Updating workflows/variant-calling/variation-reporting from 0.1 to 0.2

[planemo-autoupdate]

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 I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated: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/devteam/column_maker/Add_a_column1/1.6 should be updated to toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0
• toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3 should be updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4

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

[gxydevbot]

There are new updates, they have been integrated to the PR, check the file diff.

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ Generic-variation-analysis-reporting.ga_0

  Execution Problem:

  • Failed to run workflow, at least one job is in [error] state.
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Variation data to report:

      • step_state: scheduled

    • Step 2: AF Filter:

      • step_state: scheduled

    • Step 11: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            grouping	"1,2,3,4,5,6,19,7,8,9"
            header_in	true
            header_out	true
            ignore_case	false
            narm	false
            need_sort	false
            operations	[{"__index__": 0, "op_column": "10", "op_name": "collapse"}, {"__index__": 1, "op_column": "11", "op_name": "collapse"}, {"__index__": 2, "op_column": "12", "op_name": "collapse"}, {"__index__": 3, "op_column": "13", "op_name": "collapse"}, {"__index__": 4, "op_column": "14", "op_name": "collapse"}, {"__index__": 5, "op_column": "15", "op_name": "collapse"}, {"__index__": 6, "op_column": "16", "op_name": "collapse"}]
            print_full_line	false

    • Step 12: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            caseinsensitive	"false"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            find_and_replace	[]
            find_pattern	"\\t([^\\t,]+),[^\\t]+\\t([^\\t,]+),[^\\t]+\\t([^\\t,]+),[^\\t]+\\t([^\\t,]+),[^\\t]+\\t([^\\t,]+),[^\\t]+\\t([^\\t,]+),[^\\t]+\\t([^\\t,]+),[^\\s]+"
            global	"true"
            is_regex	"true"
            replace_pattern	"\\t$1\\t$2\\t$3\\t$4\\t$5\\t$6\\t$7"
            searchwhere	{"__current_case__": 0, "searchwhere_select": "line"}
            skip_first_line	"true"
            wholewords	"false"

    • Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            caseinsensitive	"false"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            find_and_replace	[]
            find_pattern	` "(GroupBy
            global	"true"
            is_regex	"true"
            replace_pattern	"$2"
            searchwhere	{"__current_case__": 0, "searchwhere_select": "line"}
            skip_first_line	"false"
            wholewords	"false"

    • Step 14: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            caseinsensitive	"false"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            find_and_replace	[]
            find_pattern	"AFrecalc\\tAF"
            global	"false"
            is_regex	"true"
            replace_pattern	"AF\\tAFcaller"
            searchwhere	{"__current_case__": 0, "searchwhere_select": "line"}
            skip_first_line	"false"
            wholewords	"false"

    • Step 15: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filename	{"__current_case__": 0, "add_name": true, "place_name": "same_multiple"}
            one_header	true

    • Step 16: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            avoid_scientific_notation	false
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            cond	"str(c5) + '>' + str(c6)"
            dbkey	"?"
            error_handling	{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}
            header_lines_conditional	{"__current_case__": 1, "header_lines_select": "yes", "header_new_column_name": "change"}
            ops	{"__current_case__": 0, "expressions": [], "header_lines_select": "no"}
            round	"false"

    • Step 17: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            avoid_scientific_notation	false
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            cond	"str(int(c3)) + ':' + str(c19)"
            dbkey	"?"
            error_handling	{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}
            header_lines_conditional	{"__current_case__": 1, "header_lines_select": "yes", "header_new_column_name": "change_with_pos"}
            ops	{"__current_case__": 0, "expressions": [], "header_lines_select": "no"}
            round	"false"

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

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            caseinsensitive	"false"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            find_and_replace	[]
            find_pattern	"EFF[*]."
            global	"true"
            is_regex	"false"
            replace_pattern	""
            searchwhere	{"__current_case__": 0, "searchwhere_select": "line"}
            skip_first_line	"false"
            wholewords	"false"

