Updating workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6 from 0.10.2 to 0.10.3

[gxydevbot]

Hello! This is an automated update of the following workflow: workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated: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/datamash_ops/datamash_ops/1.8+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.9+galaxy0

The workflow release number has been updated from 0.10.2 to 0.10.3.

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.

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

• ❌ Purge-duplicate-contigs-VGP6.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: Name of primary assembly:

      • step_state: scheduled

    • Step 12: Name of alternate assembly:

      • step_state: scheduled

    • Step 13: 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 running

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"48bbcc04606f11f08b816045bda9ddc2"
            chromInfo	"/tmp/tmprxa4ol4o/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 14: 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 running

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"48bbcc04606f11f08b816045bda9ddc2"
            chromInfo	"/tmp/tmprxa4ol4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "randName4", "select_param_type": "text"}}]
            dbkey	"?"

    • Step 15: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Command Line:

          • ln -f -s '/tmp/tmprxa4ol4o/files/6/b/4/dataset_6b4b48e4-d2b3-418f-9301-d3a72417171c.dat' reference.fa && minimap2 -x asm5    --q-occ-frac 0.01       -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmprxa4ol4o/files/5/8/9/dataset_5891d1cc-b0da-47d9-8757-fbf47eaaba31.dat' > '/tmp/tmprxa4ol4o/job_working_directory/000/9/outputs/dataset_ef93f0d8-b0b1-437f-9430-90454427b6a1.dat'

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
            __workflow_invocation_uuid__	"48bbcc04606f11f08b816045bda9ddc2"
            alignment_options	{"A": null, "B": null, "E": null, "E2": null, "O": null, "O2": null, "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": null, "z2": null}
            chromInfo	"/tmp/tmprxa4ol4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            fastq_input	{"__current_case__": 0, "analysis_type_selector": "asm5", "fastq_input1": {"values": [{"id": 1, "src": "dce"}]}, "fastq_input_selector": "single"}
            indexing_options	{"H": false, "I": null, "k": null, "w": null}
            io_options	{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "paf"}
            mapping_options	{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": null, "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": null, "n": null, "p": null, "q_occ_frac": "0.01", "r": null}
            reference_source	{"__current_case__": 1, "ref_file": {"values": [{"id": 1, "src": "hda"}]}, "reference_source_selector": "history"}

    • Step 16: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Command Line:

          • split_fa '/tmp/tmprxa4ol4o/files/6/b/4/dataset_6b4b48e4-d2b3-418f-9301-d3a72417171c.dat' > split.fasta

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"48bbcc04606f11f08b816045bda9ddc2"
            chromInfo	"/tmp/tmprxa4ol4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            function_select	{"__current_case__": 1, "functions": "split_fa", "input": {"values": [{"id": 1, "src": "hda"}]}}

    • Step 17: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"48bbcc04606f11f08b816045bda9ddc2"
            avoid_scientific_notation	false
            chromInfo	"/tmp/tmprxa4ol4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            error_handling	{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}
            ops	{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "1.5*c3"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "3*c7"}], "header_lines_select": "no"}

    • Step 18: Estimated genome size:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"expression.json"
            __workflow_invocation_uuid__	"48bbcc04606f11f08b816045bda9ddc2"
            chromInfo	"/tmp/tmprxa4ol4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 19: 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__	"48bbcc04606f11f08b816045bda9ddc2"
            chromInfo	"/tmp/tmprxa4ol4o/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 20: Awk command for primary assembly:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"48bbcc04606f11f08b816045bda9ddc2"
            chromInfo	"/tmp/tmprxa4ol4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "BEGIN{print \"Metric\\t", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "Primary", "select_param_type": "text"}}, {"__index__": 2, "param_type": {"__current_case__": 0, "component_value": "\"}; {print}; ", "select_param_type": "text"}}]
            dbkey	"?"

    • Step 3: Pacbio Reads Collection - Trimmed:

      • step_state: scheduled

    • Step 21: Awk command for alternate assembly 2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"48bbcc04606f11f08b816045bda9ddc2"
            chromInfo	"/tmp/tmprxa4ol4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            components	[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "BEGIN{print \"Metric\\t", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "Alternate", "select_param_type": "text"}}, {"__index__": 2, "param_type": {"__current_case__": 0, "component_value": "\"}; {print}; ", "select_param_type": "text"}}]
            dbkey	"?"

