Update MAGs-generation to 0.5

[SantaMcCloud]

FOR CONTRIBUTOR:

• I have read the Adding workflows guidelines
• License permits unrestricted use (educational + commercial)
• Please also take note of the reviewer guidelines below to facilitate a smooth review process.

FOR REVIEWERS:

• .dockstore.yml: file is present and aligned with creator metadata in workflow. ORCID identifiers are strongly encouraged in creator metadata. The .dockstore.yml file is required to run tests
• Workflow is sufficiently generic to be used with lab data and does not hardcode sample names, reference data and can be run without reading an accompanying tutorial.
• In workflow: annotation field contains short description of what the workflow does. Should start with This workflow does/runs/performs … xyz … to generate/analyze/etc …
• In workflow: workflow inputs and outputs have human readable names (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless it is generally understood. Altering input or output labels requires adjusting these labels in the the workflow-tests.yml file as well
• In workflow: name field should be human readable (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless generally understood
• Workflow folder: prefer dash (-) over underscore (_), prefer all lowercase. Folder becomes repository in iwc-workflows organization and is included in TRS id
• Readme explains what workflow does, what are valid inputs and what outputs users can expect. If a tutorial or other resources exist they can be linked. If a similar workflow exists in IWC readme should explain differences with existing workflow and when one might prefer one workflow over another
• Changelog contains appropriate entries
• Large files (> 100 KB) are uploaded to zenodo and location urls are used in test file

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ MAGs-generation.ga_0

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: __NEST__ (version 1.0.0)","err_code":0}
    

• ❌ MAGs-generation.ga_1

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: __NEST__ (version 1.0.0)","err_code":0}
    

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ MAGs-generation.ga_0

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: __NEST__ (version 1.0.0)","err_code":0}
    

• ❌ MAGs-generation.ga_1

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: __NEST__ (version 1.0.0)","err_code":0}
    

[SantaMcCloud]

strange the stated tool is installed in .org

[SantaMcCloud]

ping @paulzierep @bebatut

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ MAGs-generation.ga_0

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: __NEST__ (version 1.0.0)","err_code":0}
    

• ❌ MAGs-generation.ga_1

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: __NEST__ (version 1.0.0)","err_code":0}
    

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ MAGs-generation.ga_0

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: __NEST__ (version 1.0.0)","err_code":0}
    

• ❌ MAGs-generation.ga_1

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: __NEST__ (version 1.0.0)","err_code":0}
    

[paulzierep]

@SantaMcCloud can you replace the nest tool with the apply rules tool ? it can also nest by one level.

[paulzierep]

can you add the pick parameter tools after comebin, this is always needed if a tool is optional

[SantaMcCloud]

yes i can do this i forgot to add it sorry

[paulzierep]

why 100 ?

[SantaMcCloud]

If i use a low weight Binette favor complete bins which i dont want to happen because of dRep need more bins as input so i try to create a lot of "useless" bin for testing

[paulzierep]

this will probably fail, I would go for 99 for the test

[SantaMcCloud]

The test i did run this didnt failed since i wanted to create more MAGs so dRep get more input therefor i set the limit low.

[SantaMcCloud]

@SantaMcCloud can you replace the nest tool with the apply rules tool ? it can also nest by one level.

I can replace it yes. Maybe the tool is install now i will wait to check if this is needed or not

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ MAGs-generation.ga_0

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: __NEST__ (version 1.0.0)","err_code":0}
    

• ❌ MAGs-generation.ga_1

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: __NEST__ (version 1.0.0)","err_code":0}
    

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ MAGs-generation.ga_0

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: __NEST__ (version 1.0.0)","err_code":0}
    

• ❌ MAGs-generation.ga_1

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: __NEST__ (version 1.0.0)","err_code":0}
    

[SantaMcCloud]

@SantaMcCloud can you replace the nest tool with the apply rules tool ? it can also nest by one level.

I did change it and i hope i did it right. I also add the pick value tool. The marked changed from the box title the one you did marked is correct so i did not change this.