    • Step 19: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            grouping	"20"
            header_in	true
            header_out	true
            ignore_case	false
            narm	false
            need_sort	true
            operations	[{"__index__": 0, "op_column": "1", "op_name": "countunique"}, {"__index__": 1, "op_column": "8", "op_name": "min"}, {"__index__": 2, "op_column": "8", "op_name": "max"}, {"__index__": 3, "op_column": "1", "op_name": "collapse"}, {"__index__": 4, "op_column": "8", "op_name": "collapse"}]
            print_full_line	false

    • Step 20: Filter1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            cond	"c4=='PASS' or c4=='.'"
            dbkey	"?"
            header_lines	"1"

    • Step 3: DP Filter:

      • step_state: scheduled

    • Step 21: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            grouping	"3"
            header_in	true
            header_out	true
            ignore_case	false
            narm	false
            need_sort	true
            operations	[{"__index__": 0, "op_column": "1", "op_name": "countunique"}, {"__index__": 1, "op_column": "8", "op_name": "min"}, {"__index__": 2, "op_column": "8", "op_name": "max"}, {"__index__": 3, "op_column": "19", "op_name": "countunique"}, {"__index__": 4, "op_column": "13", "op_name": "countunique"}]
            print_full_line	false

    • Step 22: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            grouping	"20"
            header_in	true
            header_out	true
            ignore_case	false
            narm	false
            need_sort	true
            operations	[{"__index__": 0, "op_column": "1", "op_name": "countunique"}]
            print_full_line	false

    • Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            column1	"20"
            column2	"1"
            dbkey	"?"
            empty_string_filler	"0"
            header	true
            ignore_case	false
            jointype	" "

    • Step 24: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            grouping	"3"
            header_in	true
            header_out	true
            ignore_case	false
            narm	false
            need_sort	true
            operations	[{"__index__": 0, "op_column": "1", "op_name": "countunique"}]
            print_full_line	false

    • Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            column1	"20"
            column2	"1"
            dbkey	"?"
            empty_string_filler	"0"
            header	true
            ignore_case	false
            jointype	" "

    • Step 26: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            grouping	"1"
            header_in	true
            header_out	true
            ignore_case	false
            narm	false
            need_sort	true
            operations	[{"__index__": 0, "op_column": "2", "op_name": "unique"}]
            print_full_line	true

    • Step 27: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            column1	"3"
            column2	"1"
            dbkey	"?"
            empty_string_filler	"0"
            header	true
            ignore_case	false
            jointype	" "

    • Step 28: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c2,c3,c4,c5,c6,c7,c8,c9,c11,c12,c13,c14,c15,c16,c17,c18,c19"
            dbkey	"?"
            delimiter	"T"

    • Step 29: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c4,c6,c7,c13,c14,c15,c16,c17,c18,c19,c21,c22,c23,c26,c24,c25,c20"
            dbkey	"?"
            delimiter	"T"

    • Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            column1	"1"
            column2	"1"
            dbkey	"?"
            empty_string_filler	"0"
            header	true
            ignore_case	false
            jointype	" "

    • Step 4: DP_ALT Filter:

      • step_state: scheduled

    • Step 31: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            split_parms	{"__current_case__": 0, "input": {"values": [{"id": 25, "src": "hda"}]}, "select_ftype": "tabular", "split_by": {"__current_case__": 0, "id_col": "1", "match_regex": "(.*)", "select_split_by": "col", "sub_regex": "\\1"}, "top": "1"}

    • Step 32: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            caseinsensitive	"false"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            find_and_replace	[]
            find_pattern	"unique\\(Sample\\)\\tcollapse\\(Sample\\)\\tcollapse\\(AF\\)"
            global	"true"
            is_regex	"true"
            replace_pattern	"SAMPLES(above-thresholds)\\tSAMPLES(all)\\tAFs(all)"
            searchwhere	{"__current_case__": 0, "searchwhere_select": "line"}
            skip_first_line	"false"
            wholewords	"false"

