Updating workflows/scRNAseq/scanpy-clustering from 0.1 to 0.2 #656

gxydevbot · 2025-01-27T05:35:56Z

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 I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated: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/anndata_import/anndata_import/0.10.9+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.10.9+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy3
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.10.2+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.10.2+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.10.2+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.10.2+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.10.2+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.10.2+galaxy2

The workflow release number has been updated from 0.1 to 0.2.

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 · 2025-01-27T05:47:39Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ Preprocessing-and-Clustering-of-single-cell-RNA-seq-data-with-Scanpy.ga_0

Execution Problem:

Final state of invocation 103dbd8a42bfad25 is [failed]. Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because step 53 requires a dataset, but dataset entered a failed state.

Steps

Step 1: Minimum number of cells expressed:
- step_state: scheduled
Step 2: Barcodes:
- step_state: scheduled
Step 11: Louvain resolution:
- step_state: scheduled
Step 12: Manually annotate celltypes?:
- step_state: scheduled
Step 13: Annotate louvain clusters with these cell types:
- step_state: scheduled

Step 14: 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__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 1, "param_type": "integer", "pick_from": [{"__index__": 0, "value": "3"}, {"__index__": 1, "value": "3"}]}}`

Step 15: Anndata from 10x v2 or earlier:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir mtx && cp '/tmp/tmp1rjsjs18/files/f/0/7/dataset_f072c050-a1b4-4a0d-9a44-cd4de5c9eb86.dat' 'mtx/matrix.mtx' && cp '/tmp/tmp1rjsjs18/files/e/2/f/dataset_e2fc0e42-f893-4b08-ba55-1da7fe589982.dat' 'mtx/genes.tsv' && cp '/tmp/tmp1rjsjs18/files/e/c/d/dataset_ecd30058-65c3-4a1f-9073-e1cba7bff700.dat' 'mtx/barcodes.tsv' &&   cat '/tmp/tmp1rjsjs18/job_working_directory/000/5/configs/tmpmsg2lltc' && python '/tmp/tmp1rjsjs18/job_working_directory/000/5/configs/tmpmsg2lltc'

Exit Code:

```
0
```

Standard Output:

import anndata as ad
    
    
import scanpy as sc
adata = sc.read_10x_mtx(
    'mtx',
    var_names='gene_symbols',
    make_unique=True,
    cache=False,
    gex_only=True)

adata.write('anndata.h5ad', compression='gzip')
print(adata)
AnnData object with n_obs × n_vars = 2700 × 32738
    var: 'gene_ids'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
in	`{"__current_case__": 3, "adata_format": "mtx", "matrix": {"values": [{"id": 3, "src": "hda"}]}, "tenx": {"__current_case__": 1, "barcodes": {"values": [{"id": 1, "src": "hda"}]}, "genes": {"values": [{"id": 2, "src": "hda"}]}, "gex_only": true, "make_unique": true, "use": "legacy_10x", "var_names": "gene_symbols"}}`

Step 16: Map and switch the input CellRager version:

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__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 3, "input_param": true, "mappings": [{"__index__": 0, "from": true, "to": "False"}, {"__index__": 1, "from": false, "to": "True"}], "type": "boolean"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 0, "on_unmapped": "input"}`

Step 17: 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__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 1, "param_type": "integer", "pick_from": [{"__index__": 0, "value": "200"}, {"__index__": 1, "value": "200"}]}}`

Step 18: 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__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 1, "param_type": "integer", "pick_from": [{"__index__": 0, "value": "2500"}, {"__index__": 1, "value": "2500"}]}}`

Step 19: 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__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 1, "param_type": "integer", "pick_from": [{"__index__": 0, "value": "10"}, {"__index__": 1, "value": null}]}}`

Step 20: 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__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 2, "param_type": "float", "pick_from": [{"__index__": 0, "value": "0.45"}, {"__index__": 1, "value": "1.0"}]}}`

Step 3: Genes:
- step_state: scheduled

Step 21: Anndata from 10x V3 or later:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
in	`{"__current_case__": 3, "adata_format": "mtx", "matrix": {"values": [{"id": 3, "src": "hda"}]}, "tenx": {"__current_case__": 2, "barcodes": {"values": [{"id": 1, "src": "hda"}]}, "features": {"values": [{"id": 2, "src": "hda"}]}, "gex_only": true, "make_unique": true, "use": "v3_10x", "var_names": "gene_symbols"}}`

Step 22: Choose the Anndata:

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__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/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": 11, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 5, "src": "hda"}]}}]}}`

