Updating workflows/transcriptomics/rnaseq-de from 0.2 to 0.3 by gxydevbot · Pull Request #661 · galaxyproject/iwc

gxydevbot · 2025-02-03T05:35:30Z

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 I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated: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/volcanoplot/volcanoplot/0.0.6 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.7

The workflow release number has been updated from 0.2 to 0.3.

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 · 2025-02-03T05:50:32Z

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

❌ rnaseq-de-filtering-plotting.ga_0

Execution Problem:

Final state of invocation 210d064d00d17e2e is [failed]

Workflow invocation details

Invocation Messages
- Invocation scheduling failed because an unexpected failure occurred at step 19: 'Failed to create 1 job(s) for workflow step 19: Error executing tool with id 'toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.7': 'shape_col''
- Defined workflow output 'plot' was not found in step 19.

Steps

Step 1: Counts from changed condition:
- step_state: scheduled
Step 2: Counts from reference condition:
- step_state: scheduled

Step 11: Differential Analysis:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/deseq2/9a882d108833/deseq2/get_deseq_dataset.R' > /dev/null &&  Rscript '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/deseq2/9a882d108833/deseq2/deseq2.R' --cores ${GALAXY_SLOTS:-1} -o '/tmp/tmponqsgjpf/job_working_directory/000/10/outputs/dataset_67750552-7236-46e7-925f-90ae2bfafe56.dat' -p '/tmp/tmponqsgjpf/job_working_directory/000/10/outputs/dataset_fc8adef8-2041-4b64-9c52-6000f2b4c2b5.dat' -A 0.1 -n '/tmp/tmponqsgjpf/job_working_directory/000/10/outputs/dataset_c7b094d2-7322-453c-bda4-2b1cb7d518f5.dat'              -H  -f '[["DEFactor", [{"BaseFactor": ["/tmp/tmponqsgjpf/files/6/9/d/dataset_69d6dddf-7fcf-4f79-9253-dfed23359a5e.dat", "/tmp/tmponqsgjpf/files/c/0/2/dataset_c02775b3-7856-4392-b816-688124a23794.dat"]}, {"MainFactor": ["/tmp/tmponqsgjpf/files/e/e/1/dataset_ee1c16db-cd33-4612-9755-631752fdda6d.dat", "/tmp/tmponqsgjpf/files/d/1/5/dataset_d15f2a91-8001-4321-9e85-3c264ed0fb52.dat"]}]]]' -l '{"dataset_ee1c16db-cd33-4612-9755-631752fdda6d.dat": "SRR5085169 Counts Table", "dataset_d15f2a91-8001-4321-9e85-3c264ed0fb52.dat": "SRR5085170 Counts Table", "dataset_69d6dddf-7fcf-4f79-9253-dfed23359a5e.dat": "SRR5085167 Counts Table", "dataset_c02775b3-7856-4392-b816-688124a23794.dat": "SRR5085168 Counts Table"}' -t 1

Exit Code:

```
0
```

Standard Error:

estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Warning message:
`aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.
ℹ See also `vignette("ggplot2-in-packages")` for more information.

Standard Output:

primary factor: DEFactor 

---------------------
No size factor was used
DESeq2 run information

sample table:
                          DEFactor
SRR5085167 Counts Table BaseFactor
SRR5085168 Counts Table BaseFactor
SRR5085169 Counts Table MainFactor
SRR5085170 Counts Table MainFactor

design formula:
~DEFactor


4 samples with counts over 7127 genes
Applied default - beta prior off
[1] "use_beta_prior is set to FALSE"
using disperion fit type: parametric 
creating plots
summary of results
DEFactor: MainFactor vs BaseFactor

out of 5734 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up)       : 2, 0.035%
LFC < 0 (down)     : 13, 0.23%
outliers [1]       : 0, 0%
low counts [2]     : 2963, 52%
(mean count < 7)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results

