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[Do not merge!] Pseudo PR for first release #9

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wants to merge 195 commits into from
Closed

[Do not merge!] Pseudo PR for first release #9

wants to merge 195 commits into from

Commits on Apr 11, 2024

  1. Intall the assemblyscan module with nf-core tools

    @charles-plessy
    charles-plessy committed Apr 11, 2024
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Commits on Apr 12, 2024

  1. added module gfastats (like installation)

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  2. Sample sheet for one genome file in compressed FASTA format

    @charles-plessy
    charles-plessy committed Apr 12, 2024
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Commits on Apr 14, 2024

  1. installed a dotplot last

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  2. installed lastal

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    U13bs1125 committed Apr 14, 2024
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  3. installed lastdb lastsplit

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  4. installed last train mafswap

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Commits on Apr 15, 2024

  1. Merge branch 'dev' of github.com:oist/plessy_pairwiseGenomeComparison… 

    … into dev
    @charles-plessy
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Commits on Apr 17, 2024

  1. Added a 'target' parameter

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  2. Merge pull request #18 from oist/adtag 

    Added a 'target' parameter
    @charles-plessy
    charles-plessy authored Apr 17, 2024
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  3. Remove handling of paired-end data. 

    Keeping it causes the pipeline to crash because of our changes
in assets/schema_input.json.
    @charles-plessy
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  4. Run assemblyscan instead of fastqc

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  5. Merge pull request #19 from oist/runAssemblyScan 

    Run assembly scan
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    U13bs1125 authored Apr 17, 2024
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Commits on Apr 18, 2024

  1. Added 1st batch of new parameters 

    These includes seed, skip_dotplot___, targerName
    @U13bs1125
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  2. Merge pull request #20 from oist/1stnewparams 

    Added 1st batch of new parameters
    @charles-plessy
    charles-plessy authored Apr 18, 2024
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  3. Remove FastQC

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  4. Add an input channel for the target genome.

    @charles-plessy
    charles-plessy committed Apr 18, 2024
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  5. Run lastdb

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Commits on Apr 19, 2024

  1. Merge remote-tracking branch 'origin/addLASTDB' into dev

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  2. Inclusion of targetName parameter 

    to overide the default target parameter, which is null and now target
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  3. Inclusion of a new module: Last_train

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  4. Run lastal

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Commits on Apr 23, 2024

  1. Added modules: split and dotplot 

    Im waiting for your input concerning whether or not to use the 'if' here or nort to accomodate m2m, o2m, ...
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  2. Added modules: split and dotplot 

    Im waiting for your input concerning whether or not to use the 'if' here or nort to accomodate m2m, o2m, ...
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  3. tuple val(meta), path(maf) 

         val(format)
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  4. correction

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Commits on Apr 25, 2024

  1. ... 

    ...
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Commits on Apr 26, 2024

  1. REGULARIZATION

    @U13bs1125
    U13bs1125 committed Apr 26, 2024
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  2. Merge branch 'dev' into addedmodules

    @charles-plessy
    charles-plessy authored Apr 26, 2024
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  3. Merge pull request #24 from oist/addedmodules 

    Running more modules
    @charles-plessy
    charles-plessy authored Apr 26, 2024
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  4. Merge branch 'dev' of github.com:oist/plessy_pairwiseGenomeComparison… 

    … into dev
    @U13bs1125
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  5. Remove unwanted spaces to avoid pre-commit failures in GitHub actions.

    @charles-plessy
    charles-plessy committed Apr 26, 2024
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  6. Make YASS the default seed.

    @charles-plessy
    charles-plessy committed Apr 26, 2024
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  7. Rename the pipeline to pairgenomealign

    @charles-plessy
    charles-plessy committed Apr 26, 2024
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  8. Merge branch 'TEMPLATE' into dev

    @charles-plessy
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  9. Also rename files accordingly.

    @charles-plessy
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  10. Merge branch 'TEMPLATE' into dev

    @charles-plessy
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  11. Refreshed logos with nf-core create-logo

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    charles-plessy committed Apr 26, 2024
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  12. Put the refreshed logos in the correct directory.

    @charles-plessy
    charles-plessy committed Apr 26, 2024
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  13. Finish overlooked merge.

    @charles-plessy
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  14. Put the files in correct folder.

    @charles-plessy
    charles-plessy committed Apr 26, 2024
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Commits on Apr 30, 2024

  1. Added modules for m2m, o2o, o2m modules

    @U13bs1125
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  2. REGULARIZATION

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  3. Reduce test time so that it is easier to run on OISTs short queue

    @charles-plessy
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Commits on May 2, 2024

  1. ignore that are difficult to reproducibly generate

    @U13bs1125
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  2. Changed the prefices

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  3. Merge branch 'dev' into m2mdotplotsmodules

    @charles-plessy
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  4. Fix whitespace issues.

