Add annotation workflow with Braker3

[rlibouba]

Hello,
I would like to propose this workflow for annotating a genome from the GTN "Genome annotation with Braker3 ".
Thank you! Have a nice day!
Romane

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ Genome_annotation_with_braker3.ga_0

  Execution Problem:

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

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: BUSCO lineage:

      • step_state: scheduled

    • Step 2: Genome sequence masked:

      • step_state: scheduled

    • Step 11: BUSCO on the predicted protein sequences:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"b11a35c8096311f08a577c1e5258711c"
            adv	{"contig_break": "10", "evalue": "0.001", "limit": "3"}
            busco_mode	{"__current_case__": 1, "mode": "tran"}
            chromInfo	"/tmp/tmpd6ow920l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            lineage	{"__current_case__": 1, "lineage_dataset": "mucorales_odb10", "lineage_mode": "select_lineage"}
            lineage_conditional	{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}
            outputs	["short_summary", "image", "gff", "missing"]

    • Step 3: Alignments from RNA-seq:

      • step_state: scheduled

    • Step 4: Protein sequences:

      • step_state: scheduled

    • **Step 5: Fasta Statistics **:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/0dbb995c7d35/fasta_stats/fasta-stats.py' --fasta '/tmp/tmpd6ow920l/files/a/1/4/dataset_a146fbe2-8e88-4748-a103-fbaf427b6931.dat' --stats_output '/tmp/tmpd6ow920l/job_working_directory/000/4/outputs/dataset_ff264281-2a08-4cf4-93f8-ba97f261687f.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"b11a35c8096311f08a577c1e5258711c"
            chromInfo	"/tmp/tmpd6ow920l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            gaps_option	false
            genome_size	None

    • Step 6: BUSCO on the genome sequences:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Command Line:

          • busco --in '/tmp/tmpd6ow920l/files/a/1/4/dataset_a146fbe2-8e88-4748-a103-fbaf427b6931.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'mucorales_odb10'  --miniprot  && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"b11a35c8096311f08a577c1e5258711c"
            adv	{"contig_break": "10", "evalue": "0.001", "limit": "3"}
            busco_mode	{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 1, "use_augustus_selector": "miniprot"}}
            chromInfo	"/tmp/tmpd6ow920l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            lineage	{"__current_case__": 1, "lineage_dataset": "mucorales_odb10", "lineage_mode": "select_lineage"}
            lineage_conditional	{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}
            outputs	["short_summary", "image", "gff", "missing"]

    • Step 7: Braker3:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Command Line:

          • if [ -z "$GENEMARK_PATH" ] ; then echo "GeneMark is not installed on this Galaxy server." >&2 ; exit 1 ; fi && if [ ! -f "$GENEMARK_PATH/gmes/gmes_petap.pl" ] ; then echo "GeneMark is not installed properly on this Galaxy server." >&2 ; exit 1 ; fi &&   export PATH="$GENEMARK_PATH/../tools/:$PATH" &&  cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&  braker.pl --genome '/tmp/tmpd6ow920l/files/a/1/4/dataset_a146fbe2-8e88-4748-a103-fbaf427b6931.dat'   --bam /tmp/tmpd6ow920l/files/7/e/0/dataset_7e0f0928-399f-4896-a80d-a81cc5b3f027.dat  --prot_seq /tmp/tmpd6ow920l/files/a/c/8/dataset_ac8778fd-ee01-41ea-b719-3d29852470af.dat   --gff3  --fungus   --rounds 5          --alternatives-from-evidence=true    --gc_probability 0.001 --downsampling_lambda 2   --threads  ${GALAXY_SLOTS:-2} --useexisting

          Exit Code:

          • 1

          Standard Error:

          • /tmp/tmpd6ow920l/job_working_directory/000/6/tool_script.sh: line 23: /gmes/gmes_petap.pl: No such file or directory
            

          Standard Output:

          • braker.pl version 3.0.8
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"b11a35c8096311f08a577c1e5258711c"
            advanced	{"alternatives_from_evidence": true, "eval": null, "eval_pseudo": null, "filterOutShort": false}
            augustus	{"AUGUSTUS_ab_initio": false, "crf": false, "keepCrf": false, "rounds": "5"}
            chromInfo	"/tmp/tmpd6ow920l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            dev	{"downsampling_lambda": "2", "gc_probability": "0.001", "gm_max_intergenic": null, "min_contig": null, "splice_sites": null}
            evidences	{"bam": {"values": [{"id": 2, "src": "hda"}]}, "prot_seq": {"values": [{"id": 3, "src": "hda"}]}}
            genemark	{"fungus": true}
            output_format	"gff3"
            softmasking	true
            species	None

    • Step 8: GFFRead:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"b11a35c8096311f08a577c1e5258711c"
            chr_replace	None
            chromInfo	"/tmp/tmpd6ow920l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            decode_url	false
            expose	false
            filtering	None
            full_gff_attribute_preservation	false
            gffs	{"__current_case__": 0, "gff_fmt": "none"}
            maxintron	None
            merging	{"__current_case__": 0, "merge_sel": "none"}
            reference_genome	{"__current_case__": 2, "fa_outputs": ["-y pep.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}
            region	{"__current_case__": 0, "region_filter": "none"}