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ MAGs-generation.ga_0

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: __NEST__ (version 1.0.0)","err_code":0}
    

• ❌ MAGs-generation.ga_1

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: __NEST__ (version 1.0.0)","err_code":0}
    

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ MAGs-generation.ga_0

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: __NEST__ (version 1.0.0)","err_code":0}
    

• ❌ MAGs-generation.ga_1

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: __NEST__ (version 1.0.0)","err_code":0}
    

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ MAGs-generation.ga_0

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: __NEST__ (version 1.0.0)","err_code":0}
    

• ❌ MAGs-generation.ga_1

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: __NEST__ (version 1.0.0)","err_code":0}
    

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ MAGs-generation.ga_0

  Execution Problem:

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

  Workflow invocation details

  • Invocation Messages

    • Invocation scheduling failed because an unexpected failure occurred.
  • Steps

    • Step 1: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy3):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"ce3ca2644bff11f1898a7ced8ddaf5b1"
            chromInfo	"/tmp/tmpuznh19uo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            token_set	[{"__index__": 0, "line": null, "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]

    • Step 2: Trimmed nanopore reads from grouped samples:

      • step_state: scheduled

    • Step 3: Trimmed PacBio reads from grouped samples:

      • step_state: scheduled

    • Step 4: Trimmed paired reads from grouped samples:

      • step_state: scheduled

    • Step 5: Choose Assembler:

      • step_state: scheduled

    • Step 6: Trimmed reads:

      • step_state: scheduled

    • Step 7: Minimum length of contigs to output:

      • step_state: scheduled

    • Step 8: Custom Assemblies:

      • step_state: scheduled

    • Step 9: Environment for the built-in model (SemiBin):

      • step_state: scheduled

    • Step 10: Unlabelled step:

      • step_state: new
  • Other invocation details

    • error_message

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

    • history_id

      • f176a3fc40629837

    • history_state

      • new

    • invocation_id

      • f176a3fc40629837

    • invocation_state

      • failed

    • messages

      • [{'details': None, 'reason': 'unexpected_failure', 'workflow_step_id': None}]

    • workflow_id

      • c763bdf6f099a977
• ❌ MAGs-generation.ga_1

  Execution Problem:

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

  Workflow invocation details

  • Invocation Messages

    • Invocation scheduling failed because an unexpected failure occurred.
  • Steps

    • Step 1: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy3):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"e0384c2a4bff11f1898a7ced8ddaf5b1"
            chromInfo	"/tmp/tmpuznh19uo/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            token_set	[{"__index__": 0, "line": null, "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]

    • Step 2: Trimmed nanopore reads from grouped samples:

      • step_state: scheduled

    • Step 3: Trimmed PacBio reads from grouped samples:

      • step_state: scheduled

    • Step 4: Trimmed paired reads from grouped samples:

      • step_state: scheduled

    • Step 5: Choose Assembler:

      • step_state: scheduled

    • Step 6: Trimmed reads:

      • step_state: scheduled

    • Step 7: Minimum length of contigs to output:

      • step_state: scheduled

    • Step 8: Custom Assemblies:

      • step_state: scheduled

    • Step 9: Environment for the built-in model (SemiBin):

      • step_state: scheduled

    • Step 10: Unlabelled step:

      • step_state: new
  • Other invocation details

    • error_message

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

    • history_id

      • c763bdf6f099a977

    • history_state

      • new

    • invocation_id

      • c763bdf6f099a977

    • invocation_state

      • failed

    • messages

      • [{'details': None, 'reason': 'unexpected_failure', 'workflow_step_id': None}]

    • workflow_id

      • c763bdf6f099a977

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ MAGs-generation.ga_0

  Execution Problem:

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

  Workflow invocation details

  • Invocation Messages

    • Invocation scheduling failed because an unexpected failure occurred at step 34: 'Failed to create 1 job(s) for workflow step 34: Error executing tool with id 'FILTER_EMPTY_DATASETS': dict.copy() takes no keyword arguments'
  • Steps

    • Step 1: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy3):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/coreutils:9.5

          Command Line:

          • times=1; yes -- '' 2>/dev/null | head -n $times >> '/tmp/tmpp7vopu41/job_working_directory/000/5/outputs/dataset_6ddd3e23-655f-417d-98ef-6822641695e0.dat';

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"ae81847e4ca611f1898a7ced8d819316"
            chromInfo	"/tmp/tmpp7vopu41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            token_set	[{"__index__": 0, "line": null, "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]

    • Step 2: Trimmed nanopore reads from grouped samples:

      • step_state: scheduled

    • Step 3: Trimmed PacBio reads from grouped samples:

      • step_state: scheduled

    • Step 4: Trimmed paired reads from grouped samples:

      • step_state: scheduled

    • Step 5: Choose Assembler:

      • step_state: scheduled

    • Step 6: Trimmed reads:

      • step_state: scheduled

    • Step 7: Minimum length of contigs to output:

      • step_state: scheduled

    • Step 8: Custom Assemblies:

      • step_state: scheduled

    • Step 9: Environment for the built-in model (SemiBin):

