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

[gxydevbot]

Hello! This is an automated update of the following workflow: workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

• toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.20+galaxy2 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.21+galaxy0

The workflow release number has been updated from 1.0beta6 to 1.0b7.

If you want to skip this change, close this PR without deleting the branch. It will be reopened if another change is detected.
Any commit from another author than 'planemo-autoupdate' will prevent more auto-updates.
To ignore manual changes and allow autoupdates, delete the branch.

[gxydevbot]

There are new updates, they have been integrated to the PR, check the file diff.

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	2
Passed	0
Error	2
Failure	0
Skipped	0

Errored Tests

• ❌ hi-c-map-for-assembly-manual-curation.ga_0

  Execution Problem:

  • Failed to run workflow, invocation ended in [failed] state.
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Haplotype 1:

      • step_state: scheduled

    • Step 2: Will you use a second haplotype?:

      • step_state: scheduled

    • Step 11: Telomere repeat to suit species:

      • step_state: scheduled

    • Step 12: Hap2 not provided:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is running

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"864979fc556d11f0a520000d3a02b12d"
            chromInfo	"/tmp/tmpkfixsbvd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            input_param_type	{"__current_case__": 3, "input_param": false, "mappings": [{"__index__": 0, "from": false, "to": "true"}, {"__index__": 1, "from": true, "to": "false"}], "type": "boolean"}
            output_param_type	"boolean"
            unmapped	{"__current_case__": 2, "default_value": "false", "on_unmapped": "default"}

    • Step 13: Unlabelled step:

      • step_state: scheduled

      • Subworkflow Steps

        • Step 1: Hap1:

          • step_state: scheduled

        • Step 2: Hap2:

          • step_state: scheduled

        • Step 11: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"864979fd556d11f0a520000d3a02b12d"
                chromInfo	"/tmp/tmpkfixsbvd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                style_cond	{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 10, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 2, "src": "hda"}]}}]}}

        • Step 12: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy2:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"864979fd556d11f0a520000d3a02b12d"
                chromInfo	"/tmp/tmpkfixsbvd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                queries	[{"__index__": 0, "inputs2": {"values": [{"id": 12, "src": "hda"}]}}]

        • Step 3: Do you want to add suffixes to the scaffold names?:

          • step_state: scheduled

        • Step 4: Hap1 suffix:

          • step_state: scheduled

        • Step 5: Hap2 suffix:

          • step_state: scheduled

        • Step 6: Expression for hap1 suffixing:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"864979fd556d11f0a520000d3a02b12d"
                chromInfo	"/tmp/tmpkfixsbvd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H1", "select_param_type": "text"}}]
                dbkey	"?"

        • Step 7: Expression for hap2 suffixing:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"864979fd556d11f0a520000d3a02b12d"
                chromInfo	"/tmp/tmpkfixsbvd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H2", "select_param_type": "text"}}]
                dbkey	"?"

        • Step 8: add hap1 suffix:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"864979fd556d11f0a520000d3a02b12d"
                chromInfo	"/tmp/tmpkfixsbvd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                replacements	[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null, "sed_options": null}]

        • Step 9: add hap2 suffix:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"864979fd556d11f0a520000d3a02b12d"
                chromInfo	"/tmp/tmpkfixsbvd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                replacements	[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null, "sed_options": null}]

        • Step 10: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"864979fd556d11f0a520000d3a02b12d"
                chromInfo	"/tmp/tmpkfixsbvd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                style_cond	{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 9, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 1, "src": "hda"}]}}]}}

    • Step 14: concatenate HiFi:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Command Line:

          • cat '/tmp/tmpkfixsbvd/files/2/9/4/dataset_29417a63-0cdb-4e79-a9f7-2de8a9a4c491.dat' >> '/tmp/tmpkfixsbvd/job_working_directory/000/14/outputs/dataset_e72b2ba8-41f6-4116-91a2-d5bd8765a518.dat' && exit 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"864979fc556d11f0a520000d3a02b12d"
            chromInfo	"/tmp/tmpkfixsbvd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            queries	[]

    • Step 3: Haplotype 2:

      • step_state: scheduled

    • Step 4: Do you want to add suffixes to the scaffold names?:

      • step_state: scheduled

    • Step 5: First Haplotype suffix:

      • step_state: scheduled

    • Step 6: Second Haplotype suffix:

      • step_state: scheduled

    • Step 7: Hi-C reads:

      • step_state: scheduled

    • Step 8: Do you want to trim the Hi-C data?:

      • step_state: scheduled

    • Step 9: Minimum Mapping Quality:

      • step_state: scheduled

    • Step 10: PacBio reads:

      • step_state: scheduled
  • Other invocation details

    • error_message

      • Failed to run workflow, invocation ended in [failed] state.