    • Step 22: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
            __workflow_invocation_uuid__	"48bbcc04606f11f08b816045bda9ddc2"
            alignment_options	{"A": "1", "B": "19", "E": "3", "E2": "1", "O": "39", "O2": "81", "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": "200", "z2": null}
            chromInfo	"/tmp/tmprxa4ol4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            fastq_input	{"__current_case__": 0, "analysis_type_selector": "self-homology", "fastq_input1": {"values": [{"id": 10, "src": "hda"}]}, "fastq_input_selector": "single"}
            indexing_options	{"H": false, "I": null, "k": null, "w": null}
            io_options	{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "paf"}
            mapping_options	{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": "40", "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": "100", "n": null, "p": null, "q_occ_frac": "0.01", "r": null}
            reference_source	{"__current_case__": 1, "ref_file": {"values": [{"id": 10, "src": "hda"}]}, "reference_source_selector": "history"}

    • Step 23: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"48bbcc04606f11f08b816045bda9ddc2"
            chromInfo	"/tmp/tmprxa4ol4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c8"
            dbkey	"?"
            delimiter	"T"

    • Step 24: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"48bbcc04606f11f08b816045bda9ddc2"
            chromInfo	"/tmp/tmprxa4ol4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c7"
            dbkey	"?"
            delimiter	"T"

    • Step 25: param_value_from_file:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"48bbcc04606f11f08b816045bda9ddc2"
            chromInfo	"/tmp/tmprxa4ol4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 26: param_value_from_file:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"48bbcc04606f11f08b816045bda9ddc2"
            chromInfo	"/tmp/tmprxa4ol4o/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 27: Unlabelled step:

      • step_state: new

    • Step 28: Unlabelled step:

      • step_state: new

    • Step 29: Unlabelled step:

      • step_state: new

    • Step 30: Unlabelled step:

      • step_state: new

    • Step 4: Hifiasm Primary assembly:

      • step_state: scheduled

    • Step 31: Busco on purged primary/hap1 assembly:

      • step_state: new

    • Step 32: Unlabelled step:

      • step_state: new

    • Step 33: Compleasm on purged primary/hap1 assembly:

      • step_state: new

    • Step 34: Unlabelled step:

      • step_state: new

    • Step 35: Unlabelled step:

      • step_state: new

    • Step 36: Unlabelled step:

      • step_state: new

    • Step 37: Unlabelled step:

      • step_state: new

    • Step 38: Unlabelled step:

      • step_state: new

    • Step 39: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

    • Step 40: Unlabelled step:

      • step_state: new

    • Step 5: Hifiasm Alternate assembly:

      • step_state: scheduled

    • Step 41: Unlabelled step:

      • step_state: new

    • Step 42: Unlabelled step:

      • step_state: new

    • Step 43: Unlabelled step:

      • step_state: new

    • Step 44: Unlabelled step:

      • step_state: new

    • Step 45: Unlabelled step:

      • step_state: new

    • Step 46: Unlabelled step:

      • step_state: new

    • Step 47: Unlabelled step:

      • step_state: new

    • Step 48: Unlabelled step:

      • step_state: new

    • Step 49: Compleasm on purged alternate/hap2 assembly:

      • step_state: new

    • Step 50: Unlabelled step:

      • step_state: new

    • Step 6: Meryl Database:

      • step_state: scheduled

    • Step 51: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

    • Step 52: merqury_QV:

      • step_state: new

    • Step 53: output_merqury.spectra-cn.fl:

      • step_state: new

    • Step 54: output_merqury.spectra-asm.fl:

      • step_state: new

    • Step 55: output_merqury.assembly_01.spectra-cn.fl:

      • step_state: new

    • Step 56: merqury_stats:

      • step_state: new

    • Step 57: output_merqury.assembly_02.spectra-cn.fl:

      • step_state: new

    • Step 58: Unlabelled step:

      • step_state: new

    • Step 59: Unlabelled step:

      • step_state: new

      • Subworkflow Steps

    • Step 60: Unlabelled step:

      • step_state: new

    • Step 7: Genomescope model parameters:

      • step_state: scheduled

    • Step 61: Unlabelled step:

      • step_state: new

    • Step 8: Estimated genome size - Parameter File:

      • step_state: scheduled

    • Step 9: Database for Busco Lineage:

      • step_state: scheduled

    • Step 10: Lineage:

      • step_state: scheduled
  • Other invocation details

    • error_message

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

    • history_id

      • cc20944ddc4fae0d

    • history_state

      • ok

    • invocation_id

      • cc20944ddc4fae0d

    • invocation_state

      • failed

    • workflow_id

      • f273ba1ed5b0be0b