NULL
closing plot device
null device 
          1 
Session information:

R version 4.3.1 (2023-06-16)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)

Matrix products: default
BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.23.so;  LAPACK version 3.11.0

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

time zone: NA
tzcode source: system (glibc)

attached base packages:
[1] stats4    tools     stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] pheatmap_1.0.12             ggrepel_0.9.3              
 [3] ggplot2_3.4.2               rjson_0.2.21               
 [5] gplots_3.1.3                RColorBrewer_1.1-3         
 [7] DESeq2_1.40.2               SummarizedExperiment_1.30.2
 [9] Biobase_2.60.0              MatrixGenerics_1.12.2      
[11] matrixStats_1.0.0           GenomicRanges_1.52.0       
[13] GenomeInfoDb_1.36.1         IRanges_2.34.1             
[15] S4Vectors_0.38.1            BiocGenerics_0.46.0        
[17] getopt_1.20.3              

loaded via a namespace (and not attached):
 [1] utf8_1.2.3              generics_0.1.3          bitops_1.0-7           
 [4] KernSmooth_2.23-22      gtools_3.9.4            lattice_0.21-8         
 [7] caTools_1.18.2          magrittr_2.0.3          grid_4.3.1             
[10] Matrix_1.6-0            fansi_1.0.4             scales_1.2.1           
[13] codetools_0.2-19        cli_3.6.1               rlang_1.1.1            
[16] crayon_1.5.2            XVector_0.40.0          munsell_0.5.0          
[19] withr_2.5.0             DelayedArray_0.26.6     S4Arrays_1.0.4         
[22] parallel_4.3.1          BiocParallel_1.34.2     dplyr_1.1.2            
[25] colorspace_2.1-0        locfit_1.5-9.8          GenomeInfoDbData_1.2.10
[28] vctrs_0.6.3             R6_2.5.1                lifecycle_1.0.3        
[31] zlibbioc_1.46.0         pkgconfig_2.0.3         pillar_1.9.0           
[34] gtable_0.3.3            glue_1.6.2              Rcpp_1.0.11            
[37] tibble_3.2.1            tidyselect_1.2.0        farver_2.1.1           
[40] labeling_0.4.2          compiler_4.3.1          RCurl_1.98-1.12

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69c46416e1f211efb9ab7c1e521c3844"`
advanced_options	`{"auto_mean_filter_off": false, "esf_cond": {"__current_case__": 0, "esf": ""}, "fit_type": "1", "outlier_filter_off": false, "outlier_replace_off": false, "prefilter_conditional": {"__current_case__": 1, "prefilter": ""}, "use_beta_priors": false}`
batch_factors	`None`
chromInfo	`"/tmp/tmponqsgjpf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`true`
output_options	`{"alpha_ma": "0.1", "output_selector": ["pdf", "normCounts"]}`
select_data	`{"__current_case__": 1, "how": "datasets_per_level", "rep_factorName": [{"__index__": 0, "factorName": "DEFactor", "rep_factorLevel": [{"__index__": 0, "countsFile": {"values": [{"id": 1, "src": "hdca"}]}, "factorLevel": "MainFactor"}, {"__index__": 1, "countsFile": {"values": [{"id": 2, "src": "hdca"}]}, "factorLevel": "BaseFactor"}]}]}`
tximport	`{"__current_case__": 1, "tximport_selector": "count"}`

Step 12: 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 ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69c46416e1f211efb9ab7c1e521c3844"`
chromInfo	`"/tmp/tmponqsgjpf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c7<", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 2, "component_value": "0.1", "select_param_type": "float"}}]`
dbkey	`"?"`