    • history_id

      • 4fdfa144a7cb773a

    • history_state

      • ok

    • invocation_id

      • 4fdfa144a7cb773a

    • invocation_state

      • failed

    • workflow_id

      • 6568b3022b000cb0
• ❌ hi-c-map-for-assembly-manual-curation.ga_1

  Execution Problem:

  • Failed to run workflow, invocation ended in [failed] state.
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Haplotype 1:

      • step_state: scheduled

    • Step 2: Will you use a second haplotype?:

      • step_state: scheduled

    • Step 11: Telomere repeat to suit species:

      • step_state: scheduled

    • Step 12: Hap2 not provided:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"b3883994556d11f0a520000d3a02b12d"
            chromInfo	"/tmp/tmpkfixsbvd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            input_param_type	{"__current_case__": 3, "input_param": false, "mappings": [{"__index__": 0, "from": false, "to": "true"}, {"__index__": 1, "from": true, "to": "false"}], "type": "boolean"}
            output_param_type	"boolean"
            unmapped	{"__current_case__": 2, "default_value": "false", "on_unmapped": "default"}

    • Step 13: Unlabelled step:

      • step_state: scheduled

      • Subworkflow Steps

        • Step 1: Hap1:

          • step_state: scheduled

        • Step 2: Hap2:

          • step_state: scheduled

        • Step 11: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"b3883995556d11f0a520000d3a02b12d"
                chromInfo	"/tmp/tmpkfixsbvd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                style_cond	{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 50, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 42, "src": "hda"}]}}]}}

        • Step 12: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy2:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"b3883995556d11f0a520000d3a02b12d"
                chromInfo	"/tmp/tmpkfixsbvd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                queries	[{"__index__": 0, "inputs2": {"values": [{"id": 52, "src": "hda"}]}}]

        • Step 3: Do you want to add suffixes to the scaffold names?:

          • step_state: scheduled

        • Step 4: Hap1 suffix:

          • step_state: scheduled

        • Step 5: Hap2 suffix:

          • step_state: scheduled

        • Step 6: Expression for hap1 suffixing:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"b3883995556d11f0a520000d3a02b12d"
                chromInfo	"/tmp/tmpkfixsbvd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H1", "select_param_type": "text"}}]
                dbkey	"?"

        • Step 7: Expression for hap2 suffixing:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"b3883995556d11f0a520000d3a02b12d"
                chromInfo	"/tmp/tmpkfixsbvd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H2", "select_param_type": "text"}}]
                dbkey	"?"

        • Step 8: add hap1 suffix:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"b3883995556d11f0a520000d3a02b12d"
                chromInfo	"/tmp/tmpkfixsbvd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                replacements	[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null, "sed_options": null}]

        • Step 9: add hap2 suffix:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"b3883995556d11f0a520000d3a02b12d"
                chromInfo	"/tmp/tmpkfixsbvd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                replacements	[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null, "sed_options": null}]

        • Step 10: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"b3883995556d11f0a520000d3a02b12d"
                chromInfo	"/tmp/tmpkfixsbvd/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                style_cond	{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 49, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 15, "src": "hda"}]}}]}}

    • Step 3: Haplotype 2:

      • step_state: scheduled

    • Step 4: Do you want to add suffixes to the scaffold names?:

      • step_state: scheduled

    • Step 5: First Haplotype suffix:

      • step_state: scheduled

    • Step 6: Second Haplotype suffix:

      • step_state: scheduled

    • Step 7: Hi-C reads:

      • step_state: scheduled

    • Step 8: Do you want to trim the Hi-C data?:

      • step_state: scheduled

    • Step 9: Minimum Mapping Quality:

      • step_state: scheduled

    • Step 10: PacBio reads:

      • step_state: scheduled
  • Other invocation details

    • error_message

      • Failed to run workflow, invocation ended in [failed] state.

