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Refactoring, arg list handling, add two parameters #11

Merged
merged 18 commits into from
Mar 1, 2024
Merged

Refactoring, arg list handling, add two parameters #11

merged 18 commits into from
Mar 1, 2024

Commits on Feb 21, 2024

  1. (1) Fix handling of ks_peaks.tsv; (2) shorten 19_pan_aug_leftover_mer… 

    …ged_prot to 19_palm to reduce length of arglist; (3) move small families to the side in alignment step; (4) correct printing of header for counts per accession
    Steven Cannon committed Feb 21, 2024
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Commits on Feb 23, 2024

  1. MANY changes in the course of moving alignment & modeling steps to -c… 

    …ommon.sh. Likely breakages. Incomplete.
    Steven Cannon committed Feb 23, 2024
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  2. Various fixes in alignment and modeling steps, after moving this code… 

    … to -common
    @StevenCannon-USDA
    StevenCannon-USDA committed Feb 23, 2024
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Commits on Feb 26, 2024

  1. Handle argument list too long errors around augment_cluster_sets.awk

    @StevenCannon-USDA
    StevenCannon-USDA committed Feb 26, 2024
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  2. Add Wm82.gnm6 annotation to Glycine pangene config & make file

    @StevenCannon-USDA
    StevenCannon-USDA committed Feb 26, 2024
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  3. Remove 04_dag at start of filter, to avoid problems of leftover files… 

    … from previous runs
    @StevenCannon-USDA
    StevenCannon-USDA committed Feb 26, 2024
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Commits on Feb 27, 2024

  1. Minor cosmetic change in stats/ks_histplots.tsv

    @StevenCannon-USDA
    StevenCannon-USDA committed Feb 27, 2024
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  2. Add two params, min_align_count min_annots_in_align, to the reporting… 

    … in the summarize step
    @StevenCannon-USDA
    StevenCannon-USDA committed Feb 27, 2024
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Commits on Feb 28, 2024

  1. Fix listing of pandagma_conf_params reported in summarize step, and o… 

    …ther minor cleanup
    @StevenCannon-USDA
    StevenCannon-USDA committed Feb 28, 2024
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  2. Add two alignment parameters to config files; and minor changes to pa… 

    …ndagma-fsup.sh to work with the pandagma driver script and pandagma-common.sh
    @StevenCannon-USDA
    StevenCannon-USDA committed Feb 28, 2024
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Commits on Feb 29, 2024

  1. Changes in step xfr_aligns_trees to handle output from fsup

    @StevenCannon-USDA
    StevenCannon-USDA committed Feb 29, 2024
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  2. Remove optional steps align_cds, align_protein, model_and_trim, calc_… 

    …trees, and xfr_aligns_trees from commandlist in -pan and -fam workflows
    @StevenCannon-USDA
    StevenCannon-USDA committed Feb 29, 2024
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  3. Bug fix & documentation tweaks in pandagma-fsup.sh

    @StevenCannon-USDA
    StevenCannon-USDA committed Feb 29, 2024
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  4. Minor change to handling of directory/file transfer in pandagma-fsup.sh

    @StevenCannon-USDA
    StevenCannon-USDA committed Feb 29, 2024
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  5. Minor change in stats reporting

    @StevenCannon-USDA
    StevenCannon-USDA committed Feb 29, 2024
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  6. Restructure ks_filter step so that ks_block_wgd_cutoff and max_pair_k… 

    …s are used if stats/ks_histplots.tsv isn't provided
    @StevenCannon-USDA
    StevenCannon-USDA committed Feb 29, 2024
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  7. Handle transfer of 19_pan_aug_leftover_merged_prot in -common rather … 

    …than in -fam
    @StevenCannon-USDA
    StevenCannon-USDA committed Feb 29, 2024
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  8. Tweak output of counts-per-accession header in stats.txt file

    @StevenCannon-USDA
    StevenCannon-USDA committed Feb 29, 2024
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