Updating workflows/scRNAseq/pseudobulk-worflow-decoupler-edger from 0.1.1 to 0.1.2

[gxydevbot]

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 I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated: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 0.1.1 to 0.1.2.

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]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ pseudo-bulk_edgeR.ga_0

  Execution Problem:

  • Final state of invocation b8611f776925d626 is [failed]
    

  Workflow invocation details

  • Invocation Messages

    • Invocation scheduling failed because an unexpected failure occurred at step 21: 'Failed to create 1 job(s) for workflow step 21: Error executing tool with id 'toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.7': 'shape_col''
  • Steps

    • Step 1: Source AnnData file:

      • step_state: scheduled

    • Step 2: Pseudo-bulk: Fields to merge:

      • step_state: scheduled

    • Step 11: Sanitize factors:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • sed -r --sandbox -e 's/[ --+*^]+/_/g' '/tmp/tmpi12dzmqi/files/2/7/9/dataset_27981267-1656-4980-b2bc-8e931c738eb8.dat' > '/tmp/tmpi12dzmqi/job_working_directory/000/4/outputs/dataset_be758055-c29c-42ca-9449-3a5ce8aefc87.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c1d2dc4ce1f111efb9ab00224805eb1b"
            chromInfo	"/tmp/tmpi12dzmqi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            replacements	[{"__index__": 0, "find_pattern": "[ --+*^]+", "replace_pattern": "_"}]

    • Step 12: Remove start, end, width:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/2040e4c2750a/column_remove_by_header/column_remove_by_header.py' -i '/tmp/tmpi12dzmqi/files/e/5/b/dataset_e5b2a2d9-2458-4974-8731-a7df87fb0cc6.dat' -o '/tmp/tmpi12dzmqi/job_working_directory/000/5/outputs/dataset_579dd841-41a8-40e4-964b-56c2c8078bbc.dat' -d '	'  -s '#' --unicode-escaped-cols --columns 'start' 'end' 'width'

          Exit Code:

          • 0

          Standard Output:

          • Kept 10 of 10 columns.
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"c1d2dc4ce1f111efb9ab00224805eb1b"
            chromInfo	"/tmp/tmpi12dzmqi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            headers	[{"__index__": 0, "name": "start"}, {"__index__": 1, "name": "end"}, {"__index__": 2, "name": "width"}]
            keep_columns	false
            strip_characters	"#"

    • Step 13: Sanitize first factor for leading digits:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • awk -v OFS="\t" -v FS="\t" --re-interval --sandbox '{ $2 = gensub( /^([0-9])(.+)/, "GG_\\1\\2", "g", $2 ) ; print $0 ; }' '/tmp/tmpi12dzmqi/files/b/e/7/dataset_be758055-c29c-42ca-9449-3a5ce8aefc87.dat' > '/tmp/tmpi12dzmqi/job_working_directory/000/6/outputs/dataset_9f15b088-566a-4869-b41e-633ad3751a2b.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c1d2dc4ce1f111efb9ab00224805eb1b"
            chromInfo	"/tmp/tmpi12dzmqi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            replacements	[{"__index__": 0, "column": "2", "find_pattern": "^([0-9])(.+)", "replace_pattern": "GG_\\\\1\\\\2"}]

    • Step 14: 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/tmpi12dzmqi/job_working_directory/000/7/configs/tmpdo8e5vlc' '/tmp/tmpi12dzmqi/files/9/f/1/dataset_9f15b088-566a-4869-b41e-633ad3751a2b.dat' > '/tmp/tmpi12dzmqi/job_working_directory/000/7/outputs/dataset_8a1c9465-4956-4fe8-9ec4-fbddaae89f5f.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c1d2dc4ce1f111efb9ab00224805eb1b"
            chromInfo	"/tmp/tmpi12dzmqi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"BEGIN { print \"header\" } NR > 1 { if (!seen[$2]++) words[++count]=$2 } END { for (i=1; i<=count; i++) for (j=i+1; j<=count; j++) print words[i]\"-\"words[j] }"
            dbkey	"?"

