Updating workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling from 0.1.5 to 0.1.6

[gxydevbot]

Hello! This is an automated update of the following workflow: workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated: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/bowtie2/bowtie2/2.5.3+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1

The workflow release number has been updated from 0.1.5 to 0.1.6.

[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

• ❌ se-wgs-variation.ga_0

  Execution Problem:

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

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Single End Collection:

      • step_state: scheduled

    • Step 2: NC_045512.2 FASTA sequence of SARS-CoV-2:

      • step_state: scheduled

    • Step 11: SnpEff eff covid19 version:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"vcf"
            __workflow_invocation_uuid__	"7dbe08f679be11efb0af2d237307951c"
            annotations	["-formatEff", "-classic"]
            chr	""
            chromInfo	"/tmp/tmp3lbo38ju/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            csvStats	false
            dbkey	"?"
            filter	{"__current_case__": 0, "specificEffects": "no"}
            filterOut	["-no-downstream", "-no-intergenic", "-no-upstream", "-no-utr"]
            generate_stats	true
            genome_version	"NC_045512.2"
            inputFormat	"vcf"
            intervals	None
            noLog	true
            offset	"default"
            outputConditional	{"__current_case__": 0, "outputFormat": "vcf"}
            transcripts	None
            udLength	"0"

    • Step 3: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Command Line:

          • ln -sf '/tmp/tmp3lbo38ju/files/a/f/c/dataset_afcee5b7-a176-4a8d-9ac9-313c1fd0c102.dat' 'SRR11605118.fastq' &&     fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for SRR11605118.fastq'   -i 'SRR11605118.fastq' -o first.fastq                                                 &&  mv first.fastq '/tmp/tmp3lbo38ju/job_working_directory/000/3/outputs/dataset_a8d47fb6-cf63-457a-a79f-dee2050a0f9c.dat'

          Exit Code:

          • 255

          Standard Error:

          • Expected '+', got �B���
            >O��g��r
            C9���f��h�UV���P�T��){,����ؑ�p�6
            ����:��mR%�Y?[gjk^�叐��Mf��+��V-T���h������:��3��,
            ]�kY �/�����m7G�J
            "�Hy�'����K��O�En
            ERROR: '+' expected
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7dbe08f679be11efb0af2d237307951c"
            chromInfo	"/tmp/tmp3lbo38ju/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_options	{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}
            output_options	{"report_html": true, "report_json": true}
            overrepresented_sequence_analysis	{"overrepresentation_analysis": false, "overrepresentation_sampling": null}
            read_mod_options	{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}
            single_paired	{"__current_case__": 0, "adapter_trimming_options": {"adapter_sequence1": "", "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_tail1": null}, "in1": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "single"}

    • Step 4: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7dbe08f679be11efb0af2d237307951c"
            analysis_type	{"__current_case__": 0, "analysis_type_selector": "simple", "presets": "--very-sensitive"}
            chromInfo	"/tmp/tmp3lbo38ju/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            library	{"__current_case__": 0, "aligned_file": false, "input_1": {"values": [{"id": 2, "src": "dce"}]}, "type": "single", "unaligned_file": false}
            reference_genome	{"__current_case__": 1, "own_file": {"values": [{"id": 1, "src": "hda"}]}, "source": "history"}
            rg	{"__current_case__": 2, "rg_selector": "set_id_auto"}
            sam_options	{"__current_case__": 1, "sam_options_selector": "no"}
            save_mapping_stats	true

    • Step 5: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7dbe08f679be11efb0af2d237307951c"
            assume_sorted	true
            barcode_tag	""
            chromInfo	"/tmp/tmp3lbo38ju/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            comments	[]
            dbkey	"?"
            duplicate_scoring_strategy	"SUM_OF_BASE_QUALITIES"
            inputFile	__identifier__
            optical_duplicate_pixel_distance	"100"
            read_name_regex	""
            remove_duplicates	true
            validation_stringency	"LENIENT"

    • Step 6: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7dbe08f679be11efb0af2d237307951c"
            chromInfo	"/tmp/tmp3lbo38ju/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            comment	""
            dbkey	"?"
            export	false
            flat	false
            results	[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 3, "input": {"values": [{"id": 6, "src": "hdca"}]}, "software": "bowtie2"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
            saveLog	"false"
            title	""

    • Step 7: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7dbe08f679be11efb0af2d237307951c"
            adv_options	{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}
            chromInfo	"/tmp/tmp3lbo38ju/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            reference_source	{"__current_case__": 1, "ref": {"values": [{"id": 1, "src": "hda"}]}, "ref_selector": "history"}

    • Step 8: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7dbe08f679be11efb0af2d237307951c"
            chromInfo	"/tmp/tmp3lbo38ju/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            strategy	{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 1, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}