    • history_id

      • 26afbb45b30ed2f5

    • history_state

      • ok

    • invocation_id

      • 7e210109176d9cbf

    • invocation_state

      • failed

    • workflow_id

      • 6568b3022b000cb0

[gxydevbot]

There are new updates, they have been integrated to the PR, check the file diff.

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	2
Passed	0
Error	2
Failure	0
Skipped	0

Errored Tests

• ❌ hi-c-map-for-assembly-manual-curation.ga_0

  Execution Problem:

  • Failed to run workflow, invocation ended in [failed] state.
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Haplotype 1:

      • step_state: scheduled

    • Step 2: Will you use a second haplotype?:

      • step_state: scheduled

    • Step 11: Telomere repeat to suit species:

      • step_state: scheduled

    • Step 12: Hap2 not provided:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"77f721e8607011f08b810022485495c9"
            chromInfo	"/tmp/tmpaw7urigl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            input_param_type	{"__current_case__": 3, "input_param": false, "mappings": [{"__index__": 0, "from": false, "to": "true"}, {"__index__": 1, "from": true, "to": "false"}], "type": "boolean"}
            output_param_type	"boolean"
            unmapped	{"__current_case__": 2, "default_value": "false", "on_unmapped": "default"}

    • Step 13: Unlabelled step:

      • step_state: scheduled

      • Subworkflow Steps

        • Step 1: Hap1:

          • step_state: scheduled

        • Step 2: Hap2:

          • step_state: scheduled

        • Step 11: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"77f721e9607011f08b810022485495c9"
                chromInfo	"/tmp/tmpaw7urigl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                style_cond	{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 10, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 2, "src": "hda"}]}}]}}

        • Step 12: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy2:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"77f721e9607011f08b810022485495c9"
                chromInfo	"/tmp/tmpaw7urigl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                queries	[{"__index__": 0, "inputs2": {"values": [{"id": 12, "src": "hda"}]}}]

        • Step 3: Do you want to add suffixes to the scaffold names?:

          • step_state: scheduled

        • Step 4: Hap1 suffix:

          • step_state: scheduled

        • Step 5: Hap2 suffix:

          • step_state: scheduled

        • Step 6: Expression for hap1 suffixing:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"77f721e9607011f08b810022485495c9"
                chromInfo	"/tmp/tmpaw7urigl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H1", "select_param_type": "text"}}]
                dbkey	"?"

        • Step 7: Expression for hap2 suffixing:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"77f721e9607011f08b810022485495c9"
                chromInfo	"/tmp/tmpaw7urigl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H2", "select_param_type": "text"}}]
                dbkey	"?"

        • Step 8: add hap1 suffix:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"77f721e9607011f08b810022485495c9"
                chromInfo	"/tmp/tmpaw7urigl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                replacements	[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null, "sed_options": null}]

        • Step 9: add hap2 suffix:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"77f721e9607011f08b810022485495c9"
                chromInfo	"/tmp/tmpaw7urigl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                replacements	[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null, "sed_options": null}]

        • Step 10: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"77f721e9607011f08b810022485495c9"
                chromInfo	"/tmp/tmpaw7urigl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                style_cond	{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 9, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 1, "src": "hda"}]}}]}}

    • Step 14: concatenate HiFi:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Command Line:

          • cat '/tmp/tmpaw7urigl/files/f/2/4/dataset_f24ed7eb-43f4-4fff-b78c-efe5204ecc4d.dat' >> '/tmp/tmpaw7urigl/job_working_directory/000/14/outputs/dataset_1249b5f0-950c-4db5-af87-ee2eee7651e7.dat' && exit 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"77f721e8607011f08b810022485495c9"
            chromInfo	"/tmp/tmpaw7urigl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            queries	[]

    • Step 3: Haplotype 2:

      • step_state: scheduled

    • Step 4: Do you want to add suffixes to the scaffold names?:

      • step_state: scheduled

    • Step 5: First Haplotype suffix:

      • step_state: scheduled

    • Step 6: Second Haplotype suffix:

      • step_state: scheduled

    • Step 7: Hi-C reads:

      • step_state: scheduled

    • Step 8: Do you want to trim the Hi-C data?:

      • step_state: scheduled

    • Step 9: Minimum Mapping Quality:

      • step_state: scheduled

    • Step 10: PacBio reads:

      • step_state: scheduled
  • Other invocation details

    • error_message

      • Failed to run workflow, invocation ended in [failed] state.