      • step_state: scheduled

    • Step 10: Run COMEBin:

      • step_state: scheduled

    • Step 11: Minimum MAG completeness percentage:

      • step_state: scheduled

    • Step 12: Contamination weight (Binette):

      • step_state: scheduled

    • Step 13: Read length (CONCOCT):

      • step_state: scheduled

    • Step 14: CheckM2 Database:

      • step_state: scheduled

    • Step 15: Minimum MAG length:

      • step_state: scheduled

    • Step 16: Maximum MAG contamination percentage:

      • step_state: scheduled

    • Step 17: ANI threshold for dereplication:

      • step_state: scheduled

    • Step 18: Unlabelled step (Grep1):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/grep:3.4--hf43ccf4_4

          Command Line:

          • set -eo pipefail; cat '/tmp/tmpp7vopu41/files/6/d/d/dataset_6ddd3e23-655f-417d-98ef-6822641695e0.dat' | grep -P -f '/tmp/tmpp7vopu41/job_working_directory/000/6/configs/tmp1_r232aa'  >> '/tmp/tmpp7vopu41/job_working_directory/000/6/outputs/dataset_077b7001-0a4a-460a-ac91-b9c4ce3ba62c.dat'

          Exit Code:

          • 1

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"ae81847e4ca611f1898a7ced8d819316"
            chromInfo	"/tmp/tmpp7vopu41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            invert	""
            keep_header	false
            pattern	"^chr([0-9A-Za-z])+"

    • Step 19: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • mv '/tmp/tmpp7vopu41/job_working_directory/000/7/configs/tmpqi30v5kw' '/tmp/tmpp7vopu41/job_working_directory/000/7/outputs/dataset_58a898a2-219d-44f2-8285-539fb546b36a.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fastqsanger.gz"
            __workflow_invocation_uuid__	"ae81847e4ca611f1898a7ced8d819316"
            chromInfo	"/tmp/tmpp7vopu41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            input_collection	{"values": [{"id": 2, "src": "hdca"}]}

    • Step 20: Unlabelled step (__APPLY_RULES__):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __workflow_invocation_uuid__	"ae81847e4ca611f1898a7ced8d819316"
            input	{"values": [{"id": 2, "src": "hdca"}]}
            rules	{"mapping": [{"columns": [0, 2], "editing": false, "type": "list_identifiers"}, {"columns": [1], "type": "paired_identifier"}], "rules": [{"error": null, "type": "add_column_metadata", "value": "identifier0", "warn": null}, {"error": null, "type": "add_column_metadata", "value": "identifier1", "warn": null}, {"error": null, "type": "add_column_metadata", "value": "identifier0", "warn": null}]}

    • Step 21: Unlabelled step (__UNZIP_COLLECTION__):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __workflow_invocation_uuid__	"ae81847e4ca611f1898a7ced8d819316"
            input	{"values": [{"id": 4, "src": "dce"}]}

    • Step 22: Unlabelled step (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 ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"ae81847e4ca611f1898a7ced8d819316"
            chromInfo	"/tmp/tmpp7vopu41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            input_param_type	{"__current_case__": 0, "input_param": "MEGAHIT", "mappings": [{"__index__": 0, "from": "MEGAHIT", "to": "True"}], "type": "text"}
            output_param_type	"boolean"
            unmapped	{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}

    • Step 23: Unlabelled step (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 ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"ae81847e4ca611f1898a7ced8d819316"
            chromInfo	"/tmp/tmpp7vopu41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            input_param_type	{"__current_case__": 0, "input_param": "MEGAHIT", "mappings": [{"__index__": 0, "from": "metaSPAdes", "to": "True"}], "type": "text"}
            output_param_type	"boolean"
            unmapped	{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}

    • Step 24: Unlabelled step (wc_gnu):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cat '/tmp/tmpp7vopu41/files/5/8/a/dataset_58a898a2-219d-44f2-8285-539fb546b36a.dat' | wc -l | awk '{ print $1 }' >> /tmp/tmpp7vopu41/job_working_directory/000/12/outputs/dataset_eb689f07-16d5-4cd2-bdb9-c59c87216772.dat

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"ae81847e4ca611f1898a7ced8d819316"
            chromInfo	"/tmp/tmpp7vopu41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            include_header	false
            options	["lines"]

    • Step 25: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/megahit:1.2.9--haf24da9_8

          Command Line:

