCHROMOSOMAL[chr19--chr4]"]
+MALT1--IGH-@-ext	3	3	3.00	3.00	INCL_NON_REF_SPLICE	MALT1^ENSG00000172175.15	chr18:58669909:+	IGH-@-ext^IGH-.g@-ext	chr14:105888559:+	9M6,9M5,9M4	9M2,9M3,9M1	YES_LDAS	478.24	CA	1.8892	GC	1.7056	["INTERCHROMOSOMAL[chr18--chr14]"]

workflow.wdl

@@ -0,0 +1,25 @@
+import "./tasks/starfusion.wdl" as starfusion
+workflow {{project_name}} {
+	String sample_id
+        File fastq1
+        File fastq2
+        File starfusion_database_dir
+
+        String starfusion_docker
+	String starfusion_cluster
+	String disk_size
+
+	call starfusion.starfusion as starfusion {
+	input:	
+	sample_id=sample_id,
+	fastq1=fastq1,
+	fastq2=fastq2,
+	database_dir=starfusion_database_dir,
+	docker=starfusion_docker,
+	cluster = starfusion_cluster,
+	disk_size = disk_size
+
+	}
+
+
+}