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Updating workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation from 1.0beta6 to 1.0b7
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‎workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/CHANGELOG.md‎

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# Changelog
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## [1.0b7] - 2025-06-23
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### Automatic update
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- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.21+galaxy0`
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## [1.0beta6] - 2025-06-09
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### Changes

‎workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation.ga‎

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],
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"format-version": "0.1",
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"license": "MIT",
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"release": "1.0beta6",
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"name": "PretextMap Generation from 1 or 2 haplotypes",
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"report": {
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"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"
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"output_name": "output"
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}
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},
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"inputs": [],
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"inputs": [
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{
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"description": "runtime parameter for tool Map parameter value",
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"name": "input_param_type"
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}
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],
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"label": "Hap2 not provided",
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"name": "Map parameter value",
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"outputs": [
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}
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},
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"tags": [],
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"uuid": "8fb65374-0776-4aa9-80d8-eb0b8c69f274"
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"uuid": "4cc91963-eaf1-4bb1-a514-9ebf8572f6f4"
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},
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"tool_id": null,
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"type": "subworkflow",
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}
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},
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"tags": [],
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"uuid": "c32e34b2-4390-4bf2-9048-411280d63ddd"
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"uuid": "60352e06-ad4a-43c9-b97d-95d70f3b1c36"
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},
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"tool_id": null,
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"type": "subworkflow",
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"output_name": "output"
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}
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},
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"inputs": [],
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"inputs": [
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{
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"description": "runtime parameter for tool Cutadapt",
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"name": "library"
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}
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],
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"label": "Trim Hi-C reads 2",
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"name": "Cutadapt",
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"outputs": [
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"output_name": "output"
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}
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},
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"inputs": [],
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"inputs": [
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{
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"description": "runtime parameter for tool BWA-MEM2",
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"name": "fastq_input"
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},
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{
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"description": "runtime parameter for tool BWA-MEM2",
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"name": "reference_source"
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}
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],
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"label": null,
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"name": "BWA-MEM2",
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"outputs": [
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},
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"6": {
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"annotation": "",
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"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2",
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"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.21+galaxy0",
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"errors": null,
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"id": 6,
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"input_connections": {
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"output_name": "bam_output"
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}
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},
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"inputs": [],
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"inputs": [
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{
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"description": "runtime parameter for tool Samtools merge",
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"name": "bed_file"
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},
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{
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"description": "runtime parameter for tool Samtools merge",
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"name": "headerbam"
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}
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],
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"label": null,
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"name": "Samtools merge",
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"outputs": [
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"output_name": "output"
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}
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},
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"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2",
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"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.21+galaxy0",
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"tool_shed_repository": {
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"changeset_revision": "cae2794d2deb",
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"changeset_revision": "a7617eb92baf",
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"name": "samtools_merge",
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"owner": "iuc",
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"tool_shed": "toolshed.g2.bx.psu.edu"
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},
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"tool_state": "{\"bamfiles\": {\"__class__\": \"ConnectedValue\"}, \"bed_file\": {\"__class__\": \"RuntimeValue\"}, \"headerbam\": {\"__class__\": \"RuntimeValue\"}, \"idpg\": false, \"idrg\": false, \"region\": null, \"seed\": \"1\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
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"tool_version": "1.20+galaxy2",
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"tool_version": "1.21+galaxy0",
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"type": "tool",
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"uuid": "f536be00-adc2-4f1f-a167-f3fd44466290",
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"when": null,
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}
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},
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"tags": [],
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"uuid": "52451b6f-5046-4926-b61e-a16cae121c1e"
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"uuid": "9151e9dd-9909-4f6c-9ba8-a48e3b3b8953"
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},
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"tool_id": null,
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"type": "subworkflow",
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"output_name": "data_param"
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}
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},
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"inputs": [],
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"inputs": [
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{
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"description": "runtime parameter for tool Map with minimap2",
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"name": "fastq_input"
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},
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{
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"description": "runtime parameter for tool Map with minimap2",
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"name": "reference_source"
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}
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],
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"label": null,
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"name": "Map with minimap2",
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"outputs": [
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"output_name": "alignment_output"
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}
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},
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"inputs": [],
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"inputs": [
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{
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"description": "runtime parameter for tool bedtools Genome Coverage",
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"name": "input_type"
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}
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],
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"label": null,
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"name": "bedtools Genome Coverage",
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"outputs": [
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"output_name": "text_param"
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}
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},
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"inputs": [],
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"inputs": [
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{
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"description": "runtime parameter for tool Map parameter value",
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"name": "input_param_type"
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}
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],
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"label": "False if telomere track is empty",
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"name": "Map parameter value",
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"outputs": [
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}
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},
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"tags": [],
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"uuid": "34226708-cba3-421c-809f-6ba105b3812c",
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"version": 4
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"uuid": "1f756adc-099e-4a58-b484-865d43ad832c",
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"version": 1,
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"release": "1.0b7"
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}

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