          • if [[ -n "$GALAXY_MEMORY_MB" ]]; then MEMORY="-m $((GALAXY_MEMORY_MB * 1024))"; fi;  megahit --num-cpu-threads ${GALAXY_SLOTS:-4}  -1 '/tmp/tmpp7vopu41/files/3/7/e/dataset_37e414e8-943f-40f8-ada5-24f2af1ce8eb.dat' -2 '/tmp/tmpp7vopu41/files/3/d/7/dataset_3d7aa0ae-e6fb-439b-a04a-e2fc5f445ecf.dat' --min-count '2' --k-list '21,29,39,59,79,99,119,141'  --bubble-level '2' --merge-level '20,0.95' --prune-level '2' --prune-depth '2' --disconnect-ratio '0.1' --low-local-ratio '0.2' --cleaning-rounds '5'   --min-contig-len '100' $MEMORY

          Exit Code:

          • 0

          Standard Error:

          • 2026-05-10 19:31:56 - MEGAHIT v1.2.9
            2026-05-10 19:31:56 - Using megahit_core with POPCNT and BMI2 support
            2026-05-10 19:31:56 - Convert reads to binary library
            2026-05-10 19:31:56 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 0 (/tmp/tmpp7vopu41/files/3/7/e/dataset_37e414e8-943f-40f8-ada5-24f2af1ce8eb.dat,/tmp/tmpp7vopu41/files/3/d/7/dataset_3d7aa0ae-e6fb-439b-a04a-e2fc5f445ecf.dat): pe, 100000 reads, 126 max length'
            2026-05-10 19:31:56 - b'INFO  utils/utils.h                 :  152 - Real: 0.1492\tuser: 0.1417\tsys: 0.0090\tmaxrss: 16764'
            2026-05-10 19:31:56 - Start assembly. Number of CPU threads 1 
            2026-05-10 19:31:56 - k list: 21,29,39,59,79,99,119,141 
            2026-05-10 19:31:56 - Memory used: 15089788108
            2026-05-10 19:31:56 - Extract solid (k+1)-mers for k = 21 
            2026-05-10 19:31:59 - Build graph for k = 21 
            2026-05-10 19:32:00 - Assemble contigs from SdBG for k = 21
            2026-05-10 19:32:03 - Local assembly for k = 21
            2026-05-10 19:32:06 - Extract iterative edges from k = 21 to 29 
            2026-05-10 19:32:07 - Build graph for k = 29 
            2026-05-10 19:32:08 - Assemble contigs from SdBG for k = 29
            2026-05-10 19:32:10 - Local assembly for k = 29
            2026-05-10 19:32:14 - Extract iterative edges from k = 29 to 39 
            2026-05-10 19:32:14 - Build graph for k = 39 
            2026-05-10 19:32:15 - Assemble contigs from SdBG for k = 39
            2026-05-10 19:32:17 - Local assembly for k = 39
            2026-05-10 19:32:22 - Extract iterative edges from k = 39 to 59 
            2026-05-10 19:32:23 - Build graph for k = 59 
            2026-05-10 19:32:24 - Assemble contigs from SdBG for k = 59
            2026-05-10 19:32:26 - Local assembly for k = 59
            2026-05-10 19:32:32 - Extract iterative edges from k = 59 to 79 
            2026-05-10 19:32:32 - Build graph for k = 79 
            2026-05-10 19:32:33 - Assemble contigs from SdBG for k = 79
            2026-05-10 19:32:36 - Local assembly for k = 79
            2026-05-10 19:32:42 - Extract iterative edges from k = 79 to 99 
            2026-05-10 19:32:43 - Build graph for k = 99 
            2026-05-10 19:32:43 - Assemble contigs from SdBG for k = 99
            2026-05-10 19:32:46 - Local assembly for k = 99
            2026-05-10 19:32:53 - Extract iterative edges from k = 99 to 119 
            2026-05-10 19:32:54 - Build graph for k = 119 
            2026-05-10 19:32:55 - Assemble contigs from SdBG for k = 119
            2026-05-10 19:32:57 - Local assembly for k = 119
            2026-05-10 19:33:04 - Extract iterative edges from k = 119 to 141 
            2026-05-10 19:33:04 - Build graph for k = 141 
            2026-05-10 19:33:05 - Assemble contigs from SdBG for k = 141
            2026-05-10 19:33:07 - Merging to output final contigs 
            2026-05-10 19:33:07 - 610 contigs, total 1803740 bp, min 145 bp, max 117788 bp, avg 2956 bp, N50 10728 bp
            2026-05-10 19:33:07 - ALL DONE. Time elapsed: 70.838932 seconds 
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fastqsanger.gz"
            __workflow_invocation_uuid__	"ae81847e4ca611f1898a7ced8d819316"
            advanced_section	{"bubble_level": "2", "cleaning_rounds": "5", "disconnect_ratio": "0.1", "kmin1pass": false, "low_local_ratio": "0.2", "merge_level": "20,0.95", "nolocal": false, "nomercy": false, "prune_depth": "2", "prune_level": "2"}
            basic_section	{"k_mer": {"__current_case__": 0, "k_list": "21,29,39,59,79,99,119,141", "k_mer_method": "klist_method"}, "min_count": "2"}
            chromInfo	"/tmp/tmpp7vopu41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            input_option	{"__current_case__": 3, "batchmode": {"__current_case__": 0, "pair_input": {"values": [{"id": 4, "src": "dce"}]}, "processmode": "individual"}, "choice": "paired_collection"}
            output_section	{"log_file": false, "min_contig_len": "100", "show_intermediate_contigs": false}

