Remove the Count task

defaults

@@ -5,6 +5,5 @@
     "docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bamreadcount:v0.8.0",
     "cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
     "min_base_quality": "0",
-    "min_mapping_quality": "0",
-    "count_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/coverage_count:v1.0"
+    "min_mapping_quality": "0"
 }

inputs

@@ -9,6 +9,5 @@
   "{{ project_name }}.min_base_quality": "{{ min_base_quality }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.cluster_config": "{{ cluster_config }}",
-  "{{ project_name }}.sample_id": "{{ sample_id }}",
-  "{{ project_name }}.count_docker": "{{ count_docker }}"
+  "{{ project_name }}.sample_id": "{{ sample_id }}"
 }

tasks/ selected_covered.csv

@@ -1,91 +0,0 @@
-sample_id,bam,bai,bed
-CBCGA218577_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA218577_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA218577_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA218577_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA218577_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA218577_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA242560_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA242560_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA242560_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA242560_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA242560_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA242560_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA266398_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA266398_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA266398_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA266398_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA266398_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA266398_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA266806_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA266806_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA266806_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA266806_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA266806_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA266806_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA269277_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA269277_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA269277_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA269277_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA269277_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA269277_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA269751_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA269751_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA269751_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA269751_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA269751_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA269751_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA270297_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA270297_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA270297_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA270297_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA270297_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA270297_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA273358_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA273358_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA273358_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA273358_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA273358_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA273358_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA274535_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA274535_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA274535_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA274535_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA274535_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA274535_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA275481_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA275481_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA275481_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA275481_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA275481_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA275481_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA275548_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA275548_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA275548_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA275548_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA275548_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA275548_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA276514_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA276514_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA276514_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA276514_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA276514_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA276514_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA277215_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA277215_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA277215_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA277215_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA277215_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA277215_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA277372_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA277372_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA277372_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA277372_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA277372_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA277372_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA287737_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA287737_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA287737_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA287737_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA287737_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA287737_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA288015_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA288015_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA288015_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA288015_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA288015_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA288015_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA288107_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA288107_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA288107_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA288107_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA288107_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA288107_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA289219_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA289219_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA289219_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA289219_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA289219_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA289219_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA289858_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA289858_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA289858_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA289858_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA289858_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA289858_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA302358-1_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA302358-1_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA302358-1_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA302358-2_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA302358-2_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA302358-2_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA302358-2_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA302358-2_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA302358-2_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA312324-1_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA312324-1_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA312324-1_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA312324-1_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA312324-1_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA312324-1_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA312324-2_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA312324-2_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA312324-2_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA312324-2_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA312324-2_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA312324-2_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA313347_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA313347_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA313347_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA313347_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA313347_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA313347_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA315277_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA315277_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA315277_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA315277_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA315277_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA315277_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA316225_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA316225_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA316225_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA316225_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA316225_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA316225_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA316570_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA316570_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA316570_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA316570_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA316570_