    • Step 33: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c2,c1,c4,c5,c6,c7,c8,c9,c11,c10,c12,c13,c14,c15,c16,c17,c18,c23,c24,c25,c26,c19"
            dbkey	"?"
            delimiter	"T"

    • Step 34: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            header	"1"
            ignore_case	false
            sortkeys	[{"__index__": 0, "column": "1", "order": "", "style": "g"}]
            unique	false

    • Step 35: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            header	"1"
            ignore_case	false
            sortkeys	[{"__index__": 0, "column": "1", "order": "", "style": ""}, {"__index__": 1, "column": "2", "order": "", "style": "n"}]
            unique	false

    • Step 5: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • SnpSift -Xmx6G filter -f '/tmp/tmpiraiu3v5/files/9/7/2/dataset_972f5b8b-edd8-4feb-8268-25da86b2ff46.dat' -e '/tmp/tmpiraiu3v5/job_working_directory/000/2/configs/tmp3uzf0i92' > '/tmp/tmpiraiu3v5/job_working_directory/000/2/outputs/dataset_bf090267-b216-455b-8c8d-2c826ca55ca8.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"vcf"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_expression	{"__current_case__": 0, "expr": "DP >= 1", "type": "simple"}
            filtering	{"__current_case__": 0, "mode": "entries"}
            inverse	false

    • Step 6: 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__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            components	` [{"index": 0, "param_type": {"current_case": 0, "component_value": "( ( DP4[2] + DP4[3] ) < ( ", "select_param_type": "text"}}, {"index": 1, "param_type": {"current_case": 2, "component_value": "0.05", "select_param_type": "float"}}, {"index": 2, "param_type": {"current_case": 0, "component_value": " * DP ) )
            dbkey	"?"

    • Step 7: 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__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            components	` [{"index": 0, "param_type": {"current_case": 0, "component_value": "min_af_", "select_param_type": "text"}}, {"index": 1, "param_type": {"current_case": 2, "component_value": "0.05", "select_param_type": "float"}}, {"index": 2, "param_type": {"current_case": 0, "component_value": "
            dbkey	"?"

    • Step 8: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • SnpSift -Xmx6G filter -f '/tmp/tmpiraiu3v5/files/b/f/0/dataset_bf090267-b216-455b-8c8d-2c826ca55ca8.dat' -e '/tmp/tmpiraiu3v5/job_working_directory/000/5/configs/tmp0ihy_qtk' --addFilter min_af_0.05Xmin_dp_1Xmin_dp_alt_10 > '/tmp/tmpiraiu3v5/job_working_directory/000/5/outputs/dataset_ad9d210a-e424-4c9a-9430-7e85fce551eb.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"vcf"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_expression	` {"current_case": 0, "expr": "( ( DP4[2] + DP4[3] ) < ( 0.05 * DP ) )
            filtering	` {"current_case": 3, "add_filter": "min_af_0.05
            inverse	false

    • Step 9: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • if [ -z "$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=$(dirname $(readlink -e $(which SnpSift))); fi && cat '/tmp/tmpiraiu3v5/files/a/d/9/dataset_ad9d210a-e424-4c9a-9430-7e85fce551eb.dat' | perl "$SNPSIFT_JAR_PATH/scripts/vcfEffOnePerLine.pl" | SnpSift -Xmx6G extractFields -e '.' - "CHROM" "POS" "FILTER" "REF" "ALT" "DP" "AF" "DP4" "SB" "EFF[*].IMPACT" "EFF[*].FUNCLASS" "EFF[*].EFFECT" "EFF[*].GENE" "EFF[*].CODON" "EFF[*].AA" "EFF[*].TRID" "DP4[2]" "DP4[3]"> '/tmp/tmpiraiu3v5/job_working_directory/000/6/outputs/dataset_9e07b4cc-fc98-4b78-86c7-50e3ba959ce1.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"vcf"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            empty_text	"."
            extract	"CHROM POS FILTER REF ALT DP AF DP4 SB EFF[*].IMPACT EFF[*].FUNCLASS EFF[*].EFFECT EFF[*].GENE EFF[*].CODON EFF[*].AA EFF[*].TRID DP4[2] DP4[3]"
            one_effect_per_line	true
            separator	""