    • history_id

      • 6d5f409a0ddfeeed

    • history_state

      • ok

    • invocation_id

      • 6d5f409a0ddfeeed

    • invocation_state

      • failed

    • workflow_id

      • c5e8069666ade2d8
• ❌ hi-c-map-for-assembly-manual-curation.ga_1

  Execution Problem:

  • Failed to run workflow, invocation ended in [failed] state.
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Haplotype 1:

      • step_state: scheduled

    • Step 2: Will you use a second haplotype?:

      • step_state: scheduled

    • Step 11: Telomere repeat to suit species:

      • step_state: scheduled

    • Step 12: Hap2 not provided:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is running

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"cc06fc2c607011f08b810022485495c9"
            chromInfo	"/tmp/tmpaw7urigl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            input_param_type	{"__current_case__": 3, "input_param": false, "mappings": [{"__index__": 0, "from": false, "to": "true"}, {"__index__": 1, "from": true, "to": "false"}], "type": "boolean"}
            output_param_type	"boolean"
            unmapped	{"__current_case__": 2, "default_value": "false", "on_unmapped": "default"}

    • Step 13: Unlabelled step:

      • step_state: scheduled

      • Subworkflow Steps

        • Step 1: Hap1:

          • step_state: scheduled

        • Step 2: Hap2:

          • step_state: scheduled

        • Step 11: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"cc06fc2d607011f08b810022485495c9"
                chromInfo	"/tmp/tmpaw7urigl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                style_cond	{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 50, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 42, "src": "hda"}]}}]}}

        • Step 12: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy2:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"cc06fc2d607011f08b810022485495c9"
                chromInfo	"/tmp/tmpaw7urigl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                queries	[{"__index__": 0, "inputs2": {"values": [{"id": 52, "src": "hda"}]}}]

        • Step 3: Do you want to add suffixes to the scaffold names?:

          • step_state: scheduled

        • Step 4: Hap1 suffix:

          • step_state: scheduled

        • Step 5: Hap2 suffix:

          • step_state: scheduled

        • Step 6: Expression for hap1 suffixing:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"cc06fc2d607011f08b810022485495c9"
                chromInfo	"/tmp/tmpaw7urigl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H1", "select_param_type": "text"}}]
                dbkey	"?"

        • Step 7: Expression for hap2 suffixing:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"cc06fc2d607011f08b810022485495c9"
                chromInfo	"/tmp/tmpaw7urigl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H2", "select_param_type": "text"}}]
                dbkey	"?"

        • Step 8: add hap1 suffix:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"cc06fc2d607011f08b810022485495c9"
                chromInfo	"/tmp/tmpaw7urigl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                replacements	[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null, "sed_options": null}]

        • Step 9: add hap2 suffix:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"cc06fc2d607011f08b810022485495c9"
                chromInfo	"/tmp/tmpaw7urigl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                replacements	[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null, "sed_options": null}]

        • Step 10: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"cc06fc2d607011f08b810022485495c9"
                chromInfo	"/tmp/tmpaw7urigl/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                style_cond	{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 49, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 15, "src": "hda"}]}}]}}

    • Step 3: Haplotype 2:

      • step_state: scheduled

    • Step 4: Do you want to add suffixes to the scaffold names?:

      • step_state: scheduled

    • Step 5: First Haplotype suffix:

      • step_state: scheduled

    • Step 6: Second Haplotype suffix:

      • step_state: scheduled

    • Step 7: Hi-C reads:

      • step_state: scheduled

    • Step 8: Do you want to trim the Hi-C data?:

      • step_state: scheduled

    • Step 9: Minimum Mapping Quality:

      • step_state: scheduled

    • Step 10: PacBio reads:

      • step_state: scheduled
  • Other invocation details

    • error_message

      • Failed to run workflow, invocation ended in [failed] state.