Step 23: Filter genes by cells expressed:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmp1rjsjs18/files/5/8/c/dataset_58c1593f-543e-4c09-a159-d3fbccfa4d8d.dat' 'anndata.h5ad' && cat '/tmp/tmp1rjsjs18/job_working_directory/000/13/configs/tmp9re1swej' > 'XXXX' && python '/tmp/tmp1rjsjs18/job_working_directory/000/13/configs/tmp9re1swej' >> 'XXXX' && ls . >> 'XXXX' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g"  | sed -r 's|^\s*(.*):\s(.*)|[\1]\n-    \2|g' | sed 's|, |\n-    |g'

Exit Code:

```
0
```

Standard Output:

[n_obs × n_vars]
-    2700 × 13714
[var]
-    gene_ids
-    n_cells

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 1, "filter": {"__current_case__": 2, "filter": "min_cells", "min_cells": "3"}, "method": "pp.filter_genes"}`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp1rjsjs18/job_working_directory/000/14/configs/tmpnc26r11y' && python '/tmp/tmp1rjsjs18/job_working_directory/000/14/configs/tmpnc26r11y'

Exit Code:

```
0
```

Standard Output:

import anndata as ad
    
    
import pandas as pd
from scipy import io

pd.options.display.precision = 15

adata = ad.read_h5ad('/tmp/tmp1rjsjs18/files/5/8/c/dataset_58c1593f-543e-4c09-a159-d3fbccfa4d8d.dat')

with open('/tmp/tmp1rjsjs18/job_working_directory/000/14/outputs/dataset_fb56c575-010e-486e-aef7-b59bca5f1ede.dat', 'w', encoding="utf-8") as f:
    print(adata, file=f)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inspect	`{"__current_case__": 0, "info": "general"}`

Step 25: Flag Mitochondrial genes:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

cat '/tmp/tmp1rjsjs18/job_working_directory/000/15/configs/tmpkbabxvm1' && python '/tmp/tmp1rjsjs18/job_working_directory/000/15/configs/tmpkbabxvm1'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
manipulate	`{"__current_case__": 5, "function": "flag_genes", "gene_flags": [{"__index__": 0, "col_in": "", "col_out": null, "startswith": "MT-"}]}`

Step 26: Calculate quality metrics:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 0, "expr_type": "counts", "layer": "", "log1p": true, "method": "pp.calculate_qc_metrics", "percent_top": "", "qc_vars": "mito", "use_raw": false, "var_type": "genes"}`

Step 27: Scatter plot n_genes vs pct_mito:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format	`"png"`
method	`{"__current_case__": 0, "groups": "", "method": "pl.scatter", "plot": {"color_map": null, "components": [], "frameon": true, "legend_fontsize": null, "legend_fontweight": "normal", "legend_loc": "none", "palette": null, "projection": "2d", "size": null, "title": ""}, "sort_order": true, "type": {"__current_case__": 0, "color": "", "layers": {"__current_case__": 1, "use_layers": "false"}, "log": false, "type": "xy", "x": "n_genes_by_counts", "y": "pct_counts_mito"}, "use_raw": false}`

Step 28: Scatter plot n_counts vs n_genes:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format	`"png"`
method	`{"__current_case__": 0, "groups": "", "method": "pl.scatter", "plot": {"color_map": null, "components": [], "frameon": true, "legend_fontsize": null, "legend_fontweight": "normal", "legend_loc": "none", "palette": null, "projection": "2d", "size": null, "title": ""}, "sort_order": true, "type": {"__current_case__": 0, "color": "", "layers": {"__current_case__": 1, "use_layers": "false"}, "log": false, "type": "xy", "x": "total_counts", "y": "n_genes_by_counts"}, "use_raw": false}`

Step 29: Violin plot n_genes, n_counts, pct_mito:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format	`"png"`
method	{"__current_case__": 4, "groupby": "", "key_variables": {"__current_case__": 2, "keys": "n_genes_by_counts, total_counts, pct_counts_mito", "type": "custom"}, "layer": "", "log": false, "method": "pl.violin", "rotation": null, "seaborn_violinplot": {"bw_adjust": "1.0", "bw_method": "scott", "color": null, "linewidth": "0.0", "orient": null, "saturation": "0.75"}, "use_raw": false, "violin_plot": {"multi_panel": {"__current_case__": 1, "multi_panel": "True"}, "stripplot": {"__current_case__": 0, "jitter": {"__current_case__": 0, "jitter": "True", "size": "1.0"}, "stripplot": "True"}}, "xlabel": ""}

Step 30: Filter cells by min genes expressed:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 0, "filter": {"__current_case__": 2, "filter": "min_genes", "min_genes": "200"}, "method": "pp.filter_cells"}`

Step 4: Matrix:
- step_state: scheduled

Step 31: Filter cells by max genes expressed:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 0, "filter": {"__current_case__": 3, "filter": "max_genes", "max_genes": "2500"}, "method": "pp.filter_cells"}`

