diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/CHANGELOG.md b/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/CHANGELOG.md index 66826ae740..b900daeabb 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/CHANGELOG.md +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/CHANGELOG.md @@ -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 diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/consensus-from-variation.ga b/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/consensus-from-variation.ga index 7d19751edd..d83da10300 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/consensus-from-variation.ga +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/consensus-from-variation.ga @@ -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", @@ -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": { @@ -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, @@ -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, @@ -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, @@ -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": [ @@ -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": [ @@ -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": [ @@ -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": { @@ -709,12 +682,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Compute", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "Compute", "outputs": [ @@ -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, @@ -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": { @@ -774,12 +742,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Compute", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "Compute", "outputs": [ @@ -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, @@ -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": [ @@ -905,12 +859,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Merge", - "name": "input1" - } - ], + "inputs": [], "label": null, "name": "Merge", "outputs": [ @@ -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": [ @@ -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": { @@ -1036,12 +976,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool Compute", - "name": "input" - } - ], + "inputs": [], "label": null, "name": "Compute", "outputs": [ @@ -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, @@ -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": { @@ -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" @@ -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, @@ -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": [