    • Step 26: Unlabelled step (param_value_from_file):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"ae81847e4ca611f1898a7ced8d819316"
            chromInfo	"/tmp/tmpp7vopu41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 27: Unlabelled step (__DUPLICATE_FILE_TO_COLLECTION__):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __workflow_invocation_uuid__	"ae81847e4ca611f1898a7ced8d819316"
            element_identifier	None
            number	"1"

    • Step 28: Unlabelled step (__RELABEL_FROM_FILE__):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __workflow_invocation_uuid__	"ae81847e4ca611f1898a7ced8d819316"
            how	{"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 7, "src": "hda"}]}, "strict": false}
            input	{"values": [{"id": 7, "src": "hdca"}]}

    • Step 29: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_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__	"ae81847e4ca611f1898a7ced8d819316"
            chromInfo	"/tmp/tmpp7vopu41/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": null}, {"__index__": 1, "value": {"values": [{"id": 15, "src": "dce"}]}}]}}

    • Step 30: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"ae81847e4ca611f1898a7ced8d819316"
            chromInfo	"/tmp/tmpp7vopu41/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": null}, {"__index__": 1, "value": {"values": [{"id": 15, "src": "dce"}]}}]}}

    • Step 31: Unlabelled step:

      • step_state: new

    • Step 32: Unlabelled step (__APPLY_RULES__):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __workflow_invocation_uuid__	"ae81847e4ca611f1898a7ced8d819316"
            input	{"values": [{"id": 10, "src": "hdca"}]}
            rules	{"mapping": [{"columns": [0, 1], "editing": false, "type": "list_identifiers"}], "rules": [{"error": null, "type": "add_column_metadata", "value": "identifier0", "warn": null}, {"error": null, "type": "add_column_metadata", "value": "identifier0", "warn": null}]}

    • Step 33: Unlabelled step:

      • 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

    • Step 40: Unlabelled step:

      • step_state: new

    • Step 41: SemiBin latest:

      • 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: Unlabelled step:

      • step_state: new

    • Step 50: Unlabelled step:

      • step_state: new

    • Step 51: Unlabelled step:

      • step_state: new

    • Step 52: Unlabelled step:

      • step_state: new

    • Step 53: Unlabelled step:

      • step_state: new

    • Step 54: Unlabelled step:

      • step_state: new

    • Step 55: Unlabelled step:

      • step_state: new

    • Step 56: Unlabelled step:

      • step_state: new

    • Step 57: Unlabelled step:

      • step_state: new

    • Step 58: Unlabelled step:

      • step_state: new

    • Step 59: Pool Bins from all samples:

      • step_state: new

    • Step 60: Unlabelled step:

      • step_state: new

    • Step 61: Unlabelled step:

      • step_state: new

    • Step 62: Unlabelled step:

      • step_state: new

    • Step 63: Unlabelled step:

      • step_state: new

    • Step 64: Unlabelled step:

      • step_state: new

    • Step 65: Unlabelled step:

      • step_state: new

    • Step 66: Unlabelled step:

      • step_state: new

    • Step 67: Unlabelled step:

      • step_state: new

    • Step 68: Unlabelled step:

      • step_state: new

    • Step 69: Unlabelled step:

      • step_state: new
  • Other invocation details

    • error_message

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

    • history_id

      • 80990548fd569486

    • history_state

      • running

    • invocation_id

      • 80990548fd569486

    • invocation_state

      • failed

    • messages

      • [{'details': "Failed to create 1 job(s) for workflow step 34: Error executing tool with id 'FILTER_EMPTY_DATASETS': dict.copy() takes no keyword arguments", 'reason': 'unexpected_failure', 'workflow_step_id': 33}]

