Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Updating workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation from 0.4.2 to 0.4.3 #431

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Updating workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation from 0.4.2 to 0.4.3 #431

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 7 additions & 0 deletions ...ows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,12 @@
# Changelog

## [0.4.3] 2024-09-24

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1`
- `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1`
- `toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4`

## [0.4.2] 2024-03-06

### Automatic update
Expand Down
136 changes: 31 additions & 105 deletions ...ars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/consensus-from-variation.ga
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
"format-version": "0.1",
"license": "MIT",
"name": "COVID-19: consensus construction",
"release": "0.4.2",
"release": "0.4.3",
"steps": {
"0": {
"annotation": "Collection of VCFs produced by upstream workflows for variation analysis",
Expand Down Expand Up @@ -289,7 +289,7 @@
},
"8": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1",
"errors": null,
"id": 8,
"input_connections": {
Expand Down Expand Up @@ -325,15 +325,15 @@
"output_name": "output"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.31.1",
"tool_shed_repository": {
"changeset_revision": "a1a923cd89e8",
"changeset_revision": "64e2edfe7a2c",
"name": "bedtools",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"d\": false, \"dz\": false, \"five\": false, \"input_type\": {\"input_type_select\": \"bam\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"report\": {\"report_select\": \"bg\", \"__current_case__\": 0, \"zero_regions\": true, \"scale\": \"1.0\"}, \"split\": true, \"strand\": \"\", \"three\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.30.0",
"tool_version": "2.31.1",
"type": "tool",
"uuid": "d89684f5-5a49-4b4c-821b-6c8a87f3a46e",
"when": null,
Expand Down Expand Up @@ -409,10 +409,6 @@
{
"description": "runtime parameter for tool SnpSift Filter",
"name": "filter_expression"
},
{
"description": "runtime parameter for tool SnpSift Filter",
"name": "input"
}
],
"label": null,
Expand Down Expand Up @@ -475,10 +471,6 @@
{
"description": "runtime parameter for tool SnpSift Filter",
"name": "filter_expression"
},
{
"description": "runtime parameter for tool SnpSift Filter",
"name": "input"
}
],
"label": null,
Expand Down Expand Up @@ -537,16 +529,7 @@
"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool Filter",
"name": "cond"
},
{
"description": "runtime parameter for tool Filter",
"name": "input"
}
],
"inputs": [],
"label": null,
"name": "Filter",
"outputs": [
Expand Down Expand Up @@ -593,12 +576,7 @@
"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool SnpSift Extract Fields",
"name": "input"
}
],
"inputs": [],
"label": null,
"name": "SnpSift Extract Fields",
"outputs": [
Expand Down Expand Up @@ -651,12 +629,7 @@
"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool SnpSift Extract Fields",
"name": "input"
}
],
"inputs": [],
"label": null,
"name": "SnpSift Extract Fields",
"outputs": [
Expand Down Expand Up @@ -700,7 +673,7 @@
},
"15": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1",
"errors": null,
"id": 15,
"input_connections": {
Expand All @@ -709,12 +682,7 @@
"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool Compute",
"name": "input"
}
],
"inputs": [],
"label": null,
"name": "Compute",
"outputs": [
Expand Down Expand Up @@ -743,15 +711,15 @@
"output_name": "out_file1"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1",
"tool_shed_repository": {
"changeset_revision": "6595517c2dd8",
"changeset_revision": "aff5135563c6",
"name": "column_maker",
"owner": "devteam",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": false, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--skip-non-computable\", \"__current_case__\": 1}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"int(c2) - (len(c3) == 1)\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"2\"}}, {\"__index__\": 1, \"cond\": \"int(c2) + ((len(c3) - 1) or 1)\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"3\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.0",
"tool_version": "2.1",
"type": "tool",
"uuid": "fd260e32-723d-4a22-8d64-4795557f8159",
"when": null,
Expand All @@ -765,7 +733,7 @@
},
"16": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1",
"errors": null,
