Updating workflows/VGP-assembly-v2/Assembly-decontamination-VGP9 from 0.3 to 0.4

[gxydevbot]

Hello! This is an automated update of the following workflow: workflows/VGP-assembly-v2/Assembly-decontamination-VGP9. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated: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/bgruening/gfastats/gfastats/1.3.6+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0

The workflow release number has been updated from 0.3 to 0.4.

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	1
Error	0
Failure	0
Skipped	0

Passed Tests

• ✅ Assembly-decontamination-VGP9.ga_0

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: Scaffolded assembly (fasta):

      • step_state: scheduled

    • Step 2: Database for Kraken2:

      • step_state: scheduled

    • Step 11: concatenate scaffold lists:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • cat '/tmp/tmpm36tshk2/files/5/3/f/dataset_53fc7098-302b-4a89-aada-ef86a607b6bb.dat' >> '/tmp/tmpm36tshk2/job_working_directory/000/10/outputs/dataset_be97d550-6f41-40d0-9248-7afd6365b97a.dat' && cat '/tmp/tmpm36tshk2/files/d/7/a/dataset_d7a043b6-b8fa-4c30-ac0c-985a70c450df.dat' >> '/tmp/tmpm36tshk2/job_working_directory/000/10/outputs/dataset_be97d550-6f41-40d0-9248-7afd6365b97a.dat' && exit 0

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"edfc915689e411efb621000d3a38214b"
            chromInfo	"/tmp/tmpm36tshk2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            queries	[]

    • **Step 12: removing scaffolds **:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • gfastats '/tmp/tmpm36tshk2/files/c/8/0/dataset_c8036db4-7b6a-4d7d-a325-488b34e5bfce.dat'  --exclude-bed /tmp/tmpm36tshk2/files/b/e/9/dataset_be97d550-6f41-40d0-9248-7afd6365b97a.dat   -o dataset.fasta.gz --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

          Exit Code:

          • 0

          Standard Output:

          • +++Assembly summary+++: 
            # scaffolds: 0
            Total scaffold length: 0
            Average scaffold length: nan
            Scaffold N50: 0
            Scaffold auN: 0.00
            Scaffold L50: 0
            Largest scaffold: 0
            Smallest scaffold: 0
            # contigs: 0
            Total contig length: 0
            Average contig length: nan
            Contig N50: 0
            Contig auN: 0.00
            Contig L50: 0
            Largest contig: 0
            Smallest contig: 0
            # gaps in scaffolds: 0
            Total gap length in scaffolds: 0
            Average gap length in scaffolds: 0.00
            Gap N50 in scaffolds: 0
            Gap auN in scaffolds: 0.00
            Gap L50 in scaffolds: 0
            Largest gap in scaffolds: 0
            Smallest gap in scaffolds: 0
            Base composition (A:C:G:T): 0:0:0:0
            GC content %: 0.00
            # soft-masked bases: 0
            # segments: 0
            Total segment length: 0
            Average segment length: nan
            # gaps: 0
            # paths: 0
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"edfc915689e411efb621000d3a38214b"
            chromInfo	"/tmp/tmpm36tshk2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            mode_condition	{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 1, "line_length": null, "out_format": "fasta.gz"}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}
            target_condition	{"__current_case__": 1, "exclude_bed": {"values": [{"id": 13, "src": "hda"}]}, "include_bed": null, "target_option": "true", "target_sequence": ""}

    • **Step 3: soft-masking **:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • dustmasker -in '/tmp/tmpm36tshk2/files/c/8/0/dataset_c8036db4-7b6a-4d7d-a325-488b34e5bfce.dat' -infmt fasta -out '/tmp/tmpm36tshk2/job_working_directory/000/2/outputs/dataset_a29418e9-2758-40cc-bc87-3cf000ceee83.dat' -window 64 -level 40 -linker 1 -outfmt fasta

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fasta"
            __workflow_invocation_uuid__	"edfc915689e411efb621000d3a38214b"
            chromInfo	"/tmp/tmpm36tshk2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            db_opts	{"__current_case__": 2, "database": "", "db_opts_selector": "file", "histdb": "", "subject": {"values": [{"id": 1, "src": "hda"}]}}
            dbkey	"?"
            level	"40"
            linker	"1"
            outformat	"fasta"
            window	"64"

    • Step 4: hard-masking:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • sed --sandbox -r -f '/tmp/tmpm36tshk2/job_working_directory/000/3/configs/tmp5bp40fsu' '/tmp/tmpm36tshk2/files/a/2/9/dataset_a29418e9-2758-40cc-bc87-3cf000ceee83.dat' > '/tmp/tmpm36tshk2/job_working_directory/000/3/outputs/dataset_c4d0e10f-93d3-46a9-99bb-b8b608bfc949.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"edfc915689e411efb621000d3a38214b"
            adv_opts	{"__current_case__": 0, "adv_opts_selector": "basic"}
            chromInfo	"/tmp/tmpm36tshk2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            code	"/^>/!y/atcgn/NNNNN/"
            dbkey	"?"

