IWC Workflow Review Summary

Ran galaxy-workflow-validate and galaxy-workflow-clean-stale-state against the full IWC repository (111 native .ga workflows, 509 unique tools).

Tool Cache

Initial --populate-cache via ToolShed API cached 499/509 tools. 10 failed with HTTP 500. All 10 were resolved with galaxy-tool-cache add-local using source XML from the Galaxy repo or GitHub. Final result: 509/509 cached, 0 skips.

ToolShed API failures (all resolved via add-local)

Stock Galaxy tools (XML in Galaxy repo):

CONVERTER_gz_to_uncompressed 1.0.0 — lib/galaxy/datatypes/converters/gz_to_uncompressed.xml
CONVERTER_uncompressed_to_gz 1.16+galaxy0 — lib/galaxy/datatypes/converters/uncompressed_to_gz.xml
Convert characters1 1.0.0 / 1.0.1 — tools/filters/convert_characters.xml
Remove beginning1 1.0.0 — tools/filters/remove_beginning.xml
Show beginning1 1.0.2 — tools/filters/headWrapper.xml
Show tail1 1.0.1 — tools/filters/tailWrapper.xml
__RELABEL_FROM_FILE__ 1.0.0 — lib/galaxy/tools/relabel_from_file.xml
param_value_from_file 0.1.0 — tools/expression_tools/parse_values_from_file.xml

ToolShed tools (XML from GitHub):

map_param_value 0.2.0 — tools-iuc/tools/map_param_value/
pick_value 0.2.0 — tools-iuc/tools/pick_value/
cufflinks 2.2.1.4 — tools-iuc/tool_collections/cufflinks/cufflinks/ (needs adjacent macros)
EMBOSS: maskseq51 5.0.0 — tools-iuc/tools/emboss_5/ (needs adjacent macros)
rdock_sort_filter 2013.1-0+galaxy0 — bgruening/galaxytools/chemicaltoolbox/rdock/ (needs adjacent macros)

Root causes:

Stock tools: ToolShed API doesn’t serve stock Galaxy tools (they have no ToolShed repo)
Expression tools (map_param_value, pick_value): tracked in #22007
cufflinks: hidden_data param type not handled by parameters/factory.py
EMBOSS/rdock: unknown — likely similar parameter model factory gaps

Validation Report

Workflows: 111 | Steps: 2074 OK, 64 FAIL, 0 SKIP, 0 ERROR

Failure categories

saveLog — multiqc (14 workflows, 16 steps) Stale key saveLog in multiqc v1.24.1+galaxy0, v1.27+galaxy3, v1.33+galaxy0.

Workflow	Step	Version
Assembly-Hifi-Trio-phasing-VGP5	25	1.27+galaxy3
atacseq	30	1.24.1+galaxy0
consensus-peaks-atac-cutandrun	24	1.33+galaxy0
consensus-peaks-chip-pe	22	1.33+galaxy0
consensus-peaks-chip-sr	22	1.33+galaxy0
cutandrun	14	1.33+galaxy0
pe-artic-variation	25	1.27+galaxy3
pox-virus-half-genome	34, 36, 45	1.27+galaxy3
scrna-seq-fastq-to-matrix-10x-cellplex	8.6	1.33+galaxy0
scrna-seq-fastq-to-matrix-10x-v3	6	1.33+galaxy0
se-wgs-variation	5	1.27+galaxy3

trim_front2/trim_tail2 — fastp (4 workflows) Stale keys in fastp/0.23.2+galaxy0 paired-end trimming options.

Workflow	Step
Generic-variation-analysis-on-WGS-PE-data	3
pe-wgs-variation	2
WGS-PE-variant-calling-in-haploid-system	3

images — imagemagick_image_montage (2 workflows, 4 steps) Stale key images in imagemagick v7.1.2-2+galaxy1.

Workflow	Steps
Assembly-Hifi-HiC-phasing-VGP4	70, 73
Scaffolding-HiC-VGP8	49, 65

__workflow_invocation_uuid__ — clinicalmp-verification (1 workflow, 20 steps) Every step in clinicalmp-verification.ga carries a stale __workflow_invocation_uuid__ key.

__identifier__ — various tools (3 workflows, ~10 steps) Stale __identifier__ keys (e.g. input|__identifier__, dadaF|__identifier__).

Workflow	Tools affected
dada2_paired	dada2_mergePairs
MAGs-binning-evaluation	concoct_*, bowtie2, samtools_sort, metabat2
sra-manifest-to-concatenated-fastqs	Cut1
se-wgs-variation	picard_MarkDuplicates

Tool-specific stale keys (5 workflows)

Workflow	Tool	Stale keys
segmentation-and-counting	ip_filter_standard, ip_threshold	filter_type, radius, block_size, dark_bg
Genome-assembly-with-Flye	flye, quast, fasta-stats	i, m, mode, no_trestle, plasmids, al, circos, etc. (16 keys)
Assembly-polishing-with-long-reads	racon (×4)	e, f, g, m, q, u, w, x (32 keys)
mfassignr	mfassignr_*	cut, SN, abundance_score_threshold, etc. (9 keys)
Functional_annotation_of_protein_sequences	interproscan	licensed\|applications_licensed

Other

Workflow	Tool	Stale key
ont-artic-variation	ivar_trim/1.3.1+galaxy2	conflicting tool states for `filter_by`
pe-artic-variation	ivar_trim/1.4.4+galaxy0	`min_len`
pox-virus-half-genome	ivar_trim/1.4.4+galaxy1	`min_len`
Scaffolding-HiC-VGP8	tp_sort_header_tool	`ignore_case` (×2)
clinicalmp-verification	uniprotxml_downloader	`format`

Stale State Report

Workflows: 111 | 124 stale key(s) across 25 workflow(s), 86 clean, 0 errors

Summary

86/111 workflows are clean — all steps validate, no stale state.
25 workflows have 124 stale keys across ~50 steps.
0 skips — all 509 tools cached (10 via add-local fallback).
Top offenders by frequency:
- saveLog in multiqc — 16 steps across 14 workflows
- __workflow_invocation_uuid__ — 20 steps in clinicalmp-verification alone
- racon stale params — 32 keys across 4 steps in one workflow
The __identifier__ and __workflow_invocation_uuid__ patterns suggest systematic issues with how Galaxy serializes certain runtime values into saved workflow state.