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 ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69c46416e1f211efb9ab7c1e521c3844"`
chromInfo	`"/tmp/tmponqsgjpf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "abs(c3)>", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 2, "component_value": "0.5", "select_param_type": "float"}}]`
dbkey	`"?"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/e98d4ab5b5bc/deg_annotate/deg_annotate.py' -in '/tmp/tmponqsgjpf/files/6/7/7/dataset_67750552-7236-46e7-925f-90ae2bfafe56.dat' -m 'degseq' -g '/tmp/tmponqsgjpf/files/0/5/0/dataset_0509a756-c740-44d0-b7e9-3d1a58e85924.dat' -t 'exon' -i 'gene_id' -x 'transcript_id' -a 'gene_biotype, gene_name' -o '/tmp/tmponqsgjpf/job_working_directory/000/13/outputs/dataset_f2a8f421-faa4-481c-90aa-ef3637e9beac.dat'

Exit Code:

```
0
```

Standard Output:

DE(X)Seq output file     : /tmp/tmponqsgjpf/files/6/7/7/dataset_67750552-7236-46e7-925f-90ae2bfafe56.dat
Input file type          : degseq
Annotation file          : /tmp/tmponqsgjpf/files/0/5/0/dataset_0509a756-c740-44d0-b7e9-3d1a58e85924.dat
Feature type             : exon
ID attribute             : gene_id
Transcript attribute     : transcript_id
Attributes to include    : gene_biotype, gene_name
Annotated output file    : /tmp/tmponqsgjpf/job_working_directory/000/13/outputs/dataset_f2a8f421-faa4-481c-90aa-ef3637e9beac.dat

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"69c46416e1f211efb9ab7c1e521c3844"`
advanced_parameters	`{"gff_attributes": "gene_biotype, gene_name", "gff_feature_attribute": "gene_id", "gff_feature_type": "exon", "gff_transcript_attribute": "transcript_id"}`
chromInfo	`"/tmp/tmponqsgjpf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	`"degseq"`

Step 15: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmponqsgjpf/job_working_directory/000/14/configs/tmpw3u2usfp' '/tmp/tmponqsgjpf/files/c/7/b/dataset_c7b094d2-7322-453c-bda4-2b1cb7d518f5.dat' > '/tmp/tmponqsgjpf/job_working_directory/000/14/outputs/dataset_6fa20a77-34e8-4f88-940e-53575c41601a.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69c46416e1f211efb9ab7c1e521c3844"`
chromInfo	`"/tmp/tmponqsgjpf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"END{print NF}"`
dbkey	`"?"`

Step 16: Annotate DESeq2 table:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmponqsgjpf/files/f/3/2/dataset_f32689f4-1e9e-487e-a8fe-1f496952e909.dat' >> '/tmp/tmponqsgjpf/job_working_directory/000/15/outputs/dataset_227e0532-b053-4642-8d70-69f3a2e5525d.dat' && cat '/tmp/tmponqsgjpf/files/f/2/a/dataset_f2a8f421-faa4-481c-90aa-ef3637e9beac.dat' >> '/tmp/tmponqsgjpf/job_working_directory/000/15/outputs/dataset_227e0532-b053-4642-8d70-69f3a2e5525d.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69c46416e1f211efb9ab7c1e521c3844"`
chromInfo	`"/tmp/tmponqsgjpf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[{"__index__": 0, "inputs2": {"values": [{"id": 15, "src": "hda"}]}}]`

Step 17: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"69c46416e1f211efb9ab7c1e521c3844"`
chromInfo	`"/tmp/tmponqsgjpf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 18: Filter with p-adj threshold:
- step_state: new
Step 19: Generate Valcanot plot of DE genes:
- step_state: new
Step 20: Unlabelled step:
- step_state: new
Step 3: Count files have header:
- step_state: scheduled
Step 21: Filter with log2 FC threshold:
- step_state: new
Step 22: Unlabelled step:
- step_state: new
Step 23: Unlabelled step:
- step_state: new
Step 24: Generate Heatmap of counts:
- step_state: new
Step 25: Generate Heatmap of Z-scores:
- step_state: new
Step 4: Gene Annotaton:
- step_state: scheduled
Step 5: Adjusted p-value threshold:
- step_state: scheduled