    • Step 5: ID non-target contaminants:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • kraken2 --threads ${GALAXY_SLOTS:-1} --db '/cvmfs/data.galaxyproject.org/managed/kraken2_databases/kraken2_viral_db'    '/tmp/tmpm36tshk2/files/c/4/d/dataset_c4d0e10f-93d3-46a9-99bb-b8b608bfc949.dat'  --classified-out '/tmp/tmpm36tshk2/job_working_directory/000/4/outputs/dataset_d03399c1-1e39-415e-9060-1365536aa84a.dat' --unclassified-out '/tmp/tmpm36tshk2/job_working_directory/000/4/outputs/dataset_78aea8b4-47a9-44bd-bba8-1305dfa384b9.dat'  --confidence '0.3' --minimum-base-quality '0' --minimum-hit-groups '2'  --use-names   > '/tmp/tmpm36tshk2/job_working_directory/000/4/outputs/dataset_4c65beec-8f49-40b8-8de9-533a944f9811.dat'

          Exit Code:

          • 0

          Standard Error:

          • Loading database information... done.
            9 sequences (2.57 Mbp) processed in 0.171s (3.2 Kseq/m, 902.82 Mbp/m).
              1 sequences classified (11.11%)
              8 sequences unclassified (88.89%)
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fasta"
            __workflow_invocation_uuid__	"edfc915689e411efb621000d3a38214b"
            chromInfo	"/tmp/tmpm36tshk2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            confidence	"0.3"
            dbkey	"?"
            kraken2_database	"viral2019-03"
            min_base_quality	"0"
            minimum_hit_groups	"2"
            quick	false
            report	{"create_report": false, "report_minimizer_data": false, "report_zero_counts": false, "use_mpa_style": false}
            single_paired	{"__current_case__": 2, "input_sequences": {"values": [{"id": 3, "src": "hda"}]}, "single_paired_selector": "no"}
            split_reads	true
            use_names	true

    • Step 6: blast mitochondria DB:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • blastn  -query '/tmp/tmpm36tshk2/files/c/4/d/dataset_c4d0e10f-93d3-46a9-99bb-b8b608bfc949.dat'   -db '"/cvmfs/data.galaxyproject.org/byhand/refseq/mitochondrion/genomic/2022-03-10/mitochondrion"'  -task 'blastn' -evalue '0.001' -out '/tmp/tmpm36tshk2/job_working_directory/000/5/outputs/dataset_34eb4cef-ecaf-4ff3-bfcf-846f10b2cb57.dat' -outfmt '6 qseqid sseqid length qstart qend evalue qlen qcovs qcovhsp'  -num_threads "${GALAXY_SLOTS:-8}"

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"fasta"
            __workflow_invocation_uuid__	"edfc915689e411efb621000d3a38214b"
            adv_opts	{"__current_case__": 0, "adv_opts_selector": "basic"}
            blast_type	"blastn"
            chromInfo	"/tmp/tmpm36tshk2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            db_opts	{"__current_case__": 0, "database": ["refseq_mitochondrion"], "db_opts_selector": "db", "histdb": "", "subject": ""}
            dbkey	"?"
            evalue_cutoff	"0.001"
            output	{"__current_case__": 2, "ext_cols": ["qlen"], "ids_cols": null, "misc_cols": ["qcovs", "qcovhsp"], "out_format": "cols", "std_cols": ["qseqid", "sseqid", "length", "qstart", "qend", "evalue"], "tax_cols": null}

    • Step 7: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • perl '/tmp/tmpm36tshk2/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpm36tshk2/files/4/c/6/dataset_4c65beec-8f49-40b8-8de9-533a944f9811.dat' 'c1,c2,c3' T '/tmp/tmpm36tshk2/job_working_directory/000/6/outputs/dataset_36bfae06-bc86-42f1-94ed-8a8aff06f646.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"edfc915689e411efb621000d3a38214b"
            chromInfo	"/tmp/tmpm36tshk2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c1,c2,c3"
            dbkey	"?"
            delimiter	"T"

    • Step 8: parsing blast output:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • parse_mito_blast.py --blastout '/tmp/tmpm36tshk2/files/3/4/e/dataset_34eb4cef-ecaf-4ff3-bfcf-846f10b2cb57.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"edfc915689e411efb621000d3a38214b"
            chromInfo	"/tmp/tmpm36tshk2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"

    • Step 9: Filter1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • python '/tmp/tmpm36tshk2/galaxy-dev/tools/stats/filtering.py' '/tmp/tmpm36tshk2/files/3/6/b/dataset_36bfae06-bc86-42f1-94ed-8a8aff06f646.dat' '/tmp/tmpm36tshk2/job_working_directory/000/8/outputs/dataset_29e6f4ba-2a6b-4167-ba63-088b436c4d04.dat' '/tmp/tmpm36tshk2/job_working_directory/000/8/configs/tmpa659kidl' 3 "str,str,str" 0

          Exit Code:

          • 0

          Standard Output:

          • Filtering with c1!='U', 
            kept 11.11% of 9 valid lines (9 total lines).
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"edfc915689e411efb621000d3a38214b"
            chromInfo	"/tmp/tmpm36tshk2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            cond	"c1!='U'"
            dbkey	"?"
            header_lines	"0"

    • Step 10: Cut1:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • perl '/tmp/tmpm36tshk2/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpm36tshk2/files/2/9/e/dataset_29e6f4ba-2a6b-4167-ba63-088b436c4d04.dat' 'c2' T '/tmp/tmpm36tshk2/job_working_directory/000/9/outputs/dataset_d7a043b6-b8fa-4c30-ac0c-985a70c450df.dat'

          Exit Code:

          • 0

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"tabular"
            __workflow_invocation_uuid__	"edfc915689e411efb621000d3a38214b"
            chromInfo	"/tmp/tmpm36tshk2/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            columnList	"c2"
            dbkey	"?"
            delimiter	"T"

  • Other invocation details

    • history_id

      • ed4d2e2de0cf11c0

    • history_state

      • ok

    • invocation_id

      • ed4d2e2de0cf11c0

    • invocation_state

      • scheduled

    • workflow_id

      • ed4d2e2de0cf11c0