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Enhancement/hg38 update #128

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Enhancement/hg38 update #128

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Commits on Sep 20, 2024

  1. updating GRCh38 references

    Anne Marie Noronha committed Sep 20, 2024
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Commits on Sep 23, 2024

  1. fix gtf channel for GRCh38 mode

    @anoronh4
    anoronh4 committed Sep 23, 2024
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  2. update star/genomegenerate

    @anoronh4
    anoronh4 committed Sep 23, 2024
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Commits on Sep 25, 2024

  1. adjustments to make GRCh38 run through

    @anoronh4
    anoronh4 committed Sep 25, 2024
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  2. Merge branch 'develop' into enhancement/hg38_update

    @anoronh4
    anoronh4 committed Sep 25, 2024
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  3. fix indentation

    @anoronh4
    anoronh4 committed Sep 25, 2024
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Commits on Sep 26, 2024

  1. fix agfusion download command

    @anoronh4
    anoronh4 committed Sep 26, 2024
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  2. clean up view operator

    @anoronh4
    anoronh4 committed Sep 26, 2024
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  3. fix fillout pytest

    @anoronh4
    anoronh4 committed Sep 26, 2024
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  4. change pfam reference to stagnant release

    @anoronh4
    anoronh4 committed Sep 26, 2024
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  5. add poison pill to reference channels

    @anoronh4
    anoronh4 committed Sep 26, 2024
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  6. update md5sum in test_profile test

    @anoronh4
    anoronh4 committed Sep 26, 2024
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  7. update ensembl version to 112

    @anoronh4
    anoronh4 committed Sep 26, 2024
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  8. update CHANGELOG.md

    @anoronh4
    anoronh4 committed Sep 26, 2024
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Commits on Oct 1, 2024

  1. change ensembl version to 111

    @anoronh4
    anoronh4 committed Oct 1, 2024
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  2. update AGFusion to [email protected]

    @anoronh4
    anoronh4 committed Oct 1, 2024
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  3. fix conflicts

    @anoronh4
    anoronh4 committed Oct 1, 2024
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  4. Merge branch 'enhancement/hg38_update' of github.com:mskcc/forte into… 

    … enhancement/hg38_update
    @anoronh4
    anoronh4 committed Oct 1, 2024
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Commits on Oct 2, 2024

  1. add cpus in AGAT_SPADDINTRONS resources

    @anoronh4
    anoronh4 committed Oct 2, 2024
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  2. fix indentation

    @anoronh4
    anoronh4 committed Oct 2, 2024
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  3. Set gene_id as gene_name for lncRNAs, remove NF transcripts from gene… 

    … bed
    @pintoa1-mskcc
    pintoa1-mskcc committed Oct 2, 2024
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  4. Merge branch 'enhancement/hg38_update' of github.com:mskcc/forte into… 

    … enhancement/hg38_update
    @anoronh4
    anoronh4 committed Oct 2, 2024
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  5. fix linting error, ensure no scientific notation in gene bed

    @pintoa1-mskcc
    pintoa1-mskcc committed Oct 2, 2024
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  6. Merge branch 'enhancement/hg38_update' of github.com:mskcc/forte into… 

    … enhancement/hg38_update
    @pintoa1-mskcc
    pintoa1-mskcc committed Oct 2, 2024
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Commits on Oct 10, 2024

  1. remove deprecated arriba installation

    @anoronh4
    anoronh4 committed Oct 10, 2024
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  2. update to decoy fasta

    @anoronh4
    anoronh4 committed Oct 10, 2024
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  3. Merge branch 'develop' into enhancement/hg38_update

    @pintoa1-mskcc
    pintoa1-mskcc authored Oct 10, 2024
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  4. add storeDir directives for gunzip* and FASTAREMOVEPREFIX

    @anoronh4
    anoronh4 committed Oct 10, 2024
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  5. Merge branch 'enhancement/hg38_update' of github.com:mskcc/forte into… 

    … enhancement/hg38_update
    @anoronh4
    anoronh4 committed Oct 10, 2024
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  6. change chromosome M to MT in fasta

    @anoronh4
    anoronh4 committed Oct 10, 2024
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Commits on Oct 11, 2024

  1. add idt_v2 baits for GRCh38 to reference config

    @anoronh4
    anoronh4 committed Oct 11, 2024
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