    • Step 15: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • Rscript '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/edger/ae2aad0a6d50/edger/edger.R'  -R '/tmp/tmpi12dzmqi/job_working_directory/000/8/outputs/dataset_8c5cd1b7-8dcf-44a6-95f5-90edca1bdf50.dat' -o '/tmp/tmpi12dzmqi/job_working_directory/000/8/outputs/dataset_8c5cd1b7-8dcf-44a6-95f5-90edca1bdf50_files'  -m '/tmp/tmpi12dzmqi/files/3/f/1/dataset_3f1e38f7-65c2-442c-a40c-05fba7a19729.dat' -f '/tmp/tmpi12dzmqi/files/9/f/1/dataset_9f15b088-566a-4869-b41e-633ad3751a2b.dat'  -a '/tmp/tmpi12dzmqi/files/5/7/9/dataset_579dd841-41a8-40e4-964b-56c2c8078bbc.dat'  -F '~ 0 + disease'  -C '/tmp/tmpi12dzmqi/files/8/a/1/dataset_8a1c9465-4956-4fe8-9ec4-fbddaae89f5f.dat'    -l '0.0' -p '0.05' -d 'BH' -n 'TMM' -b  && mkdir ./output_dir  && cp '/tmp/tmpi12dzmqi/job_working_directory/000/8/outputs/dataset_8c5cd1b7-8dcf-44a6-95f5-90edca1bdf50_files'/*.tsv output_dir/

          Exit Code:

          • 0

          Standard Error:

          • Warning message:
            In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
              OS reports request to set locale to "en_US.UTF-8" cannot be honored
            Warning message:
            In plot.xy(xy, type, ...) : NAs introduced by coercion
            Warning message:
            In plot.xy(xy, type, ...) : NAs introduced by coercion
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"c1d2dc4ce1f111efb9ab00224805eb1b"
            adv	{"lfc": "0.0", "lrtOption": false, "normalisationOption": "TMM", "pAdjust": "BH", "pVal": "0.05", "robOption": true}
            anno	{"__current_case__": 0, "annoOpt": "yes", "geneanno": {"values": [{"id": 10, "src": "hda"}]}}
            chromInfo	"/tmp/tmpi12dzmqi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            contrasts	{"__current_case__": 1, "cinfo": {"values": [{"id": 12, "src": "hda"}]}, "contrastOpt": "file"}
            dbkey	"?"
            f	{"filt": {"__current_case__": 1, "filt_select": "no"}}
            formula	"~ 0 + disease"
            input	{"__current_case__": 1, "counts": {"values": [{"id": 8, "src": "hda"}]}, "fact": {"__current_case__": 0, "ffile": "yes", "finfo": {"values": [{"id": 11, "src": "hda"}]}}, "format": "matrix"}
            out	{"normCounts": false, "rdaOption": false, "rscript": false}

    • Step 16: Get contrast labels:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • mv '/tmp/tmpi12dzmqi/job_working_directory/000/9/configs/tmpm4aw1vd0' '/tmp/tmpi12dzmqi/job_working_directory/000/9/outputs/dataset_66ab622d-e096-46a3-8bcb-bffa9b95ffd6.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"c1d2dc4ce1f111efb9ab00224805eb1b"
            chromInfo	"/tmp/tmpi12dzmqi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            input_collection	{"values": [{"id": 1, "src": "hdca"}]}

    • Step 17: Select gene symbols, logFC, PValue and FDR:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/2040e4c2750a/column_remove_by_header/column_remove_by_header.py' -i '/tmp/tmpi12dzmqi/files/9/9/3/dataset_993f186b-f6a8-4c97-b2ae-f33264c8a2f4.dat' -o '/tmp/tmpi12dzmqi/job_working_directory/000/10/outputs/dataset_30a5cbb5-3a92-4e0a-a3eb-30ed10cf2f95.dat' -d '	' --keep -s '#' --unicode-escaped-cols --columns 'gene_symbol' 'logFC' 'PValue' 'FDR'

          Exit Code:

          • 0

          Standard Output:

          • Kept 4 of 15 columns.
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"c1d2dc4ce1f111efb9ab00224805eb1b"
            chromInfo	"/tmp/tmpi12dzmqi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            headers	[{"__index__": 0, "name": "gene_symbol"}, {"__index__": 1, "name": "logFC"}, {"__index__": 2, "name": "PValue"}, {"__index__": 3, "name": "FDR"}]
            keep_columns	true
            strip_characters	"#"

    • Step 18: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • sed -r --sandbox -e 's/edgeR_//g' '/tmp/tmpi12dzmqi/files/6/6/a/dataset_66ab622d-e096-46a3-8bcb-bffa9b95ffd6.dat' > '/tmp/tmpi12dzmqi/job_working_directory/000/11/outputs/dataset_e2544aa0-df7b-405e-a0d9-87dfa968a23f.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c1d2dc4ce1f111efb9ab00224805eb1b"
            chromInfo	"/tmp/tmpi12dzmqi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            replacements	[{"__index__": 0, "find_pattern": "edgeR_", "replace_pattern": ""}]

