changeset 2:facad3e66f91 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-WGS_GATK4.ga	Thu Mar 07 20:37:48 2019 -0500
@@ -0,0 +1,1 @@
+{"uuid": "e79b26c6-016b-47b0-b98e-ce26c8426fc6", "tags": [], "format-version": "0.1", "name": "WGS_GATK4", "version": 3, "steps": {"0": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{}", "id": 0, "uuid": "11b0bf05-e075-4a17-9e27-dec54d27322f", "errors": null, "name": "Input dataset", "label": "1.fq.gz", "inputs": [], "position": {"top": 113, "left": 182}, "annotation": "", "content_id": null, "type": "data_input"}, "1": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{}", "id": 1, "uuid": "9194fbeb-075f-40a0-9b8a-2d388abd4390", "errors": null, "name": "Input dataset", "label": "2.fq.gz", "inputs": [], "position": {"top": 241, "left": 172}, "annotation": "", "content_id": null, "type": "data_input"}, "2": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{}", "id": 2, "uuid": "d7c90a6b-280f-4086-a9cb-63b3f9e4b523", "errors": null, "name": "Input dataset", "label": "hg38 reference", "inputs": [], "position": {"top": 108, "left": 672}, "annotation": "", "content_id": null, "type": "data_input"}, "3": {"tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5", "tool_version": "0.36.5", "outputs": [{"type": "input", "name": "fastq_out_paired"}, {"type": "input", "name": "fastq_out_unpaired"}, {"type": "input", "name": "fastq_out_r1_paired"}, {"type": "input", "name": "fastq_out_r2_paired"}, {"type": "input", "name": "fastq_out_r1_unpaired"}, {"type": "input", "name": "fastq_out_r2_unpaired"}, {"type": "input", "name": "fastq_out"}], "workflow_outputs": [], "input_connections": {"readtype|fastq_r2_in": {"output_name": "output", "id": 1}, "readtype|fastq_r1_in": {"output_name": "output", "id": 0}}, "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"__current_case__\\\": 0, \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"required_quality\\\": \\\"20\\\", \\\"window_size\\\": \\\"4\\\"}}]\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"readtype\": \"{\\\"__current_case__\\\": 1, \\\"fastq_r1_in\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_r2_in\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"single_or_paired\\\": \\\"pair_of_files\\\"}\", \"illuminaclip\": \"{\\\"__current_case__\\\": 1, \\\"do_illuminaclip\\\": \\\"false\\\"}\"}", "id": 3, "tool_shed_repository": {"owner": "pjbriggs", "changeset_revision": "dfa082f84068", "name": "trimmomatic", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "acee0d27-8dc2-4f3d-bc24-5eaabe181bb1", "errors": null, "name": "Trimmomatic", "post_job_actions": {}, "label": null, "inputs": [], "position": {"top": 110, "left": 382}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5", "type": "tool"}, "4": {"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1", "tool_version": "0.7.17.1", "outputs": [{"type": "bam", "name": "bam_output"}], "workflow_outputs": [], "input_connections": {"fastq_input|fastq_input1": {"output_name": "fastq_out_r1_paired", "id": 3}, "fastq_input|fastq_input2": {"output_name": "fastq_out_r2_paired", "id": 3}, "reference_source|ref_file": {"output_name": "output", "id": 2}}, "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"__job_resource\": \"{\\\"__current_case__\\\": 0, \\\"__job_resource__select\\\": \\\"no\\\"}\", \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"fastq_input\": \"{\\\"__current_case__\\\": 0, \\\"fastq_input1\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input2\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"iset_stats\\\": \\\"\\\"}\", \"analysis_type\": \"{\\\"__current_case__\\\": 0, \\\"analysis_type_selector\\\": \\\"illumina\\\"}\", \"reference_source\": \"{\\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\", \\\"ref_file\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"reference_source_selector\\\": \\\"history\\\"}\"}", "id": 4, "tool_shed_repository": {"owner": "devteam", "changeset_revision": "8d2a528a9513", "name": "bwa", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "a15a664b-7531-4f11-a4c0-a168a444122f", "errors": null, "name": "Map with BWA-MEM", "post_job_actions": {}, "label": null, "inputs": [], "position": {"top": 264, "left": 759.5}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1", "type": "tool"}, "5": {"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.1", "tool_version": "2.18.2.1", "outputs": [{"type": "txt", "name": "metrics_file"}, {"type": "bam", "name": "outFile"}], "workflow_outputs": [], "input_connections": {"inputFile": {"output_name": "bam_output", "id": 4}}, "tool_state": "{\"duplicate_scoring_strategy\": \"\\\"SUM_OF_BASE_QUALITIES\\\"\", \"remove_duplicates\": \"\\\"false\\\"\", \"read_name_regex\": \"\\\"\\\"\", \"barcode_tag\": \"\\\"\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"optical_duplicate_pixel_distance\": \"\\\"100\\\"\", \"comments\": \"[]\", \"assume_sorted\": \"\\\"true\\\"\", \"validation_stringency\": \"\\\"LENIENT\\\"\", \"inputFile\": \"null\"}", "id": 5, "tool_shed_repository": {"owner": "devteam", "changeset_revision": "2a17c789e0a5", "name": "picard", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "4eb0b788-41a1-4ce7-9c4d-c9d1368679a0", "errors": null, "name": "MarkDuplicates", "post_job_actions": {}, "label": null, "inputs": [], "position": {"top": 277, "left": 1091}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.1", "type": "tool"}}, "annotation": "WGS data analysis based on GATK4", "a_galaxy_workflow": "true"}
\ No newline at end of file