Skip to content

Commit

Permalink
workflows
Browse files Browse the repository at this point in the history
  • Loading branch information
polkhe committed Jun 27, 2017
1 parent e9f6ff2 commit 3048a0c
Show file tree
Hide file tree
Showing 3 changed files with 370 additions and 8 deletions.
Original file line number Diff line number Diff line change
@@ -0,0 +1,185 @@
{
"a_galaxy_workflow": "true",
"annotation": "",
"format-version": "0.1",
"name": "quality_control",
"steps": {
"0": {
"annotation": "",
"content_id": null,
"errors": null,
"id": 0,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "GSM461178_untreat_paired_subset_1.fastq"
}
],
"label": null,
"name": "Input dataset",
"outputs": [],
"position": {
"left": 10,
"top": 10
},
"tool_id": null,
"tool_state": "{\"name\": \"GSM461178_untreat_paired_subset_1.fastq\"}",
"tool_version": null,
"type": "data_input",
"uuid": "4e4d892e-f36f-443f-a6e5-63bbe3081023",
"workflow_outputs": []
},
"1": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.67",
"errors": null,
"id": 1,
"input_connections": {
"input_file": {
"id": 0,
"output_name": "output"
}
},
"inputs": [],
"label": null,
"name": "FastQC",
"outputs": [
{
"name": "html_file",
"type": "html"
},
{
"name": "text_file",
"type": "txt"
}
],
"position": {
"left": 230,
"top": 10
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.67",
"tool_shed_repository": {
"changeset_revision": "3a458e268066",
"name": "fastqc",
"owner": "devteam",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__page__\": null, \"limits\": \"null\", \"input_file\": \"null\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
"tool_version": "0.67",
"type": "tool",
"uuid": "5d317b27-dd13-42d9-bbe1-e654071ac991",
"workflow_outputs": []
},
"2": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.0",
"errors": null,
"id": 2,
"input_connections": {
"singlePaired|input_singles": {
"id": 0,
"output_name": "output"
}
},
"inputs": [],
"label": null,
"name": "Trim Galore!",
"outputs": [
{
"name": "trimmed_reads_paired_collection",
"type": "input"
},
{
"name": "trimmed_reads_unpaired_collection",
"type": "input"
},
{
"name": "trimmed_reads_single",
"type": "input"
},
{
"name": "trimmed_reads_pair1",
"type": "input"
},
{
"name": "trimmed_reads_pair2",
"type": "input"
},
{
"name": "unpaired_reads_1",
"type": "input"
},
{
"name": "unpaired_reads_2",
"type": "input"
},
{
"name": "report_file",
"type": "txt"
}
],
"position": {
"left": 230,
"top": 130
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.0",
"tool_shed_repository": {
"changeset_revision": "1bf4789584dc",
"name": "trim_galore",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__page__\": null, \"singlePaired\": \"{\\\"three_prime_clip_R1\\\": \\\"\\\", \\\"trimming\\\": {\\\"trimming_select\\\": \\\"\\\", \\\"__current_case__\\\": 0}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0, \\\"input_singles\\\": null}\", \"__rerun_remap_job_id__\": null, \"params\": \"{\\\"min_length\\\": \\\"20\\\", \\\"stringency\\\": \\\"5\\\", \\\"error_rate\\\": \\\"0.1\\\", \\\"retain_unpaired\\\": {\\\"retain_unpaired_select\\\": \\\"no_output\\\", \\\"__current_case__\\\": 0}, \\\"__current_case__\\\": 1, \\\"report\\\": \\\"false\\\", \\\"settingsType\\\": \\\"custom\\\", \\\"quality\\\": \\\"20\\\", \\\"clip_R1\\\": \\\"\\\", \\\"clip_R2\\\": \\\"\\\"}\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"rrbs\": \"{\\\"settingsType\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\"}",
"tool_version": "0.4.3.0",
"type": "tool",
"uuid": "543a099f-61a9-4ccf-96ba-f1a5cda8cf3a",
"workflow_outputs": []
},
"3": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.67",
"errors": null,
"id": 3,
"input_connections": {
"input_file": {
"id": 2,
"output_name": "trimmed_reads_single"
}
},
"inputs": [],
"label": null,
"name": "FastQC",
"outputs": [
{
"name": "html_file",
"type": "html"
},
{
"name": "text_file",
"type": "txt"
}
],
"position": {
"left": 450,
"top": 10
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.67",
"tool_shed_repository": {
"changeset_revision": "3a458e268066",
"name": "fastqc",
"owner": "devteam",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__page__\": null, \"limits\": \"null\", \"input_file\": \"null\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
"tool_version": "0.67",
"type": "tool",
"uuid": "e681d4c5-17a5-4c4a-9ac8-884a4b554c56",
"workflow_outputs": []