    @charles-plessy
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  5. Merge pull request #26 from oist/m2mdotplotsmodules 

     M2mdotplotsmodules
    @charles-plessy
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  6. Complete pipeline 

    included 'ifs' and added module parameter like --reverse
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  7. regularization

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Commits on May 7, 2024

  1. Draft a tube map representation of the pipeline.

    @charles-plessy
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  2. Cleared TODOs

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  3. cleared some TODOs 

    Merge branch 'm2mdotplotsmodules' into dev
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  4. added svg

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  5. ..

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  6. ..

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  7. ,,

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  8. mm

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  9. m

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Commits on May 8, 2024

  1. Editing the README file

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  2. Clear TODOs

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  3. Update of subworkflos utils_nfcore_pipeline

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  4. Move the many-to-many and downstream alignments to a subworkflow

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Commits on May 9, 2024

  1. Use the new PAIRALIGN_M2M subworkflow

    @charles-plessy
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  2. New m2o subworkflow

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  3. Added alternataive statement on subworkflows

    @U13bs1125
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  4. Regularize groupinf of m2m param

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  5. mxc 

     # Please enter the commit message for your changes. Lines starting
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Commits on May 10, 2024

  1. Merge branch 'TEMPLATE' into dev

    @charles-plessy
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Commits on May 13, 2024

  1. added new params arguments; last_extr_args...

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  2. Merge branch 'subworkflow2' into dev

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Commits on May 14, 2024

  1. Added extra arguments for lastal and split: mismap...

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Commits on May 15, 2024

  1. Nf-core lint clearing

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Commits on May 21, 2024

  1. Remove whitespace

    @charles-plessy
    charles-plessy authored May 21, 2024
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  2. Ran pre-commit run --all-files by hand.

    @charles-plessy
    charles-plessy committed May 21, 2024
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  3. pick file name that does not look like unassembled reads

    @charles-plessy
    charles-plessy authored May 21, 2024
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  4. Drop the last_split_options parameter 

    [skip ci]
    @charles-plessy
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Commits on May 22, 2024

  1. Updated Documentations

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Commits on May 23, 2024

  1. Merge branch 'dev' of github.com:oist/plessy_pairwiseGenomeComparison… 

    … into dev
    @U13bs1125
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  2. implement the datasets folder to tests

    @U13bs1125
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  3. Implement dotplot_options 

    Closes #33
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  4. Implemented the issue: lastal params 

    close #31
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  5. cleared docs/Readme.md file

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Commits on May 24, 2024

  1. Fix typo

    @charles-plessy
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  2. removed the hanging "i"

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  3. Merge branch 'dev' of github.com:oist/plessy_pairwiseGenomeComparison… 

    … into dev
    @charles-plessy
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  4. chema build done

    @U13bs1125
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  5. Merge branch 'dev' of github.com:oist/plessy_pairwiseGenomeComparison… 

    … into dev
    @U13bs1125
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  6. Ran pre-commit run --all-files

    @charles-plessy
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  7. Remove Windowmasker and adjust borders

    Charles Plessy committed May 24, 2024
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  8. Simplify information already given in docs/output.md

    Charles Plessy committed May 24, 2024
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  9. Transfer information to usage page

    Charles Plessy committed May 24, 2024
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  10. Credits

    Charles Plessy committed May 24, 2024
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  11. Format reference. 

    [skip ci]
    Charles Plessy committed May 24, 2024
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  12. pre-commit run --all-files

    @charles-plessy
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  13. Brush up schema

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Commits on May 28, 2024

  1. Merge branch 'TEMPLATE' into dev

    @charles-plessy
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  2. Correct input parameter type. 

    In principle it is a number, but exponential notation is only recognised
as a string…
    @charles-plessy
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  3. Ensure last-train is ran with --revsym and the other lastal options

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  4. Add a zero to make nf-core lint happier

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  5. Show information directly in description.

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  6. Try with uppercase E like in funcscan pipeline

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  7. Typo

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  8. Prefix output file names with ${params.targetName}___

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  9. Allow for .fna and .fna.gz suffixed.

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  10. Use the nf-core repository

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  11. Whitespace changes by pre-commit

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  12. Numeric argument with non-scientific notation

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Commits on Jun 11, 2024

  1. Update nf-core modules

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  2. Adjust test config to the small size of the sequence

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  3. Set parameters of lastdb to -R01 -c -u${params.seed} -S2

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  4. Rename LAST_LASTAL LAST_LASTAL_M2M in the M2M workflow for consistency.

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Commits on Jun 18, 2024

  1. installed and run seqtk successfully

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  2. Effected the changes of Seqtk workflow to run on each channel individ… 

    …ually
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  3. Again, prettier and lint

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  4. Merge pull request #1 from charles-plessy/minus-s-option 

    Minus s option
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Commits on Jun 19, 2024

  1. Update pairgenomealign.nf 

    CHANGE IMPORT NAMES AS REQUESTED
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  2. Merge pull request #2 from charles-plessy/addseqtk 

    Add seqtk modules
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  3. Small-scale test suite with fungal genomes.

