Updating workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8 from 2.0 to 2.1

[gxydevbot]

Hello! This is an automated update of the following workflow: workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated: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/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2 should be updated to toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy3
• 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
• toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5 should be updated to toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.6

The workflow release number has been updated from 2.0 to 2.1.

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	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

• ❌ Scaffolding-HiC-VGP8.ga_0

  Execution Problem:

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

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Species Name:

      • step_state: scheduled

    • Step 2: Assembly Name:

      • step_state: scheduled

    • Step 11: Estimated genome size - Parameter File:

      • step_state: scheduled

    • **Step 12: Species Name: **:

      • 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__	"b9e16428556d11f0a520000d3a5bee96"
            chromInfo	"/tmp/tmp95j55cgq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "Random Name", "select_param_type": "text"}}]
            dbkey	"?"

    • Step 13: Assembly Name::

      • 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__	"b9e16428556d11f0a520000d3a5bee96"
            chromInfo	"/tmp/tmp95j55cgq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "randName3", "select_param_type": "text"}}]
            dbkey	"?"

    • Step 14: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Command Line:

          • gfastats '/tmp/tmp95j55cgq/files/1/c/3/dataset_1c320ebe-f0cc-492c-a7e6-e36fc406046d.dat'   -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"b9e16428556d11f0a520000d3a5bee96"
            chromInfo	"/tmp/tmp95j55cgq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 15: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0:

      • 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__	"b9e16428556d11f0a520000d3a5bee96"
            chromInfo	"/tmp/tmp95j55cgq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            input_param_type	{"__current_case__": 0, "input_param": "Haplotype 1", "mappings": [{"__index__": 0, "from": "Haplotype 1", "to": "H1"}, {"__index__": 1, "from": "Haplotype 2", "to": "H2"}, {"__index__": 2, "from": "Maternal ", "to": "mat"}, {"__index__": 3, "from": "Paternal", "to": "pat"}, {"__index__": 4, "from": "Primary", "to": "pri"}, {"__index__": 5, "from": "Alternate", "to": "alt"}, {"__index__": 6, "from": null, "to": null}], "type": "text"}
            output_param_type	"text"
            unmapped	{"__current_case__": 0, "on_unmapped": "input"}

    • Step 16: Haplotype::

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"b9e16428556d11f0a520000d3a5bee96"
            chromInfo	"/tmp/tmp95j55cgq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "Haplotype 1", "select_param_type": "text"}}]
            dbkey	"?"

    • Step 17: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"b9e16428556d11f0a520000d3a5bee96"
            chromInfo	"/tmp/tmp95j55cgq/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__": 1, "component_value": "20", "select_param_type": "integer"}}]
            dbkey	"?"

    • Step 18: Lineage used for Busco:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"b9e16428556d11f0a520000d3a5bee96"
            chromInfo	"/tmp/tmp95j55cgq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "vertebrata_odb10", "select_param_type": "text"}}]
            dbkey	"?"

    • Step 19: param_value_from_file:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"b9e16428556d11f0a520000d3a5bee96"
            chromInfo	"/tmp/tmp95j55cgq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 20: Unlabelled step:

      • step_state: scheduled

      • Subworkflow Steps

        • Step 1: Reference:

          • step_state: scheduled

        • Step 2: Hi-C reads:

          • step_state: scheduled

        • Step 3: Do you want to trim the Hi-C data?:

          • step_state: scheduled

        • Step 4: Trim Hi-C reads 2:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"b9e16429556d11f0a520000d3a5bee96"
                adapter_options	{"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "3", "revcomp": false, "times": "1"}
                chromInfo	"/tmp/tmp95j55cgq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                filter_options	{"discard_casava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "maximum_length2": null, "minimum_length": "1", "minimum_length2": null, "pair_filter": "any"}
                library	{"__current_case__": 2, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "pair_adapters": false, "r1": {"adapters": [], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [], "anywhere_adapters2": [], "front_adapters2": []}, "type": "paired_collection"}
                other_trimming_options	{"cut": "5", "cut2": "5", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "quality_cutoff2": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "shorten_options_r2": {"__current_case__": 1, "shorten_values_r2": "False"}, "trim_n": false}
                output_selector	["report"]
                read_mod_options	{"length_tag": null, "rename": null, "strip_suffix": null, "zero_cap": false}

        • Step 5: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is queued

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"b9e16429556d11f0a520000d3a5bee96"
                chromInfo	"/tmp/tmp95j55cgq/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": 6, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 2, "src": "dce"}]}}]}}

            • Job 2:

              • Job state is queued

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"b9e16429556d11f0a520000d3a5bee96"
                chromInfo	"/tmp/tmp95j55cgq/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": 7, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 3, "src": "dce"}]}}]}}