Step 32: Filter cells by percentage of mito genes:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
manipulate	`{"__current_case__": 0, "batch_key": "batch", "function": "concatenate", "index_unique": "-", "join": "inner", "other_adatas": null, "uns_merge": "None"}`

Step 33: Normalize by target sum:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 0, "exclude_highly_expressed": {"__current_case__": 1, "exclude_highly_expressed": "False"}, "key_added": "norm", "layer": "", "method": "pp.normalize_total", "target_sum": "10000.0"}`

Step 34: Logarithmize:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 6, "base": null, "layer": "", "method": "pp.log1p", "obsm": ""}`

Step 35: Freeze raw attribute:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
manipulate	`{"__current_case__": 12, "function": "save_raw"}`

Step 36: Annotate highly variable genes:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 4, "batch_key": "", "flavor": {"__current_case__": 0, "flavor": "seurat", "max_disp": null, "max_mean": "3.0", "min_disp": "0.5", "min_mean": "0.0125"}, "layer": "", "method": "pp.highly_variable_genes", "n_bins": "20", "subset": false}`

Step 37: toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
manipulate	`{"__current_case__": 0, "batch_key": "batch", "function": "concatenate", "index_unique": "-", "join": "inner", "other_adatas": null, "uns_merge": "None"}`

Step 38: Plot highly variable:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format	`"png"`
method	`{"__current_case__": 9, "highly_variable_genes": true, "log": false, "method": "pl.highly_variable_genes"}`

Step 39: Regress out:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 0, "keys": "total_counts, pct_counts_mito", "layer": "", "method": "pp.regress_out"}`

Step 40: Scale data:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 7, "layer": "", "mask_obs": "", "max_value": "10.0", "method": "pp.scale", "obsm": "", "zero_center": true}`

Step 5: Input is from Cell Ranger v2 or earlier versions:
- step_state: scheduled

Step 41: Compute PCA:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 2, "dtype": "float32", "layer": "", "mask_var": "", "method": "pp.pca", "n_comps": "50", "pca": {"__current_case__": 1, "chunked": "False", "random_state": "0", "svd_solver": null, "zero_center": true}}`

Step 42: Compute Neighborhood graph:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 1, "key_added": "", "knn": true, "method": "pp.neighbors", "metric": "euclidean", "n_neighbors": "10", "n_pcs": "10", "pp_neighbors_method": "umap", "random_state": "0", "use_rep": ""}`

Step 43: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format	`"png"`
method	`{"__current_case__": 12, "components": "1,2,3", "include_lowest": true, "method": "pl.pca_loadings", "n_points": null}`

Step 44: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format	`"png"`
method	{"__current_case__": 14, "add_outline": false, "color": "", "groups": "", "matplotlib_pyplot_scatter": {"alpha": null, "edgecolors": null, "linewidths": "0.0", "vmax": null, "vmin": null}, "method": "pl.pca_overview", "outline_color_border": null, "outline_color_gap": null, "outline_width_border": "0.3", "outline_width_gap": "0.05", "plot": {"color_map": null, "components": [{"__index__": 0, "axis1": "1", "axis2": "2"}, {"__index__": 1, "axis1": "2", "axis2": "3"}], "frameon": true, "hspace": "0.25", "legend_fontsize": null, "legend_fontweight": "normal", "legend_loc": "right margin", "ncols": "2", "palette": null, "projection": "2d", "size": null, "title": "", "wspace": "0.1"}, "sort_order": true, "use_raw": false}

Step 45: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format	`"png"`
method	`{"__current_case__": 13, "log": true, "method": "pl.pca_variance_ratio", "n_pcs": "50"}`

Step 46: Embed using UMAP:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 5, "alpha": "1.0", "gamma": "1.0", "init_pos": "spectral", "maxiter": null, "method": "tl.umap", "min_dist": "0.5", "n_components": "2", "negative_sample_rate": "5", "neighbors_key": "", "random_state": "0", "spread": "1.0"}`

Step 47: Louvain clustering:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 0, "directed": true, "flavor": {"__current_case__": 0, "flavor": "vtraag", "resolution": "0.45"}, "key_added": "louvain", "method": "tl.louvain", "neighbors_key": "", "random_state": "0", "use_weights": false}`

Step 48: UMAP of louvain:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format	`"png"`
method	{"__current_case__": 16, "add_outline": false, "arrows": false, "color": "louvain", "edges": {"__current_case__": 1, "edges": "False"}, "gene_symbols": "", "groups": "", "layer": "", "matplotlib_pyplot_scatter": {"alpha": null, "edgecolors": "face", "linewidths": "0.0", "vmax": null, "vmin": null}, "method": "pl.umap", "outline_color_border": null, "outline_color_gap": null, "outline_width_border": "0.3", "outline_width_gap": "0.05", "plot": {"color_map": null, "components": [], "frameon": true, "hspace": "0.25", "legend_fontsize": null, "legend_fontweight": "normal", "legend_loc": "right margin", "ncols": "2", "palette": null, "projection": "2d", "size": null, "title": "", "wspace": "0.1"}, "sort_order": true, "use_raw": false}