    • history_id

      • 89ae42c9a4e11c9f

    • history_state

      • ok

    • invocation_id

      • 268cadc8e61850eb

    • invocation_state

      • failed

    • workflow_id

      • c5e8069666ade2d8

[gxydevbot]

There are new updates, they have been integrated to the PR, check the file diff.

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	2
Passed	0
Error	2
Failure	0
Skipped	0

Errored Tests

• ❌ hi-c-map-for-assembly-manual-curation.ga_0

  Execution Problem:

  • Failed to run workflow, invocation ended in [failed] state.
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Haplotype 1:

      • step_state: scheduled

    • Step 2: Will you use a second haplotype?:

      • step_state: scheduled

    • Step 11: Telomere repeat to suit species:

      • step_state: scheduled

    • Step 12: Hap2 not provided:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"9aa35b90767211f081dd7c1e52b4129c"
            chromInfo	"/tmp/tmp5ol_09al/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            input_param_type	{"__current_case__": 3, "input_param": false, "mappings": [{"__index__": 0, "from": false, "to": "true"}, {"__index__": 1, "from": true, "to": "false"}], "type": "boolean"}
            output_param_type	"boolean"
            unmapped	{"__current_case__": 2, "default_value": "false", "on_unmapped": "default"}

    • Step 13: Unlabelled step:

      • step_state: scheduled

      • Subworkflow Steps

        • Step 1: Hap1:

          • step_state: scheduled

        • Step 2: Hap2:

          • step_state: scheduled

        • Step 11: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"9aa35b91767211f081dd7c1e52b4129c"
                chromInfo	"/tmp/tmp5ol_09al/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                style_cond	{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 10, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 2, "src": "hda"}]}}]}}

        • Step 12: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy2:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"9aa35b91767211f081dd7c1e52b4129c"
                chromInfo	"/tmp/tmp5ol_09al/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                queries	[{"__index__": 0, "inputs2": {"values": [{"id": 12, "src": "hda"}]}}]

        • Step 3: Do you want to add suffixes to the scaffold names?:

          • step_state: scheduled

        • Step 4: Hap1 suffix:

          • step_state: scheduled

        • Step 5: Hap2 suffix:

          • step_state: scheduled

        • Step 6: Expression for hap1 suffixing:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"9aa35b91767211f081dd7c1e52b4129c"
                chromInfo	"/tmp/tmp5ol_09al/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H1", "select_param_type": "text"}}]
                dbkey	"?"

        • Step 7: Expression for hap2 suffixing:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"9aa35b91767211f081dd7c1e52b4129c"
                chromInfo	"/tmp/tmp5ol_09al/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H2", "select_param_type": "text"}}]
                dbkey	"?"

        • Step 8: add hap1 suffix:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"9aa35b91767211f081dd7c1e52b4129c"
                chromInfo	"/tmp/tmp5ol_09al/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                replacements	[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null, "sed_options": null}]

        • Step 9: add hap2 suffix:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"9aa35b91767211f081dd7c1e52b4129c"
                chromInfo	"/tmp/tmp5ol_09al/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                replacements	[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null, "sed_options": null}]

        • Step 10: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"9aa35b91767211f081dd7c1e52b4129c"
                chromInfo	"/tmp/tmp5ol_09al/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                style_cond	{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 9, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 1, "src": "hda"}]}}]}}

    • Step 3: Haplotype 2:

      • step_state: scheduled

    • Step 4: Do you want to add suffixes to the scaffold names?:

      • step_state: scheduled

    • Step 5: First Haplotype suffix:

      • step_state: scheduled

    • Step 6: Second Haplotype suffix:

      • step_state: scheduled

    • Step 7: Hi-C reads:

      • step_state: scheduled

    • Step 8: Do you want to trim the Hi-C data?:

      • step_state: scheduled

    • Step 9: Minimum Mapping Quality:

      • step_state: scheduled

    • Step 10: PacBio reads:

      • step_state: scheduled
  • Other invocation details

    • error_message

      • Failed to run workflow, invocation ended in [failed] state.