    • Step 9: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7dbe08f679be11efb0af2d237307951c"
            call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "20", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
            chromInfo	"/tmp/tmp3lbo38ju/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_control	{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}
            reference_source	{"__current_case__": 1, "ref": {"values": [{"id": 1, "src": "hda"}]}, "ref_selector": "history"}
            regions	{"__current_case__": 0, "restrict_to_region": "genome"}
            variant_types	"--call-indels"

    • Step 10: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7dbe08f679be11efb0af2d237307951c"
            af	{"af_max": "0.0", "af_min": "0.0"}
            chromInfo	"/tmp/tmp3lbo38ju/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	{"cov_max": "0", "cov_min": "0"}
            dbkey	"?"
            filter_by_type	{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}
            flag_or_drop	"--print-all"
            sb	{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}

  • Other invocation details

    • error_message

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

    • history_id

      • d52bafc72fd3d302

    • history_state

      • error

    • invocation_id

      • d52bafc72fd3d302

    • invocation_state

      • scheduled

    • workflow_id

      • d52bafc72fd3d302

[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

• ❌ se-wgs-variation.ga_0

  Execution Problem:

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

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Single End Collection:

      • step_state: scheduled

    • Step 2: NC_045512.2 FASTA sequence of SARS-CoV-2:

      • step_state: scheduled

    • Step 11: SnpEff eff covid19 version:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"vcf"
            __workflow_invocation_uuid__	"c6d337fa7a8111efae09a1b535a11c9c"
            annotations	["-formatEff", "-classic"]
            chr	""
            chromInfo	"/tmp/tmpttc56a5y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            csvStats	false
            dbkey	"?"
            filter	{"__current_case__": 0, "specificEffects": "no"}
            filterOut	["-no-downstream", "-no-intergenic", "-no-upstream", "-no-utr"]
            generate_stats	true
            genome_version	"NC_045512.2"
            inputFormat	"vcf"
            intervals	None
            noLog	true
            offset	"default"
            outputConditional	{"__current_case__": 0, "outputFormat": "vcf"}
            transcripts	None
            udLength	"0"

    • Step 3: toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Command Line:

          • ln -sf '/tmp/tmpttc56a5y/files/a/b/7/dataset_ab7495b6-aec1-476f-a9b6-b640a490e374.dat' 'SRR11605118.fastq' &&     fastp  --thread ${GALAXY_SLOTS:-1} --report_title 'fastp report for SRR11605118.fastq'   -i 'SRR11605118.fastq' -o first.fastq                                                 &&  mv first.fastq '/tmp/tmpttc56a5y/job_working_directory/000/3/outputs/dataset_cdfeb723-86ab-46c3-a7c5-02e8c895e5b2.dat'

          Exit Code:

          • 255

          Standard Error:

          • Expected '+', got �B���
            >O��g��r
            C9���f��h�UV���P�T��){,����ؑ�p�6
            ����:��mR%�Y?[gjk^�叐��Mf��+��V-T���h������:��3��,
            ]�kY �/�����m7G�J
            "�Hy�'����K��O�En
            ERROR: '+' expected
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c6d337fa7a8111efae09a1b535a11c9c"
            chromInfo	"/tmp/tmpttc56a5y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_options	{"length_filtering_options": {"disable_length_filtering": false, "length_limit": null, "length_required": null}, "low_complexity_filter": {"complexity_threshold": null, "enable_low_complexity_filter": false}, "quality_filtering_options": {"disable_quality_filtering": false, "n_base_limit": null, "qualified_quality_phred": null, "unqualified_percent_limit": null}}
            output_options	{"report_html": true, "report_json": true}
            overrepresented_sequence_analysis	{"overrepresentation_analysis": false, "overrepresentation_sampling": null}
            read_mod_options	{"base_correction_options": {"correction": false}, "cutting_by_quality_options": {"cut_by_quality3": false, "cut_by_quality5": false, "cut_mean_quality": null, "cut_window_size": null}, "polyg_tail_trimming": {"__current_case__": 1, "poly_g_min_len": null, "trimming_select": ""}, "polyx_tail_trimming": {"__current_case__": 1, "polyx_trimming_select": ""}, "umi_processing": {"umi": false, "umi_len": null, "umi_loc": "", "umi_prefix": ""}}
            single_paired	{"__current_case__": 0, "adapter_trimming_options": {"adapter_sequence1": "", "disable_adapter_trimming": false}, "global_trimming_options": {"trim_front1": null, "trim_tail1": null}, "in1": {"values": [{"id": 1, "src": "dce"}]}, "single_paired_selector": "single"}