}
},
"uuid": "7ec27c57-b341-47c3-a4bc-f48e0d58b861"
}
Original file line number Diff line number Diff line change
@@ -0,0 +1,185 @@
{
"a_galaxy_workflow": "true",
"annotation": "",
"format-version": "0.1",
"name": "quality_control_2",
"steps": {
"0": {
"annotation": "",
"content_id": null,
"errors": null,
"id": 0,
"input_connections": {},
"inputs": [
{
"description": "",
"name": "GSM461182_untreat_single_subset.fastq"
}
],
"label": null,
"name": "Input dataset",
"outputs": [],
"position": {
"left": 10,
"top": 10
},
"tool_id": null,
"tool_state": "{\"name\": \"GSM461182_untreat_single_subset.fastq\"}",
"tool_version": null,
"type": "data_input",
"uuid": "81439cbe-9216-482e-8dc9-885a5d1a4fdc",
"workflow_outputs": []
},
"1": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.67",
"errors": null,
"id": 1,
"input_connections": {
"input_file": {
"id": 0,
"output_name": "output"
}
},
"inputs": [],
"label": null,
"name": "FastQC",
"outputs": [
{
"name": "html_file",
"type": "html"
},
{
"name": "text_file",
"type": "txt"
}
],
"position": {
"left": 230,
"top": 10
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.67",
"tool_shed_repository": {
"changeset_revision": "3a458e268066",
"name": "fastqc",
"owner": "devteam",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__page__\": null, \"limits\": \"null\", \"input_file\": \"null\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
"tool_version": "0.67",
"type": "tool",
"uuid": "0e214447-f28b-4a12-8857-c9f78853e8f4",
"workflow_outputs": []
},
"2": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.0",
"errors": null,
"id": 2,
"input_connections": {
"singlePaired|input_singles": {
"id": 0,
"output_name": "output"
}
},
"inputs": [],
"label": null,
"name": "Trim Galore!",
"outputs": [
{
"name": "trimmed_reads_paired_collection",
"type": "input"
},
{
"name": "trimmed_reads_unpaired_collection",
"type": "input"
},
{
"name": "trimmed_reads_single",
"type": "input"
},
{
"name": "trimmed_reads_pair1",
"type": "input"
},
{
"name": "trimmed_reads_pair2",
"type": "input"
},
{
"name": "unpaired_reads_1",
"type": "input"
},
{
"name": "unpaired_reads_2",
"type": "input"
},
{
"name": "report_file",
"type": "txt"
}
],
"position": {
"left": 230,
"top": 130
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.0",
"tool_shed_repository": {
"changeset_revision": "1bf4789584dc",
"name": "trim_galore",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__page__\": null, \"singlePaired\": \"{\\\"three_prime_clip_R1\\\": \\\"\\\", \\\"trimming\\\": {\\\"trimming_select\\\": \\\"\\\", \\\"__current_case__\\\": 0}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0, \\\"input_singles\\\": null}\", \"__rerun_remap_job_id__\": null, \"params\": \"{\\\"min_length\\\": \\\"20\\\", \\\"stringency\\\": \\\"5\\\", \\\"error_rate\\\": \\\"0.1\\\", \\\"retain_unpaired\\\": {\\\"retain_unpaired_select\\\": \\\"no_output\\\", \\\"__current_case__\\\": 0}, \\\"__current_case__\\\": 1, \\\"report\\\": \\\"false\\\", \\\"settingsType\\\": \\\"custom\\\", \\\"quality\\\": \\\"20\\\", \\\"clip_R1\\\": \\\"\\\", \\\"clip_R2\\\": \\\"\\\"}\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"rrbs\": \"{\\\"settingsType\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\"}",
"tool_version": "0.4.3.0",
"type": "tool",
"uuid": "86cbff7f-75f8-4558-8913-1f777827b0f5",
"workflow_outputs": []
},
"3": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.68",
"errors": null,
"id": 3,
"input_connections": {
"input_file": {
"id": 2,
"output_name": "trimmed_reads_single"
}
},
"inputs": [],
"label": null,
"name": "FastQC",
"outputs": [
{
"name": "html_file",
"type": "html"
},
{
"name": "text_file",
"type": "txt"
}
],
"position": {
"left": 450,
"top": 10
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.68",
"tool_shed_repository": {
"changeset_revision": "484e86282f4b",
"name": "fastqc",
"owner": "devteam",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"__page__\": null, \"limits\": \"null\", \"input_file\": \"null\", \"__rerun_remap_job_id__\": null, \"contaminants\": \"null\", \"chromInfo\": \"\\\"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
"tool_version": "0.68",
"type": "tool",
"uuid": "69a9b5af-afa4-4df2-878f-88ec024156b1",
"workflow_outputs": []
}
},
"uuid": "ef06ceb9-385d-400e-9f22-4b061c9bcc66"
}

This file was deleted.

0 comments on commit 3048a0c

Please sign in to comment.