    • Step 10: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,str,str,str,int,float,list,int,str,str,str,str,str,str,str,int,int  --file '/tmp/tmpiraiu3v5/job_working_directory/000/7/configs/tmpcqzgmnq6' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpiraiu3v5/files/9/e/0/dataset_9e07b4cc-fc98-4b78-86c7-50e3ba959ce1.dat' '/tmp/tmpiraiu3v5/job_working_directory/000/7/outputs/dataset_3fb9e6ba-fc4e-4175-9253-2e406763490a.dat'

          Exit Code:

          • 1

          Standard Error:

          • Failed to convert some of the columns in line #0 to their expected types.  The error was: "invalid literal for int() with base 10: 'POS'" for the line: "CHROM	POS	FILTER	REF	ALT	DP	AF	DP4	SB	EFF[*].IMPACT	EFF[*].FUNCLASS	EFF[*].EFFECT	EFF[*].GENE	EFF[*].CODON	EFF[*].AA	EFF[*].TRID	DP4[2]	DP4[3]"
            

          Standard Output:

          • Computing 0 new columns with instructions []
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"d61956ea79be11ef8f39d97def0909d8"
            avoid_scientific_notation	false
            chromInfo	"/tmp/tmpiraiu3v5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            cond	"round((c17 + c18) / c6, 6)"
            dbkey	"?"
            error_handling	{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}
            header_lines_conditional	{"__current_case__": 1, "header_lines_select": "yes", "header_new_column_name": "AFrecalc"}
            ops	{"__current_case__": 0, "expressions": [], "header_lines_select": "no"}
            round	"false"

  • Other invocation details

    • error_message

      • Failed to run workflow, at least one job is in [error] state.

    • history_id

      • 71a71f7f128ce926

    • history_state

      • error

    • invocation_id

      • 71a71f7f128ce926

    • invocation_state

      • scheduled

    • workflow_id

      • 71a71f7f128ce926

[gxydevbot]

There are new updates, they have been integrated to the PR, check the file diff.

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ Generic-variation-analysis-reporting.ga_0

  Execution Problem:

  • Failed to run workflow, at least one job is in [error] state.
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Variation data to report:

      • step_state: scheduled

    • Step 2: AF Filter:

      • step_state: scheduled

    • Step 11: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            grouping	"1,2,3,4,5,6,19,7,8,9"
            header_in	true
            header_out	true
            ignore_case	false
            narm	false
            need_sort	false
            operations	[{"__index__": 0, "op_column": "10", "op_name": "collapse"}, {"__index__": 1, "op_column": "11", "op_name": "collapse"}, {"__index__": 2, "op_column": "12", "op_name": "collapse"}, {"__index__": 3, "op_column": "13", "op_name": "collapse"}, {"__index__": 4, "op_column": "14", "op_name": "collapse"}, {"__index__": 5, "op_column": "15", "op_name": "collapse"}, {"__index__": 6, "op_column": "16", "op_name": "collapse"}]
            print_full_line	false

    • Step 12: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            caseinsensitive	"false"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            find_and_replace	[]
            find_pattern	"\\t([^\\t,]+),[^\\t]+\\t([^\\t,]+),[^\\t]+\\t([^\\t,]+),[^\\t]+\\t([^\\t,]+),[^\\t]+\\t([^\\t,]+),[^\\t]+\\t([^\\t,]+),[^\\t]+\\t([^\\t,]+),[^\\s]+"
            global	"true"
            is_regex	"true"
            replace_pattern	"\\t$1\\t$2\\t$3\\t$4\\t$5\\t$6\\t$7"
            searchwhere	{"__current_case__": 0, "searchwhere_select": "line"}
            skip_first_line	"true"
            wholewords	"false"