    • Step 4: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c6d337fa7a8111efae09a1b535a11c9c"
            analysis_type	{"__current_case__": 0, "analysis_type_selector": "simple", "presets": "--very-sensitive"}
            chromInfo	"/tmp/tmpttc56a5y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            library	{"__current_case__": 0, "aligned_file": false, "input_1": {"values": [{"id": 2, "src": "dce"}]}, "type": "single", "unaligned_file": false}
            reference_genome	{"__current_case__": 1, "own_file": {"values": [{"id": 1, "src": "hda"}]}, "source": "history"}
            rg	{"__current_case__": 2, "rg_selector": "set_id_auto"}
            sam_options	{"__current_case__": 1, "sam_options_selector": "no"}
            save_mapping_stats	true

    • Step 5: toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c6d337fa7a8111efae09a1b535a11c9c"
            assume_sorted	true
            barcode_tag	""
            chromInfo	"/tmp/tmpttc56a5y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            comments	[]
            dbkey	"?"
            duplicate_scoring_strategy	"SUM_OF_BASE_QUALITIES"
            inputFile	__identifier__
            optical_duplicate_pixel_distance	"100"
            read_name_regex	""
            remove_duplicates	true
            validation_stringency	"LENIENT"

    • Step 6: toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c6d337fa7a8111efae09a1b535a11c9c"
            chromInfo	"/tmp/tmpttc56a5y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            comment	""
            dbkey	"?"
            export	false
            flat	false
            results	[{"__index__": 0, "software_cond": {"__current_case__": 7, "input": {"values": [{"id": 4, "src": "hdca"}]}, "software": "fastp"}}, {"__index__": 1, "software_cond": {"__current_case__": 3, "input": {"values": [{"id": 6, "src": "hdca"}]}, "software": "bowtie2"}}, {"__index__": 2, "software_cond": {"__current_case__": 17, "output": [{"__index__": 0, "input": {"values": [{"id": 7, "src": "hdca"}]}, "type": "markdups"}], "software": "picard"}}]
            saveLog	"false"
            title	""

    • Step 7: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c6d337fa7a8111efae09a1b535a11c9c"
            adv_options	{"bq2_handling": {"__current_case__": 0, "defqual": "2", "replace_bq2": "keep"}, "keepflags": false}
            chromInfo	"/tmp/tmpttc56a5y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            reference_source	{"__current_case__": 1, "ref": {"values": [{"id": 1, "src": "hda"}]}, "ref_selector": "history"}

    • Step 8: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c6d337fa7a8111efae09a1b535a11c9c"
            chromInfo	"/tmp/tmpttc56a5y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            strategy	{"__current_case__": 1, "reference_source": {"__current_case__": 1, "ref": {"values": [{"id": 1, "src": "hda"}]}, "ref_selector": "history"}, "selector": "dindel"}

    • Step 9: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c6d337fa7a8111efae09a1b535a11c9c"
            call_control	{"__current_case__": 1, "align_quals": {"alnqual": {"__current_case__": 0, "alnqual_choice": {"__current_case__": 1, "alnquals_to_use": "", "extended_baq": true}, "use_alnqual": ""}}, "bc_quals": {"alt_bq": {"__current_case__": 0, "modify": ""}, "min_alt_bq": "30", "min_bq": "30"}, "coverage": {"max_depth": "1000000", "min_cov": "5"}, "joint_qual": {"def_alt_jq": "0", "min_alt_jq": "0", "min_jq": "0"}, "map_quals": {"min_mq": "20", "use_mq": {"__current_case__": 0, "max_mq": "255", "no_mq": ""}}, "pe": {"use_orphan": false}, "set_call_options": "yes", "source_qual": {"use_src_qual": {"__current_case__": 0, "src_qual": ""}}}
            chromInfo	"/tmp/tmpttc56a5y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            filter_control	{"__current_case__": 3, "bonf": "0", "filter_type": "set_custom", "others": false, "sig": "0.0005"}
            reference_source	{"__current_case__": 1, "ref": {"values": [{"id": 1, "src": "hda"}]}, "ref_selector": "history"}
            regions	{"__current_case__": 0, "restrict_to_region": "genome"}
            variant_types	"--call-indels"

    • Step 10: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c6d337fa7a8111efae09a1b535a11c9c"
            af	{"af_max": "0.0", "af_min": "0.0"}
            chromInfo	"/tmp/tmpttc56a5y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            coverage	{"cov_max": "0", "cov_min": "0"}
            dbkey	"?"
            filter_by_type	{"__current_case__": 0, "keep_only": "", "qual": {"indelqual_filter": {"__current_case__": 0, "indelqual": "no"}, "snvqual_filter": {"__current_case__": 0, "snvqual": "no"}}}
            flag_or_drop	"--print-all"
            sb	{"sb_filter": {"__current_case__": 2, "sb_alpha": "0.001", "sb_compound": true, "sb_indels": false, "sb_mtc": "fdr", "strand_bias": "mtc"}}

  • Other invocation details

    • error_message

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

    • history_id

      • 35ad36521520aef7

    • history_state

      • error

    • invocation_id

      • 35ad36521520aef7

    • invocation_state

      • scheduled

    • workflow_id

      • 35ad36521520aef7