Updating workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6 from 0.10.2 to 0.10.3 by gxydevbot · Pull Request #915 · galaxyproject/iwc

gxydevbot · 2025-07-14T04:47:44Z

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 I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated: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 · 2025-07-14T05:00:30Z

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": "1.5c3"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "3c7"}], "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

…0.10.2 to 0.10.3

gxydevbot · 2025-08-11T04:53:33Z

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

github-actions · 2025-08-11T05:08:39Z

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__	`"0c79c1fc767111f081dd7c1e52ada28f"`
chromInfo	`"/tmp/tmp61ewz8nd/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__	`"0c79c1fc767111f081dd7c1e52ada28f"`
chromInfo	`"/tmp/tmp61ewz8nd/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+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is queued

Command Line:

ln -f -s '/tmp/tmp61ewz8nd/files/f/3/c/dataset_f3ce6f82-e38e-4b07-8822-c268a356b38b.dat' reference.fa && minimap2 -x asm5    --q-occ-frac 0.01       -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmp61ewz8nd/files/e/6/3/dataset_e63f1db1-6e37-4d0c-9e5d-bc532f027c99.dat' > '/tmp/tmp61ewz8nd/job_working_directory/000/9/outputs/dataset_66782f07-aebd-473e-888a-60ad6fffd7f2.dat'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
__workflow_invocation_uuid__	`"0c79c1fc767111f081dd7c1e52ada28f"`
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/tmp61ewz8nd/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/tmp61ewz8nd/files/f/3/c/dataset_f3ce6f82-e38e-4b07-8822-c268a356b38b.dat' > split.fasta

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0c79c1fc767111f081dd7c1e52ada28f"`
chromInfo	`"/tmp/tmp61ewz8nd/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__	`"0c79c1fc767111f081dd7c1e52ada28f"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmp61ewz8nd/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": "1.5c3"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "3c7"}], "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__	`"0c79c1fc767111f081dd7c1e52ada28f"`
chromInfo	`"/tmp/tmp61ewz8nd/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__	`"0c79c1fc767111f081dd7c1e52ada28f"`
chromInfo	`"/tmp/tmp61ewz8nd/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__	`"0c79c1fc767111f081dd7c1e52ada28f"`
chromInfo	`"/tmp/tmp61ewz8nd/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__	`"0c79c1fc767111f081dd7c1e52ada28f"`
chromInfo	`"/tmp/tmp61ewz8nd/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+galaxy2:

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__	`"0c79c1fc767111f081dd7c1e52ada28f"`
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/tmp61ewz8nd/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__	`"0c79c1fc767111f081dd7c1e52ada28f"`
chromInfo	`"/tmp/tmp61ewz8nd/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__	`"0c79c1fc767111f081dd7c1e52ada28f"`
chromInfo	`"/tmp/tmp61ewz8nd/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__	`"0c79c1fc767111f081dd7c1e52ada28f"`
chromInfo	`"/tmp/tmp61ewz8nd/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__	`"0c79c1fc767111f081dd7c1e52ada28f"`
chromInfo	`"/tmp/tmp61ewz8nd/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
  - 6b815c8179b16d99
- history_state
  - ok
- invocation_id
  - 6b815c8179b16d99
- invocation_state
  - failed
- workflow_id
  - 71a6c7399b1700c5

Updating workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6 from …

ce14bc0

…0.10.2 to 0.10.3

gxydevbot force-pushed the workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6 branch from 9988751 to ce14bc0 Compare August 11, 2025 04:53

gxydevbot changed the title ~~Updating workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6 from 0.10.2 to 0.10.3~~ Updating workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6 from 0.10.2 to 0.10.3 Aug 11, 2025

remove runtime parameters

81b7f06

Delphine-L approved these changes Aug 25, 2025

View reviewed changes

Delphine-L merged commit a01161f into galaxyproject:main Aug 25, 2025
7 checks passed

gxydevbot deleted the workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6 branch September 29, 2025 04:27

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Updating workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6 from 0.10.2 to 0.10.3 #915

Updating workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6 from 0.10.2 to 0.10.3 #915
Delphine-L merged 2 commits intogalaxyproject:mainfrom
planemo-autoupdate:workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6

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gxydevbot commented Jul 14, 2025

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github-actions bot commented Aug 11, 2025

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Test Summary

Workflow invocation details

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