    • Step 13: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            caseinsensitive	"false"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            find_and_replace	[]
            find_pattern	` "(GroupBy
            global	"true"
            is_regex	"true"
            replace_pattern	"$2"
            searchwhere	{"__current_case__": 0, "searchwhere_select": "line"}
            skip_first_line	"false"
            wholewords	"false"

    • Step 14: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            caseinsensitive	"false"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            find_and_replace	[]
            find_pattern	"AFrecalc\\tAF"
            global	"false"
            is_regex	"true"
            replace_pattern	"AF\\tAFcaller"
            searchwhere	{"__current_case__": 0, "searchwhere_select": "line"}
            skip_first_line	"false"
            wholewords	"false"

    • Step 15: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filename	{"__current_case__": 0, "add_name": true, "place_name": "same_multiple"}
            one_header	true

    • Step 16: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            avoid_scientific_notation	false
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            cond	"str(c5) + '>' + str(c6)"
            dbkey	"?"
            error_handling	{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}
            header_lines_conditional	{"__current_case__": 1, "header_lines_select": "yes", "header_new_column_name": "change"}
            ops	{"__current_case__": 0, "expressions": [], "header_lines_select": "no"}
            round	"false"

    • Step 17: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            avoid_scientific_notation	false
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            cond	"str(int(c3)) + ':' + str(c19)"
            dbkey	"?"
            error_handling	{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}
            header_lines_conditional	{"__current_case__": 1, "header_lines_select": "yes", "header_new_column_name": "change_with_pos"}
            ops	{"__current_case__": 0, "expressions": [], "header_lines_select": "no"}
            round	"false"

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

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            caseinsensitive	"false"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            find_and_replace	[]
            find_pattern	"EFF[*]."
            global	"true"
            is_regex	"false"
            replace_pattern	""
            searchwhere	{"__current_case__": 0, "searchwhere_select": "line"}
            skip_first_line	"false"
            wholewords	"false"

    • Step 19: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            grouping	"20"
            header_in	true
            header_out	true
            ignore_case	false
            narm	false
            need_sort	true
            operations	[{"__index__": 0, "op_column": "1", "op_name": "countunique"}, {"__index__": 1, "op_column": "8", "op_name": "min"}, {"__index__": 2, "op_column": "8", "op_name": "max"}, {"__index__": 3, "op_column": "1", "op_name": "collapse"}, {"__index__": 4, "op_column": "8", "op_name": "collapse"}]
            print_full_line	false

    • Step 20: Filter1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            cond	"c4=='PASS' or c4=='.'"
            dbkey	"?"
            header_lines	"1"

    • Step 3: DP Filter:

      • step_state: scheduled

    • Step 21: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            grouping	"3"
            header_in	true
            header_out	true
            ignore_case	false
            narm	false
            need_sort	true
            operations	[{"__index__": 0, "op_column": "1", "op_name": "countunique"}, {"__index__": 1, "op_column": "8", "op_name": "min"}, {"__index__": 2, "op_column": "8", "op_name": "max"}, {"__index__": 3, "op_column": "19", "op_name": "countunique"}, {"__index__": 4, "op_column": "13", "op_name": "countunique"}]
            print_full_line	false

    • Step 22: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            grouping	"20"
            header_in	true
            header_out	true
            ignore_case	false
            narm	false
            need_sort	true
            operations	[{"__index__": 0, "op_column": "1", "op_name": "countunique"}]
            print_full_line	false

    • Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            column1	"20"
            column2	"1"
            dbkey	"?"
            empty_string_filler	"0"
            header	true
            ignore_case	false
            jointype	" "

    • Step 24: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            grouping	"3"
            header_in	true
            header_out	true
            ignore_case	false
            narm	false
            need_sort	true
            operations	[{"__index__": 0, "op_column": "1", "op_name": "countunique"}]
            print_full_line	false

    • Step 25: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            column1	"20"
            column2	"1"
            dbkey	"?"
            empty_string_filler	"0"
            header	true
            ignore_case	false
            jointype	" "

