workflow import failed (Cannot add dummy datasets)

[bernt-matthias]

Imported this workflow: https://raw.githubusercontent.com/galaxyproject/training-material/master/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/workflows/rna-seq-counts-to-genes.ga

On import there were messages that newer versions are used, and one parameter had no default (therefore I set it in the workflow run form).

When executing it I get the following box in the UI (no messages in the log):

The server could not complete the request. Please contact the Galaxy Team if this error persists. "Tool join1 missing. Cannot add dummy datasets."

{
    "new_history_name": null,
    "history_id": "b674da18ed29f393",
    "resource_params": {},
    "replacement_params": {},
    "parameters": {
        "0": {
            "input": {
                "values": [
                    {
                        "id": "f5b226c544b888ef",
                        "hid": 3,
                        "name": "seqdata",
                        "tags": [],
                        "src": "hda",
                        "keep": false
                    }
                ],
                "batch": false
            }
        },
        "1": {
            "input": {
                "values": [
                    {
                        "id": "dcb2c6ed117dc88a",
                        "hid": 5,
                        "name": "factordata",
                        "tags": [],
                        "src": "hda",
                        "keep": false
                    }
                ],
                "batch": false
            }
        },
        "2": {
            "input": {
                "values": [
                    {
                        "id": "6a98125571fbc10b",
                        "hid": 9,
                        "name": "limma",
                        "src": "hdca",
                        "tags": []
                    }
                ],
                "batch": false
            }
        },
        "3": {
            "input": {
                "values": [
                    {
                        "id": "99cb541a5db9e488",
                        "hid": 4,
                        "name": "mouse_hallmark_sets",
                        "tags": [],
                        "src": "hda",
                        "keep": false
                    }
                ],
                "batch": false
            }
        },
        "4": {
            "input": {
                "values": [
                    {
                        "id": "f6ad4c9cf784dead",
                        "hid": 6,
                        "name": "limma-voom_filtered_counts",
                        "tags": [],
                        "src": "hda",
                        "keep": false
                    }
                ],
                "batch": false
            }
        },
        "5": {
            "cond": "bool(c8<0.01) and bool(abs(c4)>0.58)",
            "round": "no"
        },
        "6": {
            "columnList": "c1,c6",
            "delimiter": "T"
        },
        "7": {
            "complement": "--complement",
            "delimiter": "",
            "cut_type_options|cut_element": "-f",
            "cut_type_options|list": ""
        },
        "8": {
            "complement": "",
            "delimiter": "",
            "cut_type_options|cut_element": "-f",
            "cut_type_options|list": ""
        },
        "9": {
            "field1": "1",
            "field2": "1",
            "unmatched": "",
            "partial": "",
            "fill_empty_columns|fill_empty_columns_switch": "no_fill",
            "header": ""
        },
        "10": {
            "header": "1",
            "sortkeys_0|column": "2",
            "sortkeys_0|order": "r",
            "sortkeys_0|style": "n",
            "unique": "false",
            "ignore_case": "false"
        },
        "11": {
            "input|format": "matrix",
            "input|fact|ffile": "yes",
            "rep_contrast_0|contrast": "basalpregnant-basallactate",
            "rep_contrast_1|contrast": "luminalpregnant-luminallactate",
            "species": "mouse",
            "base_methods": [
                "camera",
                "safe",
                "gage",
                "zscore",
                "gsva",
                "globaltest",
                "ora",
                "ssgsea",
                "padog",
                "plage",
                "fry"
            ],
            "msigdb|msigdb_gsets": [
                "h"
            ],
            "keggdb|keggdb_gsets": [
                "keggmet",
                "keggsig"
            ],
            "keggdb|kegg_updated": "false",
            "gsdb|gsdb_gsets": null,
            "advanced|display_top": "5",
            "advanced|min_size": "2",
            "advanced|fdr_cutoff": "0.05",
            "advanced|combine_method": "wilkinson",
            "advanced|sort_method": "med.rank",
            "advanced|rscriptOpt": "false",
            "advanced|rdaOpt": "false",
            "non_commercial_use": "true"
        },
        "12": {
            "columnList": "c1,c9",
            "delimiter": "T"
        },
        "13": {
            "columnList": "c1,c11",
            "delimiter": "T"
        },
        "14": {
            "header": "true",
            "min_size": "15",
            "max_size": "500",
            "n_perm": "1000",
            "plot_opt": "true",
            "top_num": "10",
            "rda_opt": "false"
        },
        "15": {
            "categorySource|catSource": "getgo",
            "categorySource|genome": "mm10",
            "categorySource|gene_id": "knownGene",
            "categorySource|fetchcats": [
                "GO:BP"
            ],
            "methods|wallenius": "true",
            "methods|hypergeometric": "false",
            "methods|repcnt": "0",
            "adv|p_adj_method": "BH",
            "adv|use_genes_without_cat": "false",
            "out|topgo_plot": "true",
            "out|make_plots": "false",
            "out|cat_genes": "true",
            "out|rdata_out": "false"
        }
    },
    "parameters_normalized": true,
    "batch": true
}

[jmchilton]

This workflow in its latest incarnation worked fine for me on EU.

[bernt-matthias]

I still get a note on a missing value

No value found for 'Input Contrast information from file?'. Using default: 'no'.
Input Contrast information from file?
No

Maybe I should update to 20.09 soon.