Step 6: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

times=1; yes -- 'GeneID__tc__Base mean__tc__log2(FC)__tc__StdErr__tc__Wald-Stats__tc__P-value__tc__P-adj__tc__Chromosome__tc__Start__tc__End__tc__Strand__tc__Feature__tc__Gene name' 2>/dev/null | head -n $times >> '/tmp/tmponqsgjpf/job_working_directory/000/6/outputs/dataset_f86a6429-06df-41c3-8c83-681638bf436a.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69c46416e1f211efb9ab7c1e521c3844"`
chromInfo	`"/tmp/tmponqsgjpf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": "GeneID\tBase mean\tlog2(FC)\tStdErr\tWald-Stats\tP-value\tP-adj\tChromosome\tStart\tEnd\tStrand\tFeature\tGene name", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]`

Step 7: log2 fold change threshold:
- step_state: scheduled

Step 8: 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__	`"69c46416e1f211efb9ab7c1e521c3844"`
chromInfo	`"/tmp/tmponqsgjpf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 1, "pick_style": "first_or_default", "type_cond": {"__current_case__": 2, "default_value": "0.05", "param_type": "float", "pick_from": [{"__index__": 0, "value": "0.1"}]}}`

Step 9: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed --sandbox -r -f '/tmp/tmponqsgjpf/job_working_directory/000/8/configs/tmphg2dsion' '/tmp/tmponqsgjpf/files/f/8/6/dataset_f86a6429-06df-41c3-8c83-681638bf436a.dat' > '/tmp/tmponqsgjpf/job_working_directory/000/8/outputs/dataset_f32689f4-1e9e-487e-a8fe-1f496952e909.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"69c46416e1f211efb9ab7c1e521c3844"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmponqsgjpf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"s/__tc__/\\t/g"`
dbkey	`"?"`

Step 10: 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__	`"69c46416e1f211efb9ab7c1e521c3844"`
chromInfo	`"/tmp/tmponqsgjpf/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 1, "pick_style": "first_or_default", "type_cond": {"__current_case__": 2, "default_value": "1.0", "param_type": "float", "pick_from": [{"__index__": 0, "value": "0.5"}]}}`

Other invocation details
- error_message
  - Final state of invocation 210d064d00d17e2e is [failed]
- history_id
  - 210d064d00d17e2e
- history_state
  - ok
- invocation_id
  - 210d064d00d17e2e
- invocation_state
  - failed
- messages
  - [{'details': "Failed to create 1 job(s) for workflow step 19: Error executing tool with id 'toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.7': 'shape_col'", 'reason': 'unexpected_failure', 'workflow_step_id': 18}, {'output_name': 'plot', 'reason': 'workflow_output_not_found', 'workflow_step_id': 18}]
- workflow_id
  - 210d064d00d17e2e

lldelisle · 2025-02-06T09:12:42Z

@pavanvidem to solve this you need to go through the graphical interface as one parameter seems to have changed name.

Updating workflows/transcriptomics/rnaseq-de from 0.2 to 0.3

23c8beb

add new shape_col param

ca381b3

bgruening merged commit 6c91869 into galaxyproject:main Feb 6, 2025
7 checks passed

gxydevbot deleted the workflows/transcriptomics/rnaseq-de branch March 10, 2025 05:46

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Updating workflows/transcriptomics/rnaseq-de from 0.2 to 0.3#661

Updating workflows/transcriptomics/rnaseq-de from 0.2 to 0.3#661
bgruening merged 2 commits intogalaxyproject:mainfrom
planemo-autoupdate:workflows/transcriptomics/rnaseq-de

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Workflow invocation details

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gxydevbot commented Feb 3, 2025

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github-actions bot commented Feb 3, 2025

Test Results (powered by Planemo)

Test Summary

Workflow invocation details

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lldelisle commented Feb 6, 2025

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4 participants