"id": 16,
"input_connections": {
Expand All @@ -774,12 +742,7 @@
"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool Compute",
"name": "input"
}
],
"inputs": [],
"label": null,
"name": "Compute",
"outputs": [
Expand Down Expand Up @@ -808,15 +771,15 @@
"output_name": "out_file1"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1",
"tool_shed_repository": {
"changeset_revision": "6595517c2dd8",
"changeset_revision": "aff5135563c6",
"name": "column_maker",
"owner": "devteam",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": false, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--skip-non-computable\", \"__current_case__\": 1}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"int(c2) - (len(c3) == 1)\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"2\"}}, {\"__index__\": 1, \"cond\": \"int(c2) + ((len(c3) - 1) or 1)\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"3\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.0",
"tool_version": "2.1",
"type": "tool",
"uuid": "116e8e99-53ca-4366-a7e1-e3a9fb0bcfc3",
"when": null,
Expand All @@ -843,16 +806,7 @@
"output_name": "out_file1"
}
},
"inputs": [
{
"description": "runtime parameter for tool Concatenate",
"name": "input1"
},
{
"description": "runtime parameter for tool Concatenate",
"name": "input2"
}
],
"inputs": [],
"label": null,
"name": "Concatenate",
"outputs": [
Expand Down Expand Up @@ -905,12 +859,7 @@
"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool Merge",
"name": "input1"
}
],
"inputs": [],
"label": null,
"name": "Merge",
"outputs": [
Expand Down Expand Up @@ -974,16 +923,7 @@
"output_name": "out_file1"
}
},
"inputs": [
{
"description": "runtime parameter for tool Subtract",
"name": "input1"
},
{
"description": "runtime parameter for tool Subtract",
"name": "input2"
}
],
"inputs": [],
"label": null,
"name": "Subtract",
"outputs": [
Expand Down Expand Up @@ -1027,7 +967,7 @@
},
"20": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
"content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1",
"errors": null,
"id": 20,
"input_connections": {
Expand All @@ -1036,12 +976,7 @@
"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool Compute",
"name": "input"
}
],
"inputs": [],
"label": null,
"name": "Compute",
"outputs": [
Expand Down Expand Up @@ -1070,15 +1005,15 @@
"output_name": "out_file1"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1",
"tool_shed_repository": {
"changeset_revision": "6595517c2dd8",
"changeset_revision": "aff5135563c6",
"name": "column_maker",
"owner": "devteam",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"int(c2) + 1\", \"add_column\": {\"mode\": \"R\", \"__current_case__\": 2, \"pos\": \"2\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.0",
"tool_version": "2.1",
"type": "tool",
"uuid": "e06fe045-f0f0-4c32-80ad-a8e070946a2f",
"when": null,
Expand All @@ -1092,7 +1027,7 @@
},
"21": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4",
"errors": null,
"id": 21,
"input_connections": {
Expand All @@ -1110,10 +1045,6 @@
}
},
"inputs": [
{
"description": "runtime parameter for tool bcftools consensus",
"name": "input_file"
},
{
"description": "runtime parameter for tool bcftools consensus",
"name": "reference_source"
Expand Down Expand Up @@ -1144,15 +1075,15 @@
"output_name": "output_file"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy3",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.15.1+galaxy4",
"tool_shed_repository": {
"changeset_revision": "147de996e34f",
"changeset_revision": "8aa352093d73",
"name": "bcftools_consensus",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"absent\": \"\", \"chain\": false, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"fasta_ref\": {\"__class__\": \"ConnectedValue\"}}, \"rename\": true, \"sec_default\": {\"mask\": {\"__class__\": \"ConnectedValue\"}, \"iupac_codes\": false, \"sample\": \"\", \"select_haplotype\": null, \"mark_del\": \"\", \"mark_ins\": null, \"mark_snv\": null, \"conditional_mask\": {\"selector\": \"disabled\", \"__current_case__\": 0}}, \"sec_restrict\": {\"include\": \"\", \"exclude\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.15.1+galaxy3",
"tool_version": "1.15.1+galaxy4",
"type": "tool",
"uuid": "698a9a8c-f6fe-430b-a7e0-cf9e1d058d02",
"when": null,
Expand All @@ -1175,12 +1106,7 @@
"output_name": "output_file"
}
},
"inputs": [
{
"description": "runtime parameter for tool Collapse Collection",
"name": "input_list"
}
],
"inputs": [],
"label": null,
"name": "Collapse Collection",
"outputs": [
Expand Down
Loading