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA316570_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA317216_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA317216_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA317216_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA317216_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA317216_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA317216_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA317438_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA317438_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA317438_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA317438_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA317438_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA317438_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA364064_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA364064_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA364064_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA364064_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA364064_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA364064_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA364330_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA364330_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA364330_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA364330_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA364330_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA364330_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA364399_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA364399_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA364399_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA364399_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA364399_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA364399_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA364819_normal,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA364819_normal.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA364819_normal.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA364819_tumor,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA364819_tumor.sorted.deduped.bam,oss://pgx-result/liuyaqing/CBCGA/dedup/CBCGA364819_tumor.sorted.deduped.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-FUSCCTNBC176_normal,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/0cb355ea-c132-4d62-b885-57bdbe2d392c/call-mapping/FUSCCTNBC176_normal.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/0cb355ea-c132-4d62-b885-57bdbe2d392c/call-mapping/FUSCCTNBC176_normal.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-FUSCCTNBC012_tumor,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/17a10ccc-0a3d-4ae9-aadb-c7555cbf3a01/call-mapping/FUSCCTNBC012_tumor.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/17a10ccc-0a3d-4ae9-aadb-c7555cbf3a01/call-mapping/FUSCCTNBC012_tumor.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-FUSCCTNBC174_normal,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/1a887567-a3c3-4dc9-8d9f-2bd23fae3bbf/call-mapping/FUSCCTNBC174_normal.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/1a887567-a3c3-4dc9-8d9f-2bd23fae3bbf/call-mapping/FUSCCTNBC174_normal.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-FUSCCTNBC422_normal,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/1e934995-64e2-46ef-b2dd-bc16e2c77b8a/call-mapping/FUSCCTNBC422_normal.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/1e934995-64e2-46ef-b2dd-bc16e2c77b8a/call-mapping/FUSCCTNBC422_normal.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-FUSCCTNBC247_normal,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/22c09c14-5175-4b11-97b7-b2c8394e69f7/call-mapping/FUSCCTNBC247_normal.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/22c09c14-5175-4b11-97b7-b2c8394e69f7/call-mapping/FUSCCTNBC247_normal.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-FUSCCTNBC255_normal,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/2c6a6389-0c11-4208-a7d9-a5370a1e8b7c/call-mapping/FUSCCTNBC255_normal.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/2c6a6389-0c11-4208-a7d9-a5370a1e8b7c/call-mapping/FUSCCTNBC255_normal.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-FUSCCTNBC422_tumor,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/2f7a4608-a6bf-453c-ad6d-b1ac32154464/call-mapping/FUSCCTNBC422_tumor.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/2f7a4608-a6bf-453c-ad6d-b1ac32154464/call-mapping/FUSCCTNBC422_tumor.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA312324_normal,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/4601aa73-f3f3-4c2c-aa58-3e6fca3b63a8/call-mapping/CBCGA312324_normal.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/4601aa73-f3f3-4c2c-aa58-3e6fca3b63a8/call-mapping/CBCGA312324_normal.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-FUSCCTNBC012_normal,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/4b687131-2951-49ed-b62e-accdc2e71c82/call-mapping/FUSCCTNBC012_normal.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/4b687131-2951-49ed-b62e-accdc2e71c82/call-mapping/FUSCCTNBC012_normal.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-FUSCCTNBC174_tumor,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/501b4b16-7990-4966-924b-65f4bf529ce1/call-mapping/FUSCCTNBC174_tumor.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/501b4b16-7990-4966-924b-65f4bf529ce1/call-mapping/FUSCCTNBC174_tumor.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-FUSCCTNBC247_tumor,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/508a6740-6d4b-4d5c-99a7-43d3af6d7d54/call-mapping/FUSCCTNBC247_tumor.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/508a6740-6d4b-4d5c-99a7-43d3af6d7d54/call-mapping/FUSCCTNBC247_tumor.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-FUSCCTNBC430_tumor,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/66cf5d4e-b0a2-4e0f-a432-de7b46f0efee/call-mapping/FUSCCTNBC430_tumor.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/66cf5d4e-b0a2-4e0f-a432-de7b46f0efee/call-mapping/FUSCCTNBC430_tumor.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-FUSCCTNBC018_normal,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/6cfc8ebc-ecdd-4566-a265-1f82638b4f76/call-mapping/FUSCCTNBC018_normal.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/6cfc8ebc-ecdd-4566-a265-1f82638b4f76/call-mapping/FUSCCTNBC018_normal.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-FUSCCTNBC018_tumor,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/9584364b-cdce-4b05-a59c-68c98ac4cb12/call-mapping/FUSCCTNBC018_tumor.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/9584364b-cdce-4b05-a59c-68c98ac4cb12/call-mapping/FUSCCTNBC018_tumor.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-FUSCCTNBC176_tumor,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/9e3e45c6-a718-4543-a2c7-88e39e0b642d/call-mapping/FUSCCTNBC176_tumor.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/9e3e45c6-a718-4543-a2c7-88e39e0b642d/call-mapping/FUSCCTNBC176_tumor.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA302358_normal,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/a5a9c828-2b43-4a72-a7a6-c29288c75b68/call-mapping/CBCGA302358_normal.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/a5a9c828-2b43-4a72-a7a6-c29288c75b68/call-mapping/CBCGA302358_normal.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-FUSCCTNBC255_tumor,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/aa18ec64-7f7a-402e-9ac1-915e9476f66b/call-mapping/FUSCCTNBC255_tumor.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/aa18ec64-7f7a-402e-9ac1-915e9476f66b/call-mapping/FUSCCTNBC255_tumor.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA302358_tumor,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/bc08bb9d-b2d8-44bc-abf6-d0b57b9aefa6/call-mapping/CBCGA302358_tumor.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/bc08bb9d-b2d8-44bc-abf6-d0b57b9aefa6/call-mapping/CBCGA302358_tumor.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-FUSCCTNBC430_normal,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/c0778ef4-809e-418a-aace-2953bc000be0/call-mapping/FUSCCTNBC430_normal.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/c0778ef4-809e-418a-aace-2953bc000be0/call-mapping/FUSCCTNBC430_normal.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-FUSCCTNBC297_normal,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/c51b48ee-34d1-43c2-b450-fca404cf86d2/call-mapping/FUSCCTNBC297_normal.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/c51b48ee-34d1-43c2-b450-fca404cf86d2/call-mapping/FUSCCTNBC297_normal.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA302358-2K_normal,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/c9231d82-e93a-4b02-b334-aef75fd67fd2/call-mapping/CBCGA302358-2K_normal.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/c9231d82-e93a-4b02-b334-aef75fd67fd2/call-mapping/CBCGA302358-2K_normal.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA312324_tumor,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/d6e73c7a-ee0f-4bfb-aec3-257ce83d20ed/call-mapping/CBCGA312324_tumor.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/d6e73c7a-ee0f-4bfb-aec3-257ce83d20ed/call-mapping/CBCGA312324_tumor.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA302358-M220_normal,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/dd0aa5dd-8076-4f64-9790-a10234091424/call-mapping/CBCGA302358-M220_normal.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/dd0aa5dd-8076-4f64-9790-a10234091424/call-mapping/CBCGA302358-M220_normal.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-FUSCCTNBC297_tumor,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/df56fa2d-daae-4c00-ba46-37af02d9cd7d/call-mapping/FUSCCTNBC297_tumor.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/df56fa2d-daae-4c00-ba46-37af02d9cd7d/call-mapping/FUSCCTNBC297_tumor.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed
-CBCGA312324-2K_tumor,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/e6fd091d-30d2-4697-8fb4-a9b9ec3987cb/call-mapping/CBCGA312324-2K_tumor.sorted.bam,oss://choppy-cromwell-result/test-choppy/WES1020_TNBC_mapping_liuyaqing/e6fd091d-30d2-4697-8fb4-a9b9ec3987cb/call-mapping/CBCGA312324-2K_tumor.sorted.bam.bai,oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/s07604514_covered_selected.bed