Step 49: Rank genes by Wilcoxon test:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 4, "get_df": {"__current_case__": 0, "get_df_select": "False"}, "groupby": "louvain", "groups": "", "key_added": "", "layer": "", "method": "tl.rank_genes_groups", "n_genes": "100", "ref": {"__current_case__": 0, "rest": "rest"}, "tl_rank_genes_groups_method": {"__current_case__": 1, "corr_method": "benjamini-hochberg", "method": "wilcoxon", "tie_correct": false}, "use_raw": true}`

Step 50: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inspect	`{"__current_case__": 5, "info": "uns", "uns_info": "rank_genes_groups"}`

Step 6: Mitochondrial genes start with pattern:
- step_state: scheduled

Step 51: Inspect clusters:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inspect	`{"__current_case__": 3, "info": "obs"}`

Step 52: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format	`"png"`
method	`{"__current_case__": 24, "fontsize": "8", "gene_symbols": "", "groups": "", "method": "pl.rank_genes_groups", "n_genes": "20", "ncols": "3", "sharey": false}`

Step 53: Unlabelled step:
- step_state: new

Step 54: General information about the final Anndata object:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inspect	`{"__current_case__": 0, "info": "general"}`

Step 55: Select top ranked genes:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"NR==2{gsub(/\\t/,\",\",$0); print}"`
dbkey	`"?"`

Step 56: Count number of clusters:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{print NF}"`
dbkey	`"?"`

Step 57: Select top ranked genes with louvain:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"NR==2{gsub(/\\t/,\",\",$0); print \"louvain,\"$0}"`
dbkey	`"?"`

Step 58: Count number of cells per cluster:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`"15"`
header_in	`true`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`true`
operations	`[{"__index__": 0, "op_column": "1", "op_name": "count"}]`
print_full_line	`false`

Step 59: Unlabelled step:
- step_state: new

Step 60: 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__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 7: Minimum number of genes expressed:
- step_state: scheduled

Step 61: 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__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 62: 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__	`"bac61d72dc7111ef96aa000d3ad4458e"`
chromInfo	`"/tmp/tmp1rjsjs18/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 63: Unlabelled step:
- step_state: new
Step 64: Violin plot of top genes on clusters:
- step_state: new
Step 65: Stacked violin of top genes on clusters:
- step_state: new
Step 66: Dotplot of top genes on clusters:
- step_state: new
Step 67: Heatmap of 20 genes:
- step_state: new
Step 68: UMAP of louvain and top ranked genes:
- step_state: new
Step 8: Maximum number of genes expressed:
- step_state: scheduled
Step 9: Number of neighbours for computing neighborhood graph:
- step_state: scheduled
Step 10: Number of PCs to use for computing neighborhood graph:
- step_state: scheduled

Other invocation details
- error_message
  - Final state of invocation 103dbd8a42bfad25 is [failed]. Failed to run workflow, at least one job is in [error] state.
- history_id
  - 103dbd8a42bfad25
- history_state
  - error
- invocation_id
  - 103dbd8a42bfad25
- invocation_state
  - failed
- messages
  - [{'dependent_workflow_step_id': None, 'hda_id': '3a8dceb8b4b6fa3f', 'reason': 'dataset_failed', 'workflow_step_id': 52}]
- workflow_id
  - 103dbd8a42bfad25

…Scanpy.ga - Replace all Manipulate Anndata tool filtering steps with Scanpy filter - Add complete URL for ORCID

github-actions · 2025-01-29T11:40:49Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ Preprocessing-and-Clustering-of-single-cell-RNA-seq-data-with-Scanpy.ga_0

Execution Problem:

Final state of invocation 5a5e20b5fe519187 is [failed]. Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because step 53 requires a dataset, but dataset entered a failed state.

Steps

Step 1: Matrix:
- step_state: scheduled
Step 2: Genes:
- step_state: scheduled
Step 11: Louvain resolution:
- step_state: scheduled
Step 12: Manually annotate celltypes?:
- step_state: scheduled
Step 13: Annotate louvain clusters with these cell types:
- step_state: scheduled

Step 14: Map and switch the input CellRager version:

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__	`"69aa0488de3511efb9ab00224823ee30"`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
input_param_type	`{"__current_case__": 3, "input_param": true, "mappings": [{"__index__": 0, "from": true, "to": "False"}, {"__index__": 1, "from": false, "to": "True"}], "type": "boolean"}`
output_param_type	`"boolean"`
unmapped	`{"__current_case__": 0, "on_unmapped": "input"}`