    • workflow_id

      • ea214b627d1bb1e9
• ❌ MAGs-generation.ga_1

  Execution Problem:

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

  Workflow invocation details

  • Invocation Messages

    • Invocation scheduling failed because an unexpected failure occurred at step 34: 'Failed to create 1 job(s) for workflow step 34: Error executing tool with id 'FILTER_EMPTY_DATASETS': dict.copy() takes no keyword arguments'
  • Steps

    • Step 1: Unlabelled step (toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.5+galaxy3):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/coreutils:9.5

          Command Line:

          • times=1; yes -- '' 2>/dev/null | head -n $times >> '/tmp/tmpp7vopu41/job_working_directory/000/25/outputs/dataset_9fd2358f-590b-4578-946c-625135a6e5bb.dat';

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"391852024ca711f1898a7ced8d819316"
            chromInfo	"/tmp/tmpp7vopu41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            token_set	[{"__index__": 0, "line": null, "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]

    • Step 2: Trimmed nanopore reads from grouped samples:

      • step_state: scheduled

    • Step 3: Trimmed PacBio reads from grouped samples:

      • step_state: scheduled

    • Step 4: Trimmed paired reads from grouped samples:

      • step_state: scheduled

    • Step 5: Choose Assembler:

      • step_state: scheduled

    • Step 6: Trimmed reads:

      • step_state: scheduled

    • Step 7: Minimum length of contigs to output:

      • step_state: scheduled

    • Step 8: Custom Assemblies:

      • step_state: scheduled

    • Step 9: Environment for the built-in model (SemiBin):

      • step_state: scheduled

    • Step 10: Run COMEBin:

      • step_state: scheduled

    • Step 11: Minimum MAG completeness percentage:

      • step_state: scheduled

    • Step 12: Contamination weight (Binette):

      • step_state: scheduled

    • Step 13: Read length (CONCOCT):

      • step_state: scheduled

    • Step 14: CheckM2 Database:

      • step_state: scheduled

    • Step 15: Minimum MAG length:

      • step_state: scheduled

    • Step 16: Maximum MAG contamination percentage:

      • step_state: scheduled

    • Step 17: ANI threshold for dereplication:

      • step_state: scheduled

    • Step 18: Unlabelled step (Grep1):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Container:

          • quay.io/biocontainers/grep:3.4--hf43ccf4_4

          Command Line:

          • set -eo pipefail; cat '/tmp/tmpp7vopu41/files/9/f/d/dataset_9fd2358f-590b-4578-946c-625135a6e5bb.dat' | grep -P -f '/tmp/tmpp7vopu41/job_working_directory/000/26/configs/tmp1wa9umg1'  >> '/tmp/tmpp7vopu41/job_working_directory/000/26/outputs/dataset_25f4d916-5420-4394-a2ef-f55dfb216f1f.dat'

          Exit Code:

          • 1

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"391852024ca711f1898a7ced8d819316"
            chromInfo	"/tmp/tmpp7vopu41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            invert	""
            keep_header	false
            pattern	"^chr([0-9A-Za-z])+"

    • Step 19: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • mv '/tmp/tmpp7vopu41/job_working_directory/000/27/configs/tmprx42blhe' '/tmp/tmpp7vopu41/job_working_directory/000/27/outputs/dataset_bf409de3-2908-47ae-907c-919085a58a79.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fastqsanger.gz"
            __workflow_invocation_uuid__	"391852024ca711f1898a7ced8d819316"
            chromInfo	"/tmp/tmpp7vopu41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            input_collection	{"values": [{"id": 14, "src": "hdca"}]}

    • Step 20: Unlabelled step (__APPLY_RULES__):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __workflow_invocation_uuid__	"391852024ca711f1898a7ced8d819316"
            input	{"values": [{"id": 14, "src": "hdca"}]}
            rules	{"mapping": [{"columns": [0, 2], "editing": false, "type": "list_identifiers"}, {"columns": [1], "type": "paired_identifier"}], "rules": [{"error": null, "type": "add_column_metadata", "value": "identifier0", "warn": null}, {"error": null, "type": "add_column_metadata", "value": "identifier1", "warn": null}, {"error": null, "type": "add_column_metadata", "value": "identifier0", "warn": null}]}

    • Step 21: Unlabelled step (__UNZIP_COLLECTION__):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __workflow_invocation_uuid__	"391852024ca711f1898a7ced8d819316"
            input	{"values": [{"id": 24, "src": "dce"}]}

