Updating workflows/variant-calling/variation-reporting from 0.1.1 to 0.1.2

[gxydevbot]

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 I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated: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_column1/2.1
• 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/1.8+galaxy0
• 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/9.5+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 should be updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0 should be updated to toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 should be updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.5+galaxy0

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

• ❌ 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__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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/9.5+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"00e8c9d8fd7611efbdfa6045bd093052"
            caseinsensitive	"false"
            chromInfo	"/tmp/tmpnqas0bqu/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/9.5+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"00e8c9d8fd7611efbdfa6045bd093052"
            caseinsensitive	"false"
            chromInfo	"/tmp/tmpnqas0bqu/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/9.5+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"00e8c9d8fd7611efbdfa6045bd093052"
            caseinsensitive	"false"
            chromInfo	"/tmp/tmpnqas0bqu/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__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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__	"00e8c9d8fd7611efbdfa6045bd093052"
            avoid_scientific_notation	false
            chromInfo	"/tmp/tmpnqas0bqu/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__	"00e8c9d8fd7611efbdfa6045bd093052"
            avoid_scientific_notation	false
            chromInfo	"/tmp/tmpnqas0bqu/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/9.5+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"00e8c9d8fd7611efbdfa6045bd093052"
            caseinsensitive	"false"
            chromInfo	"/tmp/tmpnqas0bqu/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__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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/9.5+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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/9.5+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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/9.5+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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/9.5+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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/9.5+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"00e8c9d8fd7611efbdfa6045bd093052"
            caseinsensitive	"false"
            chromInfo	"/tmp/tmpnqas0bqu/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__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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/9.5+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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/9.5+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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/tmpnqas0bqu/files/2/e/6/dataset_2e6c9ba4-eade-4fa0-b156-2b2d7ef85a60.dat' -e '/tmp/tmpnqas0bqu/job_working_directory/000/2/configs/tmp0a6vltsw' > '/tmp/tmpnqas0bqu/job_working_directory/000/2/outputs/dataset_b4d89567-ce90-4cc0-822c-47ccde380b96.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"vcf"
            __workflow_invocation_uuid__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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/tmpnqas0bqu/files/b/4/d/dataset_b4d89567-ce90-4cc0-822c-47ccde380b96.dat' -e '/tmp/tmpnqas0bqu/job_working_directory/000/5/configs/tmp02h2ttli' --addFilter min_af_0.05Xmin_dp_1Xmin_dp_alt_10 > '/tmp/tmpnqas0bqu/job_working_directory/000/5/outputs/dataset_1a6220af-ebf9-4a78-a3f3-379da1a6d633.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"vcf"
            __workflow_invocation_uuid__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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 $(which SnpSift))); fi && cat '/tmp/tmpnqas0bqu/files/1/a/6/dataset_1a6220af-ebf9-4a78-a3f3-379da1a6d633.dat' | perl "$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/tmpnqas0bqu/job_working_directory/000/6/outputs/dataset_a0fa0bb9-2622-408c-9b91-8ab23338860a.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"vcf"
            __workflow_invocation_uuid__	"00e8c9d8fd7611efbdfa6045bd093052"
            chromInfo	"/tmp/tmpnqas0bqu/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/tmpnqas0bqu/job_working_directory/000/7/configs/tmpwihxvvnt' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpnqas0bqu/files/a/0/f/dataset_a0fa0bb9-2622-408c-9b91-8ab23338860a.dat' '/tmp/tmpnqas0bqu/job_working_directory/000/7/outputs/dataset_02999cf7-552d-4ec6-9596-de9004ceafe1.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__	"00e8c9d8fd7611efbdfa6045bd093052"
            avoid_scientific_notation	false
            chromInfo	"/tmp/tmpnqas0bqu/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

      • 7aac19faf60ae10e

    • history_state

      • error

    • invocation_id

      • 7aac19faf60ae10e

    • invocation_state

      • scheduled

    • workflow_id

      • 7aac19faf60ae10e

[mvdbeek]

The problem is in step 10: 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]" . @wm75 would you have some time to look at this ?