    • Step 19: Split contrasts:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • mkdir ./out && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/2dae863c8f42/split_file_to_collection/split_file_to_collection.py' --out ./out --in '/tmp/tmpi12dzmqi/files/e/2/5/dataset_e2544aa0-df7b-405e-a0d9-87dfa968a23f.dat' --ftype 'txt' --chunksize 1 --batch --file_names 'split_file' --file_ext 'txt'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"txt"
            __workflow_invocation_uuid__	"c1d2dc4ce1f111efb9ab00224805eb1b"
            chromInfo	"/tmp/tmpi12dzmqi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            split_parms	{"__current_case__": 5, "input": {"values": [{"id": 17, "src": "hda"}]}, "newfilenames": "split_file", "select_allocate": {"__current_case__": 1, "allocate": "batch"}, "select_ftype": "txt", "select_mode": {"__current_case__": 0, "chunksize": "1", "mode": "chunk"}}

    • Step 20: Contrast as parameters:

      • 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	"txt"
            __workflow_invocation_uuid__	"c1d2dc4ce1f111efb9ab00224805eb1b"
            chromInfo	"/tmp/tmpi12dzmqi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            param_type	"text"
            remove_newlines	true

    • Step 3: Group by column:

      • step_state: scheduled

    • Step 21: Unlabelled step:

      • step_state: new

    • Step 4: Sample key column:

      • step_state: scheduled

    • Step 5: Name Your Raw Counts Layer:

      • step_state: scheduled

    • Step 6: Factor fields:

      • step_state: scheduled

    • Step 7: Formula:

      • step_state: scheduled

    • Step 8: Gene symbol column:

      • step_state: scheduled

    • Step 9: toolshed.g2.bx.psu.edu/repos/ebi-gxa/decoupler_pseudobulk/decoupler_pseudobulk/1.4.0+galaxy8:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • mkdir deseq_output_dir && mkdir plots_output_dir && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/ebi-gxa/decoupler_pseudobulk/09c833d9b03b/decoupler_pseudobulk/decoupler_pseudobulk.py' '/tmp/tmpi12dzmqi/files/0/0/e/dataset_00ef2a77-fa5a-4b64-af4c-04d9bdfd33b6.dat' --groupby 'cell_type' --sample_key 'individual' --layer 'counts' --mode 'sum' --min_cells 10 --save_path plots_output_dir --min_counts 10 --min_counts_per_sample_marking 20 --min_total_counts 1000 --filter_expr --factor_fields 'disease' --deseq2_output_path deseq_output_dir --plot_samples_figsize 13 13 --plot_filtering_figsize 13 13

          Exit Code:

          • 0

          Standard Output:

          • Using mode: sum
            Created pseudo-bulk AnnData, checking if fields still make sense.
            If this fails this check, it might mean that you asked for factors         that are not compatible with you sample identifiers (ie. asked for         phase in the factors, but each sample contains more than one phase,        try joining fields).
            Factors requested are adequate for the pseudo-bulked AnnData!
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c1d2dc4ce1f111efb9ab00224805eb1b"
            adata_obs_fields_to_merge	None
            chromInfo	"/tmp/tmpi12dzmqi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            factor_fields	"disease"
            filter_expr	true
            filter_per_contrast	{"__current_case__": 1, "filter": "no"}
            groupby	"cell_type"
            layer	"counts"
            min_cells	"10"
            min_counts	"10"
            min_counts_per_sample	"20"
            min_total_counts	"1000"
            mode	"sum"
            plot_filtering_figsize	"13 13"
            plot_samples_figsize	"13 13"
            produce_anndata	false
            produce_plots	true
            sample_key	"individual"
            use_raw	false

    • Step 10: Sanitize matrix:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • sed -r --sandbox -e 's/[ --+*^]+/_/g' '/tmp/tmpi12dzmqi/files/0/d/6/dataset_0d65b43c-581e-4f16-be44-d6f3f4a458a0.dat' > '/tmp/tmpi12dzmqi/job_working_directory/000/3/outputs/dataset_3f1e38f7-65c2-442c-a40c-05fba7a19729.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c1d2dc4ce1f111efb9ab00224805eb1b"
            chromInfo	"/tmp/tmpi12dzmqi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            replacements	[{"__index__": 0, "find_pattern": "[ --+*^]+", "replace_pattern": "_"}]

  • Other invocation details

    • error_message

      • Final state of invocation b8611f776925d626 is [failed]

    • history_id

      • b8611f776925d626

    • history_state

      • ok

    • invocation_id

      • b8611f776925d626

    • invocation_state

      • failed

    • messages

      • [{'details': "Failed to create 1 job(s) for workflow step 21: 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': 20}]

    • workflow_id

      • b8611f776925d626

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ pseudo-bulk_edgeR.ga_0

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/ (version 0.0.7)","err_code":0}
    

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ pseudo-bulk_edgeR.ga_0

  Execution Problem:

  • Unexpected HTTP status code: 400: {"err_msg":"Workflow was not invoked; the following required tools are not installed: toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/ (version 0.0.7)","err_code":0}
    

[gxydevbot]

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