    • history_id

      • ddde9811b7bad4a8

    • history_state

      • ok

    • invocation_id

      • ddde9811b7bad4a8

    • invocation_state

      • failed

    • workflow_id

      • 7a0ca5ccd5f41e30
• ❌ hi-c-map-for-assembly-manual-curation.ga_1

  Execution Problem:

  • Failed to run workflow, invocation ended in [failed] state.
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Haplotype 1:

      • step_state: scheduled

    • Step 2: Will you use a second haplotype?:

      • step_state: scheduled

    • Step 11: Telomere repeat to suit species:

      • step_state: scheduled

    • Step 12: Hap2 not provided:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is running

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"af64ee72767211f081dd7c1e52b4129c"
            chromInfo	"/tmp/tmp5ol_09al/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            input_param_type	{"__current_case__": 3, "input_param": false, "mappings": [{"__index__": 0, "from": false, "to": "true"}, {"__index__": 1, "from": true, "to": "false"}], "type": "boolean"}
            output_param_type	"boolean"
            unmapped	{"__current_case__": 2, "default_value": "false", "on_unmapped": "default"}

    • Step 13: Unlabelled step:

      • step_state: scheduled

      • Subworkflow Steps

        • Step 1: Hap1:

          • step_state: scheduled

        • Step 2: Hap2:

          • step_state: scheduled

        • Step 11: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"af64ee73767211f081dd7c1e52b4129c"
                chromInfo	"/tmp/tmp5ol_09al/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                style_cond	{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 50, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 16, "src": "hda"}]}}]}}

        • Step 12: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy2:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"af64ee73767211f081dd7c1e52b4129c"
                chromInfo	"/tmp/tmp5ol_09al/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                queries	[{"__index__": 0, "inputs2": {"values": [{"id": 52, "src": "hda"}]}}]

        • Step 3: Do you want to add suffixes to the scaffold names?:

          • step_state: scheduled

        • Step 4: Hap1 suffix:

          • step_state: scheduled

        • Step 5: Hap2 suffix:

          • step_state: scheduled

        • Step 6: Expression for hap1 suffixing:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"af64ee73767211f081dd7c1e52b4129c"
                chromInfo	"/tmp/tmp5ol_09al/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H1", "select_param_type": "text"}}]
                dbkey	"?"

        • Step 7: Expression for hap2 suffixing:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"af64ee73767211f081dd7c1e52b4129c"
                chromInfo	"/tmp/tmp5ol_09al/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "&.", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "H2", "select_param_type": "text"}}]
                dbkey	"?"

        • Step 8: add hap1 suffix:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"af64ee73767211f081dd7c1e52b4129c"
                chromInfo	"/tmp/tmp5ol_09al/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                replacements	[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null, "sed_options": null}]

        • Step 9: add hap2 suffix:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"af64ee73767211f081dd7c1e52b4129c"
                chromInfo	"/tmp/tmp5ol_09al/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                replacements	[{"__index__": 0, "find_pattern": ">.+$", "replace_pattern": null, "sed_options": null}]

        • Step 10: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"af64ee73767211f081dd7c1e52b4129c"
                chromInfo	"/tmp/tmp5ol_09al/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                style_cond	{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 4, "param_type": "data", "pick_from": [{"__index__": 0, "value": {"values": [{"id": 49, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 15, "src": "hda"}]}}]}}

    • Step 3: Haplotype 2:

      • step_state: scheduled

    • Step 4: Do you want to add suffixes to the scaffold names?:

      • step_state: scheduled

    • Step 5: First Haplotype suffix:

      • step_state: scheduled

    • Step 6: Second Haplotype suffix:

      • step_state: scheduled

    • Step 7: Hi-C reads:

      • step_state: scheduled

    • Step 8: Do you want to trim the Hi-C data?:

      • step_state: scheduled

    • Step 9: Minimum Mapping Quality:

      • step_state: scheduled

    • Step 10: PacBio reads:

      • step_state: scheduled
  • Other invocation details

    • error_message

      • Failed to run workflow, invocation ended in [failed] state.

    • history_id

      • 590ca40b89f0bac7

    • history_state

      • ok

    • invocation_id

      • a2f584685b6b0bb2

    • invocation_state

      • failed

    • workflow_id

      • 7a0ca5ccd5f41e30