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/amplicon/amplicon-mgnify/mgnify-amplicon-pipeline-v5-quality-control-paired-end from 0.2 to 0.3 #755

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open
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
Original file line number Diff line number Diff line change
@@ -1,5 +1,11 @@
# Changelog

## [0.3] - 2025-03-21

### Automatic update
- `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0`
- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3`

## [0.2] - 2025-03-10

- `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy4`
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@
"format-version": "0.1",
"license": "Apache-2.0",
"name": "MGnify's amplicon pipeline v5.0 - Quality control PE",
"release": "0.2",
"release": "0.3",
"report": {
"markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
},
Expand Down Expand Up @@ -414,7 +414,7 @@
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": {\"__class__\": \"ConnectedValue\"}, \"unqualified_percent_limit\": {\"__class__\": \"ConnectedValue\"}, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": {\"__class__\": \"ConnectedValue\"}, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": null, \"umi_len\": null, \"umi_prefix\": null}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": {\"__class__\": \"ConnectedValue\"}}}, \"single_paired\": {\"single_paired_selector\": \"paired_collection\", \"__current_case__\": 1, \"paired_input\": {\"__class__\": \"RuntimeValue\"}, \"merge_reads\": {\"merge\": \"\", \"__current_case__\": 1}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": null, \"adapter_sequence2\": null, \"detect_adapter_for_pe\": false}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
"tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": {\"__class__\": \"ConnectedValue\"}, \"unqualified_percent_limit\": {\"__class__\": \"ConnectedValue\"}, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": {\"__class__\": \"ConnectedValue\"}, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": null, \"umi_len\": null, \"umi_prefix\": null}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": {\"__class__\": \"ConnectedValue\"}}}, \"single_paired\": {\"single_paired_selector\": \"paired_collection\", \"__current_case__\": 1, \"paired_input\": {\"__class__\": \"ConnectedValue\"}, \"merge_reads\": {\"merge\": \"\", \"__current_case__\": 1}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": null, \"adapter_sequence2\": null, \"detect_adapter_for_pe\": false}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
"tool_version": "0.24.0+galaxy4",
"type": "tool",
"uuid": "9b7f1d2d-d39f-407d-a709-a5095fca62c2",
Expand Down Expand Up @@ -826,7 +826,7 @@
},
"19": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0",
"errors": null,
"id": 19,
"input_connections": {
Expand Down Expand Up @@ -855,15 +855,15 @@
"output_name": "outfile"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0",
"tool_shed_repository": {
"changeset_revision": "86755160afbf",
"changeset_revision": "3dc70b59608c",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"\\\\t(.*?)\\\\.gz\", \"replace_pattern\": \"\\\\t$1_initial_reads\", \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "9.3+galaxy1",
"tool_version": "9.5+galaxy0",
"type": "tool",
"uuid": "680b293b-0b1e-4b95-9dc9-233354651b61",
"when": null,
Expand Down Expand Up @@ -1008,7 +1008,7 @@
},
"22": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0",
"errors": null,
"id": 22,
"input_connections": {
Expand Down Expand Up @@ -1037,15 +1037,15 @@
"output_name": "outfile"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0",
"tool_shed_repository": {
"changeset_revision": "86755160afbf",
"changeset_revision": "3dc70b59608c",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"\\\\t(.*?)\\\\.gz\", \"replace_pattern\": \"\\\\t$1_trimming\", \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "9.3+galaxy1",
"tool_version": "9.5+galaxy0",
"type": "tool",
"uuid": "2bb5af38-51bd-4828-bc34-7b4c7273c9e2",
"when": null,
Expand Down Expand Up @@ -1172,7 +1172,7 @@
},
"25": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0",
"errors": null,
"id": 25,
"input_connections": {
Expand Down Expand Up @@ -1201,15 +1201,15 @@
"output_name": "outfile"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0",
"tool_shed_repository": {
"changeset_revision": "86755160afbf",
"changeset_revision": "3dc70b59608c",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"\\\\t(.*?)\\\\.gz\", \"replace_pattern\": \"\\\\t$1_length_filtering\", \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "9.3+galaxy1",
"tool_version": "9.5+galaxy0",
"type": "tool",
"uuid": "8c5dc662-6bcc-4772-bc0e-d0b747113ef3",
"when": null,
Expand Down Expand Up @@ -1270,7 +1270,7 @@
},
"27": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
"content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0",
"errors": null,
"id": 27,
"input_connections": {
Expand Down Expand Up @@ -1299,23 +1299,23 @@
"output_name": "outfile"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy0",
"tool_shed_repository": {
"changeset_revision": "86755160afbf",
"changeset_revision": "3dc70b59608c",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"\\\\t(.*?)\\\\.gz\", \"replace_pattern\": \"\\\\t$1_ambiguous_base_filtering\", \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "9.3+galaxy1",
"tool_version": "9.5+galaxy0",
"type": "tool",
"uuid": "aacb9221-34de-46f7-91ec-ff796e98db10",
"when": null,
"workflow_outputs": []
},
"28": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy0",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3",
"errors": null,
"id": 28,
"input_connections": {
Expand All @@ -1336,7 +1336,12 @@
"output_name": "outfile"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool MultiQC",
"name": "image_content_input"
}
],
"label": null,
"name": "MultiQC",
"outputs": [
Expand Down Expand Up @@ -1369,15 +1374,15 @@
"output_name": "stats"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3",
"tool_shed_repository": {
"changeset_revision": "a7e081ceb76a",
"changeset_revision": "31c42a2c02d3",
"name": "multiqc",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 2, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 3, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.27+galaxy0",
"tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"image_content_input\": {\"__class__\": \"RuntimeValue\"}, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 2, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 3, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.27+galaxy3",
"type": "tool",
"uuid": "e04ee136-c52f-4d7e-85c5-3b3ed78b0cce",
"when": null,
Expand All @@ -1403,4 +1408,4 @@
],
"uuid": "3af45a28-126d-4c9d-9948-cabfe43566f3",
"version": 21
}
}