Step 15: Anndata from 10x v2 or earlier:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir mtx && cp '/tmp/tmpd4t5srhw/files/0/9/2/dataset_0920d91c-4f8c-4675-8311-df13936b3732.dat' 'mtx/matrix.mtx' && cp '/tmp/tmpd4t5srhw/files/e/6/b/dataset_e6b57f5b-8183-4fae-b229-5253e362e84c.dat' 'mtx/genes.tsv' && cp '/tmp/tmpd4t5srhw/files/1/a/e/dataset_1aee7b83-d26b-48cd-bbe2-c1c05725ab4d.dat' 'mtx/barcodes.tsv' &&   cat '/tmp/tmpd4t5srhw/job_working_directory/000/5/configs/tmpq3dqdsv_' && python '/tmp/tmpd4t5srhw/job_working_directory/000/5/configs/tmpq3dqdsv_'

Exit Code:

```
0
```

Standard Output:

import anndata as ad
    
    
import scanpy as sc
adata = sc.read_10x_mtx(
    'mtx',
    var_names='gene_symbols',
    make_unique=True,
    cache=False,
    gex_only=True)

adata.write('anndata.h5ad', compression='gzip')
print(adata)
AnnData object with n_obs × n_vars = 2700 × 32738
    var: 'gene_ids'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
in	`{"__current_case__": 3, "adata_format": "mtx", "matrix": {"values": [{"id": 3, "src": "hda"}]}, "tenx": {"__current_case__": 1, "barcodes": {"values": [{"id": 1, "src": "hda"}]}, "genes": {"values": [{"id": 2, "src": "hda"}]}, "gex_only": true, "make_unique": true, "use": "legacy_10x", "var_names": "gene_symbols"}}`

Step 16: 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__	`"69aa0488de3511efb9ab00224823ee30"`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 1, "param_type": "integer", "pick_from": [{"__index__": 0, "value": "3"}, {"__index__": 1, "value": "3"}]}}`

Step 17: 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__	`"69aa0488de3511efb9ab00224823ee30"`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 1, "param_type": "integer", "pick_from": [{"__index__": 0, "value": "200"}, {"__index__": 1, "value": "200"}]}}`

Step 18: 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__	`"69aa0488de3511efb9ab00224823ee30"`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 1, "param_type": "integer", "pick_from": [{"__index__": 0, "value": "2500"}, {"__index__": 1, "value": "2500"}]}}`

Step 19: 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__	`"69aa0488de3511efb9ab00224823ee30"`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 1, "param_type": "integer", "pick_from": [{"__index__": 0, "value": "10"}, {"__index__": 1, "value": null}]}}`

Step 20: 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__	`"69aa0488de3511efb9ab00224823ee30"`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 0, "pick_style": "first", "type_cond": {"__current_case__": 2, "param_type": "float", "pick_from": [{"__index__": 0, "value": "0.45"}, {"__index__": 1, "value": "1.0"}]}}`

Step 3: Barcodes:
- step_state: scheduled

Step 21: Anndata from 10x V3 or later:

step_state: scheduled

Jobs

Job 1:

Job state is skipped

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
in	`{"__current_case__": 3, "adata_format": "mtx", "matrix": {"values": [{"id": 3, "src": "hda"}]}, "tenx": {"__current_case__": 2, "barcodes": {"values": [{"id": 1, "src": "hda"}]}, "features": {"values": [{"id": 2, "src": "hda"}]}, "gex_only": true, "make_unique": true, "use": "v3_10x", "var_names": "gene_symbols"}}`

Step 22: Choose the Anndata:

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__	`"69aa0488de3511efb9ab00224823ee30"`
chromInfo	`"/tmp/tmpd4t5srhw/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": 11, "src": "hda"}]}}, {"__index__": 1, "value": {"values": [{"id": 5, "src": "hda"}]}}]}}`

Step 23: Filter genes by cells expressed:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cp '/tmp/tmpd4t5srhw/files/f/2/a/dataset_f2a9e1bf-6801-4e5f-87e7-cac8b9caf1c5.dat' 'anndata.h5ad' && cat '/tmp/tmpd4t5srhw/job_working_directory/000/13/configs/tmpsmnl0rq4' > 'XXXX' && python '/tmp/tmpd4t5srhw/job_working_directory/000/13/configs/tmpsmnl0rq4' >> 'XXXX' && ls . >> 'XXXX' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g"  | sed -r 's|^\s*(.*):\s(.*)|[\1]\n-    \2|g' | sed 's|, |\n-    |g'

Exit Code:

```
0
```

Standard Output:

[n_obs × n_vars]
-    2700 × 13714
[var]
-    gene_ids
-    n_cells

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 1, "filter": {"__current_case__": 2, "filter": "min_cells", "min_cells": "3"}, "method": "pp.filter_genes"}`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpd4t5srhw/job_working_directory/000/14/configs/tmph9t5xh7z' && python '/tmp/tmpd4t5srhw/job_working_directory/000/14/configs/tmph9t5xh7z'

Exit Code:

```
0
```

Standard Output:

import anndata as ad
    
    
import pandas as pd
from scipy import io

pd.options.display.precision = 15

adata = ad.read_h5ad('/tmp/tmpd4t5srhw/files/f/2/a/dataset_f2a9e1bf-6801-4e5f-87e7-cac8b9caf1c5.dat')

with open('/tmp/tmpd4t5srhw/job_working_directory/000/14/outputs/dataset_ebc677a8-43d9-44da-852c-17055860001d.dat', 'w', encoding="utf-8") as f:
    print(adata, file=f)

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inspect	`{"__current_case__": 0, "info": "general"}`

Step 25: Flag Mitochondrial genes:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

cat '/tmp/tmpd4t5srhw/job_working_directory/000/15/configs/tmp_rl60_am' && python '/tmp/tmpd4t5srhw/job_working_directory/000/15/configs/tmp_rl60_am'

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
manipulate	`{"__current_case__": 5, "function": "flag_genes", "gene_flags": [{"__index__": 0, "col_in": "", "col_out": null, "startswith": "MT-"}]}`

Step 26: Calculate quality metrics:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 0, "expr_type": "counts", "layer": "", "log1p": true, "method": "pp.calculate_qc_metrics", "percent_top": "", "qc_vars": "mito", "use_raw": false, "var_type": "genes"}`

Step 27: Scatter plot n_genes vs pct_mito:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format	`"png"`
method	`{"__current_case__": 0, "groups": "", "method": "pl.scatter", "plot": {"color_map": null, "components": [], "frameon": true, "legend_fontsize": null, "legend_fontweight": "normal", "legend_loc": "none", "palette": null, "projection": "2d", "size": null, "title": ""}, "sort_order": true, "type": {"__current_case__": 0, "color": "", "layers": {"__current_case__": 1, "use_layers": "false"}, "log": false, "type": "xy", "x": "n_genes_by_counts", "y": "pct_counts_mito"}, "use_raw": false}`

Step 28: Scatter plot n_counts vs n_genes:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format	`"png"`
method	`{"__current_case__": 0, "groups": "", "method": "pl.scatter", "plot": {"color_map": null, "components": [], "frameon": true, "legend_fontsize": null, "legend_fontweight": "normal", "legend_loc": "none", "palette": null, "projection": "2d", "size": null, "title": ""}, "sort_order": true, "type": {"__current_case__": 0, "color": "", "layers": {"__current_case__": 1, "use_layers": "false"}, "log": false, "type": "xy", "x": "total_counts", "y": "n_genes_by_counts"}, "use_raw": false}`

Step 29: Violin plot n_genes, n_counts, pct_mito:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format	`"png"`
method	{"__current_case__": 4, "groupby": "", "key_variables": {"__current_case__": 2, "keys": "n_genes_by_counts, total_counts, pct_counts_mito", "type": "custom"}, "layer": "", "log": false, "method": "pl.violin", "rotation": null, "seaborn_violinplot": {"bw_adjust": "1.0", "bw_method": "scott", "color": null, "linewidth": "0.0", "orient": null, "saturation": "0.75"}, "use_raw": false, "violin_plot": {"multi_panel": {"__current_case__": 1, "multi_panel": "True"}, "stripplot": {"__current_case__": 0, "jitter": {"__current_case__": 0, "jitter": "True", "size": "1.0"}, "stripplot": "True"}}, "xlabel": ""}

Step 30: Filter cells by min genes expressed:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 0, "filter": {"__current_case__": 2, "filter": "min_genes", "min_genes": "200"}, "method": "pp.filter_cells"}`

Step 4: Input is from Cell Ranger v2 or earlier versions:
- step_state: scheduled

Step 31: Filter cells by max genes expressed:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 0, "filter": {"__current_case__": 3, "filter": "max_genes", "max_genes": "2500"}, "method": "pp.filter_cells"}`

Step 32: Filter cells by percentage of mito genes:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 2, "filter": {"__current_case__": 0, "filter": "key", "filter_key": {"__current_case__": 0, "filter": "less", "type": "number", "value": "5.0"}, "key": "pct_counts_mito"}, "method": "filter_any", "var_obs": "obs"}`

Step 33: Normalize by target sum:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 0, "exclude_highly_expressed": {"__current_case__": 1, "exclude_highly_expressed": "False"}, "key_added": "norm", "layer": "", "method": "pp.normalize_total", "target_sum": "10000.0"}`

Step 34: Logarithmize:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 6, "base": null, "layer": "", "method": "pp.log1p", "obsm": ""}`

