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.

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/epigenetics/consensus-peaks from 1.1 to 1.2 #527

Merged
Show file tree
Hide file tree
Changes from all commits
Commits
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
6 changes: 6 additions & 0 deletions workflows/epigenetics/consensus-peaks/CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -1,5 +1,11 @@
# Changelog

## [1.2] 2024-09-24

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3`
- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0`

## [1.1] 2024-05-27

### Automatic update
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@
],
"format-version": "0.1",
"license": "MIT",
"release": "1.1",
"release": "1.2",
"name": "Get Confident Peaks From ATAC or CUTandRUN replicates",
"steps": {
"0": {
Expand Down Expand Up @@ -239,7 +239,7 @@
},
"5": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3",
"errors": null,
"id": 5,
"input_connections": {
Expand Down Expand Up @@ -268,15 +268,15 @@
"output_name": "outputcnt"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3",
"tool_shed_repository": {
"changeset_revision": "6be888be75f9",
"changeset_revision": "32dc5f781059",
"name": "samtools_view",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"all_reads\", \"__current_case__\": 0, \"output_options\": {\"reads_report_type\": \"count\", \"__current_case__\": 1}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.15.1+galaxy2",
"tool_version": "1.20+galaxy3",
"type": "tool",
"uuid": "9cff58b2-123e-42df-b562-3b2a4a553934",
"when": null,
Expand Down Expand Up @@ -886,7 +886,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -989,7 +989,7 @@
},
"20": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3",
"errors": null,
"id": 20,
"input_connections": {
Expand Down Expand Up @@ -1022,15 +1022,15 @@
"output_name": "outputsam"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3",
"tool_shed_repository": {
"changeset_revision": "6be888be75f9",
"changeset_revision": "32dc5f781059",
"name": "samtools_view",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"quality\": null, \"library\": null, \"cigarcons\": null, \"inclusive_filter\": null, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"target\", \"__current_case__\": 1, \"target\": {\"__class__\": \"ConnectedValue\"}, \"seed\": \"1\"}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": false, \"adv_output\": {\"readtags\": [], \"collapsecigar\": false}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.15.1+galaxy2",
"tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"cond_expr\": {\"select_expr\": \"no\", \"__current_case__\": 0}, \"quality\": null, \"library\": null, \"cigarcons\": null, \"inclusive_filter\": null, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"target\", \"__current_case__\": 1, \"target\": {\"__class__\": \"ConnectedValue\"}, \"seed\": \"1\"}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": false, \"adv_output\": {\"readtags\": [], \"collapsecigar\": false}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.20+galaxy3",
"type": "tool",
"uuid": "36713e3f-6110-41f7-8df1-9a9966400fab",
"when": null,
Expand Down Expand Up @@ -1226,7 +1226,7 @@
},
"24": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0",
"errors": null,
"id": 24,
"input_connections": {
Expand All @@ -1243,13 +1243,13 @@
"label": "multiQC",
"name": "MultiQC",
"outputs": [
{
"name": "stats",
"type": "input"
},
{
"name": "html_report",
"type": "html"
},
{
"name": "stats",
"type": "tabular"
}
],
"position": {
Expand All @@ -1263,15 +1263,15 @@
"output_name": "stats"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0",
"tool_shed_repository": {
"changeset_revision": "abfd8a6544d7",
"changeset_revision": "f7e2f1eb3a16",
"name": "multiqc",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.11+galaxy1",
"tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.24.1+galaxy0",
"type": "tool",
"uuid": "f7d74248-16e3-4020-8156-caae0e7682ef",
"when": null,
Expand Down Expand Up @@ -1403,7 +1403,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down
42 changes: 21 additions & 21 deletions workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe.ga
Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@
],
"format-version": "0.1",
"license": "MIT",
"release": "1.1",
"release": "1.2",
"name": "Get Confident Peaks From ChIP_PE replicates",
"steps": {
"0": {
Expand Down Expand Up @@ -194,7 +194,7 @@
},
"4": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3",
"errors": null,
"id": 4,
"input_connections": {
Expand Down Expand Up @@ -223,15 +223,15 @@
"output_name": "outputcnt"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3",
"tool_shed_repository": {
"changeset_revision": "6be888be75f9",
"changeset_revision": "32dc5f781059",
"name": "samtools_view",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"all_reads\", \"__current_case__\": 0, \"output_options\": {\"reads_report_type\": \"count\", \"__current_case__\": 1}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.15.1+galaxy2",
"tool_version": "1.20+galaxy3",
"type": "tool",
"uuid": "a864ff43-af08-436a-aa78-54491ff0cce6",
"when": null,
Expand Down Expand Up @@ -841,7 +841,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -944,7 +944,7 @@
},
"19": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3",
"errors": null,
"id": 19,
"input_connections": {
Expand Down Expand Up @@ -977,15 +977,15 @@
"output_name": "outputsam"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3",
"tool_shed_repository": {
"changeset_revision": "6be888be75f9",
"changeset_revision": "32dc5f781059",
"name": "samtools_view",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"quality\": null, \"library\": null, \"cigarcons\": null, \"inclusive_filter\": null, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"target\", \"__current_case__\": 1, \"target\": {\"__class__\": \"ConnectedValue\"}, \"seed\": \"1\"}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": false, \"adv_output\": {\"readtags\": [], \"collapsecigar\": false}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.15.1+galaxy2",
"tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"cond_expr\": {\"select_expr\": \"no\", \"__current_case__\": 0}, \"quality\": null, \"library\": null, \"cigarcons\": null, \"inclusive_filter\": null, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"target\", \"__current_case__\": 1, \"target\": {\"__class__\": \"ConnectedValue\"}, \"seed\": \"1\"}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": false, \"adv_output\": {\"readtags\": [], \"collapsecigar\": false}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.20+galaxy3",
"type": "tool",
"uuid": "ae46e826-d985-4437-abae-152b6877eea7",
"when": null,
Expand Down Expand Up @@ -1136,7 +1136,7 @@
},
"22": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0",
"errors": null,
"id": 22,
"input_connections": {
Expand All @@ -1153,13 +1153,13 @@
"label": "multiQC",
"name": "MultiQC",
"outputs": [
{
"name": "stats",
"type": "input"
},
{
"name": "html_report",
"type": "html"
},
{
"name": "stats",
"type": "tabular"
}
],
"position": {
Expand All @@ -1173,15 +1173,15 @@
"output_name": "stats"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0",
"tool_shed_repository": {
"changeset_revision": "abfd8a6544d7",
"changeset_revision": "f7e2f1eb3a16",
"name": "multiqc",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.11+galaxy1",
"tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.24.1+galaxy0",
"type": "tool",
"uuid": "f7d74248-16e3-4020-8156-caae0e7682ef",
"when": null,
Expand Down Expand Up @@ -1313,7 +1313,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down
Loading
Loading