    • Step 9: JBrowse:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fasta"
            __workflow_invocation_uuid__	"b11a35c8096311f08a577c1e5258711c"
            action	{"__current_case__": 0, "action_select": "create"}
            chromInfo	"/tmp/tmpd6ow920l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            gencode	"1"
            jbgen	{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}
            plugins	{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}
            reference_genome	{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}
            standalone	"minimal"
            track_groups	[{"__index__": 0, "category": "Braker3 annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 10, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
            uglyTestingHack	""

    • Step 10: OMArk:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is paused

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"b11a35c8096311f08a577c1e5258711c"
            chromInfo	"/tmp/tmpd6ow920l/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            database	"LUCA-v2.0.0.h5"
            dbkey	"?"
            input_iso	None
            omark_mode	false
            outputs	"detail_sum"
            r	None
            t	None

  • Other invocation details

    • error_message

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

    • history_id

      • 85e23c94bcb17d8c

    • history_state

      • error

    • invocation_id

      • 85e23c94bcb17d8c

    • invocation_state

      • scheduled

    • workflow_id

      • 85e23c94bcb17d8c

[github-actions]

Test Results (powered by Planemo)

Test Summary

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

Errored Tests

• ❌ Genome_annotation_with_braker3.ga_0

  Execution Problem:

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

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: BUSCO lineage:

      • step_state: scheduled

    • Step 2: Genome sequence masked:

      • step_state: scheduled

    • Step 3: Alignments from RNA-seq:

      • step_state: scheduled

    • Step 4: Protein sequences:

      • step_state: scheduled

    • Step 5: BUSCO on the genome sequences:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Command Line:

          • ln -s '/tmp/tmp87j16dob/files/7/6/2/dataset_762691bf-c0ae-4fc1-9e71-cf0076d3667a.dat' input.fa &&  busco --in 'input.fa' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10 --offline --download_path '/cvmfs/data.galaxyproject.org/byhand/busco/v5'  --lineage_dataset 'mucorales_odb10'  --miniprot  && mkdir BUSCO_summaries && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && (cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true)

          Exit Code:

          • 127

          Standard Error:

          • /tmp/tmp87j16dob/job_working_directory/000/4/tool_script.sh: line 10: busco: command not found
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"8d70ba5e477d11f0bb097c1e524172af"
            adv	{"contig_break": "10", "evalue": "0.001", "limit": "3"}
            busco_mode	{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 1, "use_augustus_selector": "miniprot"}}
            cached_db	"v5"
            chromInfo	"/tmp/tmp87j16dob/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            lineage	{"__current_case__": 1, "lineage_dataset": "mucorales_odb10", "lineage_mode": "select_lineage"}
            outputs	["short_summary", "image", "gff", "missing"]
            test	None

    • Step 6: Braker3:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Command Line:

          • if [ -z "$GENEMARK_PATH" ] ; then echo "GeneMark is not installed on this Galaxy server." >&2 ; exit 1 ; fi && if [ ! -f "$GENEMARK_PATH/gmes/gmes_petap.pl" ] ; then echo "GeneMark is not installed properly on this Galaxy server." >&2 ; exit 1 ; fi &&   export PATH="$GENEMARK_PATH/../tools/:$PATH" &&  cp -r "$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&  braker.pl --genome '/tmp/tmp87j16dob/files/7/6/2/dataset_762691bf-c0ae-4fc1-9e71-cf0076d3667a.dat'   --bam /tmp/tmp87j16dob/files/1/a/4/dataset_1a4ac51e-fa2b-411b-9f1c-acfe154f5d82.dat  --prot_seq /tmp/tmp87j16dob/files/c/6/1/dataset_c6147020-bcb8-4710-a846-bdcb5a5b5482.dat   --gff3     --rounds 5          --alternatives-from-evidence=true    --gc_probability 0.001 --downsampling_lambda 2   --threads  ${GALAXY_SLOTS:-2} --useexisting

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"8d70ba5e477d11f0bb097c1e524172af"
            advanced	{"alternatives_from_evidence": true, "eval": null, "eval_pseudo": null, "filterOutShort": false}
            augustus	{"AUGUSTUS_ab_initio": false, "crf": false, "keepCrf": false, "rounds": "5"}
            chromInfo	"/tmp/tmp87j16dob/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            dev	{"downsampling_lambda": "2", "gc_probability": "0.001", "gm_max_intergenic": null, "min_contig": null, "splice_sites": null}
            evidences	{"bam": {"values": [{"id": 2, "src": "hda"}]}, "prot_seq": {"values": [{"id": 3, "src": "hda"}]}}
            genemark	{"fungus": false}
            output_format	"gff3"
            softmasking	true
            species	None