        • Step 6: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy4:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is new

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"b9e16429556d11f0a520000d3a5bee96"
                analysis_type	{"__current_case__": 4, "algorithmic_options": {"D": "0.5", "P": true, "S": true, "W": "0", "__current_case__": 0, "algorithmic_options_selector": "set", "c": "500", "d": "100", "e": false, "k": "19", "m": "50", "r": "1.5", "w": "100", "y": "20"}, "analysis_type_selector": "full", "io_options": {"C": false, "K": null, "M": false, "T": "30", "V": false, "Y": false, "__current_case__": 0, "a": false, "five": true, "h": "5", "io_options_selector": "set", "q": false}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}
                chromInfo	"/tmp/tmp95j55cgq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                fastq_input	{"__current_case__": 2, "fastq_input1": {"values": [{"id": 8, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": null}
                output_sort	"coordinate"
                reference_source	{"__current_case__": 1, "ref_file": {"values": [{"id": 7, "src": "hda"}]}, "reference_source_selector": "history"}
                rg	{"__current_case__": 3, "rg_selector": "do_not_set"}

    • Step 3: Assembly GFA:

      • step_state: scheduled

    • Step 4: Haplotype:

      • step_state: scheduled

    • Step 5: Hi-C reads:

      • step_state: scheduled

    • Step 6: Trim Hi-C Data?:

      • step_state: scheduled

    • Step 7: Minimum Mapping Quality:

      • step_state: scheduled

    • Step 8: Database for Busco Lineage:

      • step_state: scheduled

    • Step 9: Lineage:

      • step_state: scheduled

    • Step 10: Restriction enzymes:

      • step_state: scheduled
  • Other invocation details

    • error_message

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

    • history_id

      • 774c63c02b3e67b6

    • history_state

      • new

    • invocation_id

      • 774c63c02b3e67b6

    • invocation_state

      • failed

    • workflow_id

      • 93beaabd6dccee7a

[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	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

• ❌ Scaffolding-HiC-VGP8.ga_0

  Execution Problem:

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

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Species Name:

      • step_state: scheduled

    • Step 2: Assembly Name:

      • step_state: scheduled

    • Step 11: Estimated genome size - Parameter File:

      • step_state: scheduled

    • **Step 12: Species Name: **:

      • 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__	"4aabf8f8607011f08b816045bd4b14eb"
            chromInfo	"/tmp/tmpo5aosja0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "Random Name", "select_param_type": "text"}}]
            dbkey	"?"

    • Step 13: Assembly Name::

      • 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__	"4aabf8f8607011f08b816045bd4b14eb"
            chromInfo	"/tmp/tmpo5aosja0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "randName3", "select_param_type": "text"}}]
            dbkey	"?"

    • Step 14: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Command Line:

          • gfastats '/tmp/tmpo5aosja0/files/8/7/0/dataset_870c7026-e31f-4122-a209-697cfd48f720.dat'   -o dataset.fasta --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"4aabf8f8607011f08b816045bd4b14eb"
            chromInfo	"/tmp/tmpo5aosja0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 0, "line_length": null, "out_format": "fasta"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 0, "target_option": "false"}

    • Step 15: toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0:

      • 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__	"4aabf8f8607011f08b816045bd4b14eb"
            chromInfo	"/tmp/tmpo5aosja0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            input_param_type	{"__current_case__": 0, "input_param": "Haplotype 1", "mappings": [{"__index__": 0, "from": "Haplotype 1", "to": "H1"}, {"__index__": 1, "from": "Haplotype 2", "to": "H2"}, {"__index__": 2, "from": "Maternal ", "to": "mat"}, {"__index__": 3, "from": "Paternal", "to": "pat"}, {"__index__": 4, "from": "Primary", "to": "pri"}, {"__index__": 5, "from": "Alternate", "to": "alt"}, {"__index__": 6, "from": null, "to": null}], "type": "text"}
            output_param_type	"text"
            unmapped	{"__current_case__": 0, "on_unmapped": "input"}

    • Step 16: Haplotype::

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"4aabf8f8607011f08b816045bd4b14eb"
            chromInfo	"/tmp/tmpo5aosja0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "Haplotype 1", "select_param_type": "text"}}]
            dbkey	"?"

    • Step 17: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"4aabf8f8607011f08b816045bd4b14eb"
            chromInfo	"/tmp/tmpo5aosja0/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__": 1, "component_value": "20", "select_param_type": "integer"}}]
            dbkey	"?"

    • Step 18: Lineage used for Busco:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"4aabf8f8607011f08b816045bd4b14eb"
            chromInfo	"/tmp/tmpo5aosja0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "vertebrata_odb10", "select_param_type": "text"}}]
            dbkey	"?"