Step 35: Freeze raw attribute:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
manipulate	`{"__current_case__": 12, "function": "save_raw"}`

Step 36: Annotate highly variable genes:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 4, "batch_key": "", "flavor": {"__current_case__": 0, "flavor": "seurat", "max_disp": null, "max_mean": "3.0", "min_disp": "0.5", "min_mean": "0.0125"}, "layer": "", "method": "pp.highly_variable_genes", "n_bins": "20", "subset": false}`

Step 37: Filter highly variable genes:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 2, "filter": {"__current_case__": 0, "filter": "key", "filter_key": {"__current_case__": 2, "type": "boolean", "value": true}, "key": "highly_variable"}, "method": "filter_any", "var_obs": "var"}`

Step 38: Plot highly variable:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format	`"png"`
method	`{"__current_case__": 9, "highly_variable_genes": true, "log": false, "method": "pl.highly_variable_genes"}`

Step 39: Regress out:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 0, "keys": "total_counts, pct_counts_mito", "layer": "", "method": "pp.regress_out"}`

Step 40: Scale data:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 7, "layer": "", "mask_obs": "", "max_value": "10.0", "method": "pp.scale", "obsm": "", "zero_center": true}`

Step 5: Minimum number of cells expressed:
- step_state: scheduled

Step 41: Compute PCA:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 2, "dtype": "float32", "layer": "", "mask_var": "", "method": "pp.pca", "n_comps": "50", "pca": {"__current_case__": 1, "chunked": "False", "random_state": "0", "svd_solver": null, "zero_center": true}}`

Step 42: Compute Neighborhood graph:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 1, "key_added": "", "knn": true, "method": "pp.neighbors", "metric": "euclidean", "n_neighbors": "10", "n_pcs": "10", "pp_neighbors_method": "umap", "random_state": "0", "use_rep": ""}`

Step 43: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format	`"png"`
method	`{"__current_case__": 12, "components": "1,2,3", "include_lowest": true, "method": "pl.pca_loadings", "n_points": null}`

Step 44: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format	`"png"`
method	{"__current_case__": 14, "add_outline": false, "color": "", "groups": "", "matplotlib_pyplot_scatter": {"alpha": null, "edgecolors": null, "linewidths": "0.0", "vmax": null, "vmin": null}, "method": "pl.pca_overview", "outline_color_border": null, "outline_color_gap": null, "outline_width_border": "0.3", "outline_width_gap": "0.05", "plot": {"color_map": null, "components": [{"__index__": 0, "axis1": "1", "axis2": "2"}, {"__index__": 1, "axis1": "2", "axis2": "3"}], "frameon": true, "hspace": "0.25", "legend_fontsize": null, "legend_fontweight": "normal", "legend_loc": "right margin", "ncols": "2", "palette": null, "projection": "2d", "size": null, "title": "", "wspace": "0.1"}, "sort_order": true, "use_raw": false}

Step 45: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format	`"png"`
method	`{"__current_case__": 13, "log": true, "method": "pl.pca_variance_ratio", "n_pcs": "50"}`

Step 46: Embed using UMAP:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 5, "alpha": "1.0", "gamma": "1.0", "init_pos": "spectral", "maxiter": null, "method": "tl.umap", "min_dist": "0.5", "n_components": "2", "negative_sample_rate": "5", "neighbors_key": "", "random_state": "0", "spread": "1.0"}`

Step 47: Louvain clustering:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 0, "directed": true, "flavor": {"__current_case__": 0, "flavor": "vtraag", "resolution": "0.45"}, "key_added": "louvain", "method": "tl.louvain", "neighbors_key": "", "random_state": "0", "use_weights": false}`

Step 48: UMAP of louvain:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format	`"png"`
method	{"__current_case__": 16, "add_outline": false, "arrows": false, "color": "louvain", "edges": {"__current_case__": 1, "edges": "False"}, "gene_symbols": "", "groups": "", "layer": "", "matplotlib_pyplot_scatter": {"alpha": null, "edgecolors": "face", "linewidths": "0.0", "vmax": null, "vmin": null}, "method": "pl.umap", "outline_color_border": null, "outline_color_gap": null, "outline_width_border": "0.3", "outline_width_gap": "0.05", "plot": {"color_map": null, "components": [], "frameon": true, "hspace": "0.25", "legend_fontsize": null, "legend_fontweight": "normal", "legend_loc": "right margin", "ncols": "2", "palette": null, "projection": "2d", "size": null, "title": "", "wspace": "0.1"}, "sort_order": true, "use_raw": false}

