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Updating anvil-production README for prod-25-01-14-12-34-1
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actions-user committed Jan 14, 2025
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2 changes: 1 addition & 1 deletion reports/anvil-production/README.md

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10 changes: 5 additions & 5 deletions reports/anvil-production/tool-tests/chunks.json
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"date2": "Sun Jan 05 00:57:37 2025"
},
"3": {
"run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-25-01-07-12-36-1/results.html",
"date1": "Tue Jan 07 12:52:19 2025",
"tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-25-01-07-12-36-1/tools.yml",
"run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-12-31-12-34-1/results.html",
"date2": "Tue Dec 31 12:50:39 2024"
"run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/results.html",
"date1": "Tue Jan 14 12:50:36 2025",
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"date2": "Tue Jan 07 12:52:19 2025"
},
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"date1": "Tue Jan 14 12:50:36 2025",
"tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-25-01-14-12-34-1/tools.yml"
}
}
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-t split_file_to_collection --tool-version 6cbe2f30c2d7
-t reshape2_melt --tool-version 317ed0ee8bf2
-t fasta_compute_length --tool-version 7d37cfda8e00
-t bamtools --tool-version 4d343c1f606b
-t samtools_idxstats --tool-version 7a6034296ae9
-t bcftools_gtcheck --tool-version 672b6c02fbc7
-t bcftools_reheader --tool-version 9ef52d95114b
-t bcftools_plugin_tag2tag --tool-version bdfdf5f6e950
-t vcfgenotypes --tool-version a60ae8af21a1
-t flye --tool-version 3ee0ef312022
-t poretools_tabular --tool-version 2cb2feb94f0e
-t deeptools_multi_bigwig_summary --tool-version 3c9f0c486cca
-t unicycler --tool-version 9e3e80cc4ad4
-t ivar_removereads --tool-version ee2beb764a7b
-t hisat2 --tool-version 26371a1df031
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Original file line number Diff line number Diff line change
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Original file line number Diff line number Diff line change
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Original file line number Diff line number Diff line change
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"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0",
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"command_line": "ln -s '/galaxy/server/database/objects/a/8/e/dataset_a8e7667e-3e06-4941-833a-173c42cb310d.dat' fq1.fastq && ln -s '/galaxy/server/database/objects/7/3/8/dataset_738fb138-e581-4661-98b6-3d90bc357e56.dat' fq2.fastq && ln -s '/galaxy/server/database/objects/6/6/4/dataset_664606f8-030b-409a-8205-6ded7a8045fd.dat' 'lr.fasta' && unicycler -t \"${GALAXY_SLOTS:-4}\" -o ./ --verbosity 3 -1 'fq1.fastq' -2 'fq2.fastq' -l lr.fasta --mode 'normal' --min_fasta_length '100' --linear_seqs '0' --min_kmer_frac '0.2' --max_kmer_frac '0.95' --kmer_count '10' --depth_filter '0.25' --start_gene_id '90.0' --start_gene_cov '95.0' --min_component_size '1000' --min_dead_end_size '1000' --scores '3,-6,-5,-2' --keep 2 && mkdir 'spades_graphs' && mv 00*gfa './spades_graphs/' && samtools view -@ \"${GALAXY_SLOTS:-4}\" -u 'read_alignment/long_read_alignments.sam' | samtools sort -@ \"${GALAXY_SLOTS:-4}\" -o 'read_alignment/long_read_alignments.bam'",
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"keep": "\"2\"",
"lr_align": "{\"contamination\": null, \"low_score\": \"\", \"no_simple_bridges\": false, \"scores\": \"3,-6,-5,-2\"}",
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"rotation": "{\"no_rotate\": false, \"start_gene_cov\": \"95.0\", \"start_gene_id\": \"90.0\", \"start_genes\": null}",
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Original file line number Diff line number Diff line change
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"file_count": "\"auto\"",
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}
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