tasks/Count.wdl

@@ -1,24 +0,0 @@
-task Count {
-
-    String sample_id
-    File readcount
-    File bed
-    String docker
-    String cluster_config
-    String disk_size
-
-    command <<<
-        python /count.py -s ${sample_id} -i ${readcount} -c ${bed} -o ${sample_id}.coverage
-    >>>
-
-    runtime {
-        docker: docker
-        cluster: cluster_config
-        systemDisk: "cloud_ssd 40"
-        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-    }
-
-    output {
-        File Count = "${sample_id}.coverage"
-    }
-}

workflow.wdl

@@ -1,6 +1,4 @@
 import "./tasks/BAMReadCount.wdl" as BAMReadCount
-import "./tasks/Count.wdl" as Count
-
 
 workflow {{ project_name }} {
     File ref_dir
@@ -12,10 +10,8 @@ workflow {{ project_name }} {
     String min_base_quality
     String sample_id
     String docker
-    String count_docker
     String cluster_config
     String disk_size
-    
 
     call BAMReadCount.BAMReadCount as BAMReadCount {
         input:
@@ -31,14 +27,4 @@ workflow {{ project_name }} {
         cluster_config=cluster_config,
         sample_id=sample_id
     }
-
-    call Count.Count as Count {
-        input:
-        readcount=BAMReadCount.BAMReadCount,
-        bed=bed,
-        docker=count_docker,
-        disk_size=disk_size,
-        cluster_config=cluster_config,
-        sample_id=sample_id
-    }
 }