    • Step 22: Unlabelled step (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 ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"391852024ca711f1898a7ced8d819316"
            chromInfo	"/tmp/tmpp7vopu41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            input_param_type	{"__current_case__": 0, "input_param": "metaSPAdes", "mappings": [{"__index__": 0, "from": "MEGAHIT", "to": "True"}], "type": "text"}
            output_param_type	"boolean"
            unmapped	{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}

    • Step 23: Unlabelled step (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 ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"391852024ca711f1898a7ced8d819316"
            chromInfo	"/tmp/tmpp7vopu41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            input_param_type	{"__current_case__": 0, "input_param": "metaSPAdes", "mappings": [{"__index__": 0, "from": "metaSPAdes", "to": "True"}], "type": "text"}
            output_param_type	"boolean"
            unmapped	{"__current_case__": 2, "default_value": "False", "on_unmapped": "default"}

    • Step 24: Unlabelled step (wc_gnu):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cat '/tmp/tmpp7vopu41/files/b/f/4/dataset_bf409de3-2908-47ae-907c-919085a58a79.dat' | wc -l | awk '{ print $1 }' >> /tmp/tmpp7vopu41/job_working_directory/000/32/outputs/dataset_eaddd13c-3bac-4183-ab93-eb5c8583fe16.dat

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"391852024ca711f1898a7ced8d819316"
            chromInfo	"/tmp/tmpp7vopu41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            include_header	false
            options	["lines"]

    • Step 25: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is skipped

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fastqsanger.gz"
            __workflow_invocation_uuid__	"391852024ca711f1898a7ced8d819316"
            advanced_section	{"bubble_level": "2", "cleaning_rounds": "5", "disconnect_ratio": "0.1", "kmin1pass": false, "low_local_ratio": "0.2", "merge_level": "20,0.95", "nolocal": false, "nomercy": false, "prune_depth": "2", "prune_level": "2"}
            basic_section	{"k_mer": {"__current_case__": 0, "k_list": "21,29,39,59,79,99,119,141", "k_mer_method": "klist_method"}, "min_count": "2"}
            chromInfo	"/tmp/tmpp7vopu41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            input_option	{"__current_case__": 3, "batchmode": {"__current_case__": 0, "pair_input": {"values": [{"id": 24, "src": "dce"}]}, "processmode": "individual"}, "choice": "paired_collection"}
            output_section	{"log_file": false, "min_contig_len": "100", "show_intermediate_contigs": false}

    • Step 26: Unlabelled step (param_value_from_file):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"391852024ca711f1898a7ced8d819316"
            chromInfo	"/tmp/tmpp7vopu41/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"integer"
            remove_newlines	true

    • Step 27: Unlabelled step (__DUPLICATE_FILE_TO_COLLECTION__):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __workflow_invocation_uuid__	"391852024ca711f1898a7ced8d819316"
            element_identifier	None
            number	"1"

    • Step 28: Unlabelled step (__RELABEL_FROM_FILE__):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __workflow_invocation_uuid__	"391852024ca711f1898a7ced8d819316"
            how	{"__current_case__": 0, "how_select": "txt", "labels": {"values": [{"id": 29, "src": "hda"}]}, "strict": false}
            input	{"values": [{"id": 20, "src": "hdca"}]}

    • Step 29: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"391852024ca711f1898a7ced8d819316"
            chromInfo	"/tmp/tmpp7vopu41/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": 27, "src": "dce"}]}}, {"__index__": 1, "value": {"values": [{"id": 36, "src": "dce"}]}}]}}

    • Step 30: Unlabelled step (toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cd ../; python _evaluate_expression_.py

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"391852024ca711f1898a7ced8d819316"
            chromInfo	"/tmp/tmpp7vopu41/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": null}, {"__index__": 1, "value": {"values": [{"id": 36, "src": "dce"}]}}]}}

    • Step 31: Unlabelled step (__APPLY_RULES__):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __workflow_invocation_uuid__	"391852024ca711f1898a7ced8d819316"
            input	{"values": [{"id": 22, "src": "hdca"}]}
            rules	{"mapping": [{"columns": [0, 1], "editing": false, "type": "list_identifiers"}], "rules": [{"error": null, "type": "add_column_metadata", "value": "identifier0", "warn": null}, {"error": null, "type": "add_column_metadata", "value": "identifier0", "warn": null}]}

    • Step 32: Unlabelled step (__APPLY_RULES__):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __workflow_invocation_uuid__	"391852024ca711f1898a7ced8d819316"
            input	{"values": [{"id": 23, "src": "hdca"}]}
            rules	{"mapping": [{"columns": [0, 1], "editing": false, "type": "list_identifiers"}], "rules": [{"error": null, "type": "add_column_metadata", "value": "identifier0", "warn": null}, {"error": null, "type": "add_column_metadata", "value": "identifier0", "warn": null}]}