Step 49: Rank genes by Wilcoxon test:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
method	`{"__current_case__": 4, "get_df": {"__current_case__": 0, "get_df_select": "False"}, "groupby": "louvain", "groups": "", "key_added": "", "layer": "", "method": "tl.rank_genes_groups", "n_genes": "100", "ref": {"__current_case__": 0, "rest": "rest"}, "tl_rank_genes_groups_method": {"__current_case__": 1, "corr_method": "benjamini-hochberg", "method": "wilcoxon", "tie_correct": false}, "use_raw": true}`

Step 50: toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inspect	`{"__current_case__": 5, "info": "uns", "uns_info": "rank_genes_groups"}`

Step 6: Mitochondrial genes start with pattern:
- step_state: scheduled

Step 51: Inspect clusters:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inspect	`{"__current_case__": 3, "info": "obs"}`

Step 52: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
advanced_common	`{"show_log": false}`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
format	`"png"`
method	`{"__current_case__": 24, "fontsize": "8", "gene_symbols": "", "groups": "", "method": "pl.rank_genes_groups", "n_genes": "20", "ncols": "3", "sharey": false}`

Step 53: Unlabelled step:
- step_state: new

Step 54: General information about the final Anndata object:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
inspect	`{"__current_case__": 0, "info": "general"}`

Step 55: Select top ranked genes:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"NR==2{gsub(/\\t/,\",\",$0); print}"`
dbkey	`"?"`

Step 56: Count number of clusters:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{print NF}"`
dbkey	`"?"`

Step 57: Select top ranked genes with louvain:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"NR==2{gsub(/\\t/,\",\",$0); print \"louvain,\"$0}"`
dbkey	`"?"`

Step 58: Count number of cells per cluster:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69aa0488de3511efb9ab00224823ee30"`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`"15"`
header_in	`true`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`true`
operations	`[{"__index__": 0, "op_column": "1", "op_name": "count"}]`
print_full_line	`false`

Step 59: Unlabelled step:
- step_state: new

Step 60: 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__	`"69aa0488de3511efb9ab00224823ee30"`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 7: Minimum number of genes expressed:
- step_state: scheduled

Step 61: 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__	`"69aa0488de3511efb9ab00224823ee30"`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 62: 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__	`"69aa0488de3511efb9ab00224823ee30"`
chromInfo	`"/tmp/tmpd4t5srhw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 63: Unlabelled step:
- step_state: new
Step 64: Violin plot of top genes on clusters:
- step_state: new
Step 65: Stacked violin of top genes on clusters:
- step_state: new
Step 66: Dotplot of top genes on clusters:
- step_state: new
Step 67: Heatmap of 20 genes:
- step_state: new
Step 68: UMAP of louvain and top ranked genes:
- step_state: new
Step 8: Maximum number of genes expressed:
- step_state: scheduled
Step 9: Number of neighbours for computing neighborhood graph:
- step_state: scheduled
Step 10: Number of PCs to use for computing neighborhood graph:
- step_state: scheduled

Other invocation details
- error_message
  - Final state of invocation 5a5e20b5fe519187 is [failed]. Failed to run workflow, at least one job is in [error] state.
- history_id
  - 5a5e20b5fe519187
- history_state
  - error
- invocation_id
  - 5a5e20b5fe519187
- invocation_state
  - failed
- messages
  - [{'dependent_workflow_step_id': None, 'hda_id': 'b25e3dce458d1f88', 'reason': 'dataset_failed', 'workflow_step_id': 52}]
- workflow_id
  - 5a5e20b5fe519187

gxydevbot · 2025-02-03T05:34:12Z

There are new updates, if you want to integrate them, close the PR and delete branch.

...eq/scanpy-clustering/Preprocessing-and-Clustering-of-single-cell-RNA-seq-data-with-Scanpy.ga

lldelisle

Looks good to me except the name of Bérénice

…ing-of-single-cell-RNA-seq-data-with-Scanpy.ga The name was autogenerated from the workflow editor Co-authored-by: Lucille Delisle <[email protected]>

Updating workflows/scRNAseq/scanpy-clustering from 0.1 to 0.2

bc822be

pavanvidem added 2 commits January 29, 2025 12:20

Update Preprocessing-and-Clustering-of-single-cell-RNA-seq-data-with-…

aca70e7

…Scanpy.ga - Replace all Manipulate Anndata tool filtering steps with Scanpy filter - Add complete URL for ORCID

Update CHANGELOG.md

3e3b2f7

update mito annotation step

e9dc919

lldelisle reviewed Feb 6, 2025

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Updating workflows/scRNAseq/scanpy-clustering from 0.1 to 0.2 #656

Updating workflows/scRNAseq/scanpy-clustering from 0.1 to 0.2 #656

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Workflow invocation details

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Workflow invocation details

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Updating workflows/scRNAseq/scanpy-clustering from 0.1 to 0.2 #656

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Updating workflows/scRNAseq/scanpy-clustering from 0.1 to 0.2 #656

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