    • Step 19: param_value_from_file:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"4aabf8f8607011f08b816045bd4b14eb"
            chromInfo	"/tmp/tmpo5aosja0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 20: Unlabelled step:

      • step_state: scheduled

      • Subworkflow Steps

        • Step 1: Reference:

          • step_state: scheduled

        • Step 2: Hi-C reads:

          • step_state: scheduled

        • Step 3: Do you want to trim the Hi-C data?:

          • step_state: scheduled

        • Step 4: Trim Hi-C reads 2:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is skipped

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"4aabf8f9607011f08b816045bd4b14eb"
                adapter_options	{"action": "trim", "error_rate": "0.1", "match_read_wildcards": false, "no_indels": false, "no_match_adapter_wildcards": true, "overlap": "3", "revcomp": false, "times": "1"}
                chromInfo	"/tmp/tmpo5aosja0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                filter_options	{"discard_casava": false, "discard_trimmed": false, "discard_untrimmed": false, "max_average_error_rate": null, "max_expected_errors": null, "max_n": null, "maximum_length": null, "maximum_length2": null, "minimum_length": "1", "minimum_length2": null, "pair_filter": "any"}
                library	{"__current_case__": 2, "input_1": {"values": [{"id": 1, "src": "dce"}]}, "pair_adapters": false, "r1": {"adapters": [], "anywhere_adapters": [], "front_adapters": []}, "r2": {"adapters2": [], "anywhere_adapters2": [], "front_adapters2": []}, "type": "paired_collection"}
                other_trimming_options	{"cut": "5", "cut2": "5", "nextseq_trim": "0", "poly_a": false, "quality_cutoff": "0", "quality_cutoff2": "", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "shorten_options_r2": {"__current_case__": 1, "shorten_values_r2": "False"}, "trim_n": false}
                output_selector	["report"]
                read_mod_options	{"length_tag": null, "rename": null, "strip_suffix": null, "zero_cap": false}

        • Step 5: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is queued

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"4aabf8f9607011f08b816045bd4b14eb"
                chromInfo	"/tmp/tmpo5aosja0/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": 6, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 2, "src": "dce"}]}}]}}

            • Job 2:

              • Job state is queued

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"4aabf8f9607011f08b816045bd4b14eb"
                chromInfo	"/tmp/tmpo5aosja0/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": 7, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 3, "src": "dce"}]}}]}}

        • Step 6: toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.3+galaxy0:

          • step_state: scheduled

          • Jobs

            • Job 1:

              • Job state is new

              Traceback:

              Job Parameters:

              • Job parameter	Parameter value
                __input_ext	"input"
                __workflow_invocation_uuid__	"4aabf8f9607011f08b816045bd4b14eb"
                analysis_type	{"__current_case__": 4, "algorithmic_options": {"D": "0.5", "P": true, "S": true, "W": "0", "__current_case__": 0, "algorithmic_options_selector": "set", "c": "500", "d": "100", "e": false, "k": "19", "m": "50", "r": "1.5", "w": "100", "y": "20"}, "analysis_type_selector": "full", "io_options": {"C": false, "K": null, "M": false, "T": "30", "V": false, "Y": false, "__current_case__": 0, "a": false, "five": true, "h": "5", "io_options_selector": "set", "q": false}, "scoring_options": {"__current_case__": 1, "scoring_options_selector": "do_not_set"}}
                chromInfo	"/tmp/tmpo5aosja0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
                dbkey	"?"
                fastq_input	{"__current_case__": 2, "fastq_input1": {"values": [{"id": 8, "src": "dce"}]}, "fastq_input_selector": "paired_collection", "iset_stats": null}
                output_sort	"coordinate"
                reference_source	{"__current_case__": 1, "ref_file": {"values": [{"id": 7, "src": "hda"}]}, "reference_source_selector": "history"}
                rg	{"__current_case__": 3, "rg_selector": "do_not_set"}

    • Step 3: Assembly GFA:

      • step_state: scheduled

    • Step 4: Haplotype:

      • step_state: scheduled

    • Step 5: Hi-C reads:

      • step_state: scheduled

    • Step 6: Trim Hi-C Data?:

      • step_state: scheduled

    • Step 7: Minimum Mapping Quality:

      • step_state: scheduled

    • Step 8: Database for Busco Lineage:

      • step_state: scheduled

    • Step 9: Lineage:

      • step_state: scheduled

    • Step 10: Restriction enzymes:

      • step_state: scheduled
  • Other invocation details

    • error_message

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

    • history_id

      • d97a8826fafb8c73

    • history_state

      • ok

    • invocation_id

      • d97a8826fafb8c73

    • invocation_state

      • failed

    • workflow_id

      • 3f35393b86f12759