    • Step 33: Unlabelled step (__FILTER_EMPTY_DATASETS__):

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __workflow_invocation_uuid__	"391852024ca711f1898a7ced8d819316"
            input	{"values": [{"id": 39, "src": "dce"}]}
            replacement	{"__class__": "RuntimeValue"}

    • 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

    • Step 40: Unlabelled step:

      • step_state: new

    • Step 41: SemiBin latest:

      • 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: Unlabelled step:

      • step_state: new

    • Step 50: Unlabelled step:

      • step_state: new

    • Step 51: Unlabelled step:

      • step_state: new

    • Step 52: Unlabelled step:

      • step_state: new

    • Step 53: Unlabelled step:

      • step_state: new

    • Step 54: Unlabelled step:

      • step_state: new

    • Step 55: Unlabelled step:

      • step_state: new

    • Step 56: Unlabelled step:

      • step_state: new

    • Step 57: Unlabelled step:

      • step_state: new

    • Step 58: Unlabelled step:

      • step_state: new

    • Step 59: Pool Bins from all samples:

      • step_state: new

    • Step 60: Unlabelled step:

      • step_state: new

    • Step 61: Unlabelled step:

      • step_state: new

    • Step 62: Unlabelled step:

      • step_state: new

    • Step 63: Unlabelled step:

      • step_state: new

    • Step 64: Unlabelled step:

      • step_state: new

    • Step 65: Unlabelled step:

      • step_state: new

    • Step 66: Unlabelled step:

      • step_state: new

    • Step 67: Unlabelled step:

      • step_state: new

    • Step 68: Unlabelled step:

      • step_state: new

    • Step 69: Unlabelled step:

      • step_state: new
  • Other invocation details

    • error_message

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

    • history_id

      • ea214b627d1bb1e9

    • history_state

      • skipped

    • invocation_id

      • ea214b627d1bb1e9

    • invocation_state

      • failed

    • messages

      • [{'details': "Failed to create 1 job(s) for workflow step 34: Error executing tool with id 'FILTER_EMPTY_DATASETS': dict.copy() takes no keyword arguments", 'reason': 'unexpected_failure', 'workflow_step_id': 33}]

    • workflow_id

      • ea214b627d1bb1e9

[SantaMcCloud]

This is the current error cut out of the logs:

galaxy.tools ERROR 2026-05-10 19:35:39,186 [pN:main.1,p:19191,tN:WorkflowRequestMonitor.monitor_thread] Exception caught while attempting to execute tool with id '__FILTER_EMPTY_DATASETS__':
Traceback (most recent call last):
  File "/tmp/tmpp7vopu41/galaxy-dev/lib/galaxy/tools/__init__.py", line 2332, in handle_single_execution
    rval = self._execute(
           ^^^^^^^^^^^^^^
  File "/tmp/tmpp7vopu41/galaxy-dev/lib/galaxy/tools/__init__.py", line 2468, in _execute
    return self.tool_action.execute(
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpp7vopu41/galaxy-dev/lib/galaxy/tools/actions/model_operations.py", line 121, in execute
    self._produce_outputs(
  File "/tmp/tmpp7vopu41/galaxy-dev/lib/galaxy/tools/actions/model_operations.py", line 160, in _produce_outputs
    tool.produce_outputs(
  File "/tmp/tmpp7vopu41/galaxy-dev/lib/galaxy/tools/__init__.py", line 4148, in produce_outputs
    new_elements = self._get_new_elements(
                   ^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/tmpp7vopu41/galaxy-dev/lib/galaxy/tools/__init__.py", line 4097, in _get_new_elements
    new_elements[element_identifier] = replacement_dataset.copy(
                                       ^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: dict.copy() takes no keyword arguments
galaxy.tools.execute WARNING 2026-05-10 19:35:39,187 [pN:main.1,p:19191,tN:WorkflowRequestMonitor.monitor_thread] There was a failure executing a job for tool [__FILTER_EMPTY_DATASETS__] - Error executing tool with id '__FILTER_EMPTY_DATASETS__': dict.copy() takes no keyword arguments

Not sure why it does fail since testing it manually there is no such error and the WF runs without any problem on .EU. The only difference is that her this tool is downgraded from 1.1.0 to 1.0.0 this might be the problem but im not 100% just want to point it out that i did read this on the logs.

ping @paulzierep for updateing you!