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  4. Merge pull request #3 from charles-plessy/fusarium 

    Fusarium test data merged
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  5. Fix file names in modules runnign on single genomes.

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  6. Merge pull request #4 from charles-plessy/target__query 

    Fix file names in QC modules
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  7. Merge branch 'dev' of github.com:charles-plessy/pairgenomealign into dev

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Commits on Jun 28, 2024

  1. Update last/dotplot

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  2. Pass the seqtk cutN output to last-dotplot

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  3. Document the use of seqtk cutN to plot polyN regions.

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  4. Document assemblyscan and seqtk; remove postmask

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  5. Reorganise documentation of dot-plots and other outputs

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  6. Merge pull request #5 from charles-plessy/plotContigBoundaries2 

    Plot contig boundaries
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Commits on Jul 16, 2024

  1. Update modules

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  2. Collect and report training and alignment statistics.

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  3. Collect more software version numbers.

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  4. Merge pull request #7 from charles-plessy/lastal-multiqc2 

    MultiQC update: alignment stats and software versions.
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Commits on Jul 17, 2024

  1. new branch to resolve multiqc version issue

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Commits on Jul 18, 2024

  1. Combine two reports, plus minor changes.

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Commits on Jul 19, 2024

  1. Cite LAST papers.

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  2. Fix typo in output file name.

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    charles-plessy committed Jul 19, 2024
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  3. Change comments and indentation

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  4. Full tests comparing the human genome to other primates.

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  5. Name the target

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  6. Release 1.0.0

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Commits on Jul 23, 2024

  1. Remove the PSEUDO seed from the schema.

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Commits on Jul 24, 2024

  1. Correct duplicated text 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  2. Reduce redundancy with doc/output.md as suggested in PR #9.

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  3. Also cite the paper describing the original implementation. 

    As suggested in PR#9
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  4. Correct the list of accepted file suffixes 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  5. Remove mention of unported parameters.

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  6. Improve wording of docs/usage.md 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  7. Mention --input explicitely 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  8. Fix typo 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  9. Fix markdown formatting. 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  10. modified the pipeline logo, now png formatted

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  11. modified the pipeline logo, now png formatted

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  12. added the new svg formatted pipeline logo/map

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  13. Merge pull request #10 from oist/devop 

    Improve the pipeline workflow graphic/map
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  14. Merge branch 'dev' of github.com:nf-core/pairgenomealign into dev

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  15. Indent workflows/pairgenomealign.nf 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  16. Remove un-needed example 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  17. Remove dangling filename. 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  18. Show the full sample sheet as an example. 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  19. Multi-query example

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  20. Slim nextflow.config 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  21. Move LAST output to alignment/

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  22. Merge branch 'dev' of github.com:nf-core/pairgenomealign into dev

    @charles-plessy
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  23. Put seqtk cutN output in cutn/ and document it.

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  24. Remove mention of FastQC

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  25. [automated] Fix code linting

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  26. Remove duplicated documentation.

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  27. Merge branch 'dev' of github.com:nf-core/pairgenomealign into dev

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  28. Fix typo

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Commits on Jul 25, 2024

  1. Add a human–monkey alignment as example.

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  2. Update workflows/pairgenomealign.nf 

    Co-authored-by: Matthias Hörtenhuber <[email protected]>
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  3. Rename the custom module and document its output.

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  4. Merge branch 'dev' of github.com:nf-core/pairgenomealign into dev

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  5. Revert "Update workflows/pairgenomealign.nf" 

    This reverts commit 3e349a9.
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  6. Polish parameter description.

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  7. Move tube map to docs/ hoping it solves display problem. 

    Also remove old tube map file
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  8. Add an example dot-plot

    @charles-plessy
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  9. Remove FASTQC examples.

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  10. Add new multiqc examples

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  11. Merge branch 'dev' of github.com:nf-core/pairgenomealign into dev

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  12. Display example MultiQC plots

    @charles-plessy
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  13. prettier

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  14. modified the logomap again as advised by nfcore team

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Commits on Jul 26, 2024

  1. Merge pull request #13 from oist/devlogo 

    Updated the logo/map
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  2. Add a codename

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  3. Fix filename

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  4. Merge branch 'dev' of github.com:nf-core/pairgenomealign into dev

    @charles-plessy
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  5. Use a Markdown link instead of HTML.

    @charles-plessy
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  6. pre-commit fixes

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Commits on Aug 7, 2024

  1. Rename and document some table columns

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  2. Thank Martin and teammates

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Commits on Aug 8, 2024

  1. Remove mention of lastdb -P because it does not impact the alignment … 

    …files
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Commits on Aug 26, 2024

  1. Update release date in CHANGELOG.md

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