    • Step 7: JBrowse:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fasta"
            __workflow_invocation_uuid__	"8d70ba5e477d11f0bb097c1e524172af"
            action	{"__current_case__": 0, "action_select": "create"}
            chromInfo	"/tmp/tmp87j16dob/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            gencode	"1"
            jbgen	{"aboutDescription": "", "defaultLocation": "", "hideGenomeOptions": false, "shareLink": true, "show_menu": true, "show_nav": true, "show_overview": true, "show_tracklist": true, "trackPadding": "20"}
            plugins	{"BlastView": true, "ComboTrackSelector": false, "GCContent": false}
            reference_genome	{"__current_case__": 1, "genome": {"values": [{"id": 1, "src": "hda"}]}, "genome_type_select": "history"}
            standalone	"minimal"
            track_groups	[{"__index__": 0, "category": "Helixer Annotation", "data_tracks": [{"__index__": 0, "data_format": {"__current_case__": 2, "annotation": {"values": [{"id": 9, "src": "hda"}]}, "data_format_select": "gene_calls", "index": false, "jb_custom_config": {"option": []}, "jbcolor_scale": {"color_score": {"__current_case__": 0, "color": {"__current_case__": 0, "color_select": "automatic"}, "color_score_select": "none"}}, "jbmenu": {"track_menu": []}, "jbstyle": {"max_height": "600", "style_classname": "feature", "style_description": "note,description", "style_height": "10px", "style_label": "product,name,id"}, "match_part": {"__current_case__": 1, "match_part_select": false}, "override_apollo_drag": "False", "override_apollo_plugins": "False", "track_config": {"__current_case__": 3, "html_options": {"topLevelFeatures": null}, "track_class": "NeatHTMLFeatures/View/Track/NeatFeatures"}, "track_visibility": "default_off"}}]}]
            uglyTestingHack	""

    • Step 8: GFFRead:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"8d70ba5e477d11f0bb097c1e524172af"
            chr_replace	None
            chromInfo	"/tmp/tmp87j16dob/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            decode_url	false
            expose	false
            filtering	None
            full_gff_attribute_preservation	false
            gffs	{"__current_case__": 0, "gff_fmt": "none"}
            maxintron	None
            merging	{"__current_case__": 0, "merge_sel": "none"}
            reference_genome	{"__current_case__": 2, "fa_outputs": ["-y pep.fa"], "genome_fasta": {"values": [{"id": 1, "src": "hda"}]}, "ref_filtering": null, "source": "history"}
            region	{"__current_case__": 0, "region_filter": "none"}

    • Step 9: OMArk:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"8d70ba5e477d11f0bb097c1e524172af"
            chromInfo	"/tmp/tmp87j16dob/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            database	"LUCA-v2.0.0.h5"
            dbkey	"?"
            input_iso	None
            omark_mode	false
            outputs	"detail_sum"
            r	None
            t	None

    • Step 10: BUSCO on the predicted protein sequences:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is new

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"8d70ba5e477d11f0bb097c1e524172af"
            adv	{"contig_break": "10", "evalue": "0.001", "limit": "3"}
            busco_mode	{"__current_case__": 1, "mode": "tran"}
            cached_db	"v5"
            chromInfo	"/tmp/tmp87j16dob/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            lineage	{"__current_case__": 1, "lineage_dataset": "mucorales_odb10", "lineage_mode": "select_lineage"}
            outputs	["short_summary", "image", "gff", "missing"]
            test	None

  • Other invocation details

    • error_message

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

    • history_id

      • 1af438c5f7138931

    • history_state

      • error

    • invocation_id

      • 1af438c5f7138931

    • invocation_state

      • scheduled

    • workflow_id

      • 1af438c5f7138931

[mvdbeek]

You seem to have helixer changes in here, let me know if you want to remove those ?

[rlibouba]

Hi @mvdbeek, I had a conflict, so I tried a rebase to fix it.

[rlibouba]

I wanted to let users choose which database to use.

[rlibouba]

Hello @Delphine-L , Do you think these latest changes are good ?

[rlibouba]

Hello @mvdbeek and @Delphine-L, do you think this PR can be merged? Or are there other changes that need to be made?
Have a nice day!

[Copilot]

Pull request overview

This PR adds a new genome annotation workflow using Braker3 to the IWC repository. The workflow integrates RNA-seq and protein data to annotate eukaryotic genomes, with quality evaluation using BUSCO and OMArk, sequence extraction with GFFRead, and visualization via JBrowse.

Key changes:

• New workflow for genome annotation with Braker3 that combines GeneMark-ETP and AUGUSTUS predictions
• Comprehensive quality evaluation with BUSCO (on both genome and predicted proteins) and OMArk
• Support for both fungal and non-fungal genomes with configurable parameters

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
Genome_annotation_with_braker3.ga	Main workflow file defining the Braker3 annotation pipeline with quality evaluation steps
Genome_annotation_with_braker3-tests.yml	Test configuration using Zenodo-hosted test data (mucorales genome)
README.md	Documentation explaining workflow purpose, inputs, steps, and expected outputs
CHANGELOG.md	Version history documenting the initial release
.dockstore.yml	Dockstore configuration with correct file paths and author information

[mvdbeek]

@copilot open a new pull request to apply changes based on the comments in this thread

[mvdbeek]

Looks great as always, thank you @rlibouba!