    • Step 26: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            grouping	"1"
            header_in	true
            header_out	true
            ignore_case	false
            narm	false
            need_sort	true
            operations	[{"__index__": 0, "op_column": "2", "op_name": "unique"}]
            print_full_line	true

    • Step 27: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            column1	"3"
            column2	"1"
            dbkey	"?"
            empty_string_filler	"0"
            header	true
            ignore_case	false
            jointype	" "

    • Step 28: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c2,c3,c4,c5,c6,c7,c8,c9,c11,c12,c13,c14,c15,c16,c17,c18,c19"
            dbkey	"?"
            delimiter	"T"

    • Step 29: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c4,c6,c7,c13,c14,c15,c16,c17,c18,c19,c21,c22,c23,c26,c24,c25,c20"
            dbkey	"?"
            delimiter	"T"

    • Step 30: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            column1	"1"
            column2	"1"
            dbkey	"?"
            empty_string_filler	"0"
            header	true
            ignore_case	false
            jointype	" "

    • Step 4: DP_ALT Filter:

      • step_state: scheduled

    • Step 31: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            split_parms	{"__current_case__": 0, "input": {"values": [{"id": 25, "src": "hda"}]}, "select_ftype": "tabular", "split_by": {"__current_case__": 0, "id_col": "1", "match_regex": "(.*)", "select_split_by": "col", "sub_regex": "\\1"}, "top": "1"}

    • Step 32: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            caseinsensitive	"false"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            find_and_replace	[]
            find_pattern	"unique\\(Sample\\)\\tcollapse\\(Sample\\)\\tcollapse\\(AF\\)"
            global	"true"
            is_regex	"true"
            replace_pattern	"SAMPLES(above-thresholds)\\tSAMPLES(all)\\tAFs(all)"
            searchwhere	{"__current_case__": 0, "searchwhere_select": "line"}
            skip_first_line	"false"
            wholewords	"false"

    • Step 33: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c2,c1,c4,c5,c6,c7,c8,c9,c11,c10,c12,c13,c14,c15,c16,c17,c18,c23,c24,c25,c26,c19"
            dbkey	"?"
            delimiter	"T"

    • Step 34: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            header	"1"
            ignore_case	false
            sortkeys	[{"__index__": 0, "column": "1", "order": "", "style": "g"}]
            unique	false

    • Step 35: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            header	"1"
            ignore_case	false
            sortkeys	[{"__index__": 0, "column": "1", "order": "", "style": ""}, {"__index__": 1, "column": "2", "order": "", "style": "n"}]
            unique	false

    • Step 5: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • SnpSift -Xmx6G filter -f '/tmp/tmpqw2l5630/files/f/0/4/dataset_f04809ed-a172-4546-b608-eb9fb6b62fa7.dat' -e '/tmp/tmpqw2l5630/job_working_directory/000/2/configs/tmpnap77rwe' > '/tmp/tmpqw2l5630/job_working_directory/000/2/outputs/dataset_3a3562ef-4df1-4b1e-9365-c7896f102ee4.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"vcf"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_expression	{"__current_case__": 0, "expr": "DP >= 1", "type": "simple"}
            filtering	{"__current_case__": 0, "mode": "entries"}
            inverse	false

    • Step 6: 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__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            components	` [{"index": 0, "param_type": {"current_case": 0, "component_value": "( ( DP4[2] + DP4[3] ) < ( ", "select_param_type": "text"}}, {"index": 1, "param_type": {"current_case": 2, "component_value": "0.05", "select_param_type": "float"}}, {"index": 2, "param_type": {"current_case": 0, "component_value": " * DP ) )
            dbkey	"?"

    • Step 7: 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__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            components	` [{"index": 0, "param_type": {"current_case": 0, "component_value": "min_af_", "select_param_type": "text"}}, {"index": 1, "param_type": {"current_case": 2, "component_value": "0.05", "select_param_type": "float"}}, {"index": 2, "param_type": {"current_case": 0, "component_value": "
            dbkey	"?"

    • Step 8: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • SnpSift -Xmx6G filter -f '/tmp/tmpqw2l5630/files/3/a/3/dataset_3a3562ef-4df1-4b1e-9365-c7896f102ee4.dat' -e '/tmp/tmpqw2l5630/job_working_directory/000/5/configs/tmp_lz_v9xg' --addFilter min_af_0.05Xmin_dp_1Xmin_dp_alt_10 > '/tmp/tmpqw2l5630/job_working_directory/000/5/outputs/dataset_bd0cc2a6-939e-4dc3-b396-333b59d35bf1.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"vcf"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_expression	` {"current_case": 0, "expr": "( ( DP4[2] + DP4[3] ) < ( 0.05 * DP ) )
            filtering	` {"current_case": 3, "add_filter": "min_af_0.05
            inverse	false

    • Step 9: toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • if [ -z "$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=$(dirname $(readlink -e $(which SnpSift))); fi && cat '/tmp/tmpqw2l5630/files/b/d/0/dataset_bd0cc2a6-939e-4dc3-b396-333b59d35bf1.dat' | perl "$SNPSIFT_JAR_PATH/scripts/vcfEffOnePerLine.pl" | SnpSift -Xmx6G extractFields -e '.' - "CHROM" "POS" "FILTER" "REF" "ALT" "DP" "AF" "DP4" "SB" "EFF[*].IMPACT" "EFF[*].FUNCLASS" "EFF[*].EFFECT" "EFF[*].GENE" "EFF[*].CODON" "EFF[*].AA" "EFF[*].TRID" "DP4[2]" "DP4[3]"> '/tmp/tmpqw2l5630/job_working_directory/000/6/outputs/dataset_ef7ce1b0-16b3-47b8-b2d1-3cfaa2fec9f6.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"vcf"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            empty_text	"."
            extract	"CHROM POS FILTER REF ALT DP AF DP4 SB EFF[*].IMPACT EFF[*].FUNCLASS EFF[*].EFFECT EFF[*].GENE EFF[*].CODON EFF[*].AA EFF[*].TRID DP4[2] DP4[3]"
            one_effect_per_line	true
            separator	""

    • Step 10: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,str,str,str,int,float,list,int,str,str,str,str,str,str,str,int,int  --file '/tmp/tmpqw2l5630/job_working_directory/000/7/configs/tmpm38xqo1r' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpqw2l5630/files/e/f/7/dataset_ef7ce1b0-16b3-47b8-b2d1-3cfaa2fec9f6.dat' '/tmp/tmpqw2l5630/job_working_directory/000/7/outputs/dataset_1ce7912d-ff57-4645-a2d9-ded387082c7e.dat'

          Exit Code:

          • 1

          Standard Error:

          • Failed to convert some of the columns in line #0 to their expected types.  The error was: "invalid literal for int() with base 10: 'POS'" for the line: "CHROM	POS	FILTER	REF	ALT	DP	AF	DP4	SB	EFF[*].IMPACT	EFF[*].FUNCLASS	EFF[*].EFFECT	EFF[*].GENE	EFF[*].CODON	EFF[*].AA	EFF[*].TRID	DP4[2]	DP4[3]"
            

          Standard Output:

          • Computing 0 new columns with instructions []
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"a5d12ebc7a8211efb14b65e6de8472bb"
            avoid_scientific_notation	false
            chromInfo	"/tmp/tmpqw2l5630/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            cond	"round((c17 + c18) / c6, 6)"
            dbkey	"?"
            error_handling	{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}
            header_lines_conditional	{"__current_case__": 1, "header_lines_select": "yes", "header_new_column_name": "AFrecalc"}
            ops	{"__current_case__": 0, "expressions": [], "header_lines_select": "no"}
            round	"false"

  • Other invocation details

    • error_message

      • Failed to run workflow, at least one job is in [error] state.

    • history_id

      • 85ef8163134b5500

    • history_state

      • error

    • invocation_id

      • 85ef8163134b5500

    • invocation_state

      • scheduled

    • workflow_id

      • 85ef8163134b5500