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Ver2rc #98

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Ver2rc #98

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Commits on Jul 19, 2023

  1. export more cutadapt parameters.

    @jianhong
    jianhong committed Jul 19, 2023
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  2. export more cutadapt parameters.

    @jianhong
    jianhong committed Jul 19, 2023
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Commits on Aug 7, 2023

  1. push the changes for last submit.

    @jianhong
    jianhong committed Aug 7, 2023
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Commits on Aug 8, 2023

  1. add function to detect the contamination by karken2.

    @jianhong
    jianhong committed Aug 8, 2023
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  2. export pairtools_walks_policy parameter.

    @jianhong
    jianhong committed Aug 8, 2023
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  3. update changelog.

    @jianhong
    jianhong committed Aug 8, 2023
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Commits on Aug 9, 2023

  1. update the pipeline to skip cutadapt_3end by default.

    @jianhong
    jianhong committed Aug 9, 2023
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Commits on Aug 10, 2023

  1. fix the wrong input for cutadapt_3end.

    @jianhong
    jianhong committed Aug 10, 2023
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  2. update the keywords to skip cutadapt 3end.

    @jianhong
    jianhong committed Aug 10, 2023
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Commits on Aug 11, 2023

  1. use the standard kraken2 db as default.

    @jianhong
    jianhong committed Aug 11, 2023
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Commits on Aug 16, 2023

  1. change the cutadapt_action default setting.

    @jianhong
    jianhong committed Aug 16, 2023
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Commits on Aug 18, 2023

  1. Merge branch 'dev' into dev2rc; fix the file name collision for KRONA… 

    …_KTIMPORTTEXT
    @jianhong
    jianhong committed Aug 18, 2023
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Commits on Aug 22, 2023

  1. run black to fix the python script format.

    @jianhong
    jianhong committed Aug 22, 2023
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  2. change the version number to 2.0.0dev.

    @jianhong
    jianhong committed Aug 22, 2023
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  3. update to nf-core/samtools/sort

    @jianhong
    jianhong committed Aug 22, 2023
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  4. fix a typo in nextflow_schema.json.

    @jianhong
    jianhong committed Aug 22, 2023
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Commits on Aug 23, 2023

  1. try to fix the multiqc_config.yml missing report_comment error.

    @jianhong
    jianhong committed Aug 23, 2023
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  2. try again.

    @jianhong
    jianhong committed Aug 23, 2023
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Commits on Aug 28, 2023

  1. update igv.js tracks to avoid the error that if skip interaction caller.

    @jianhong
    jianhong committed Aug 28, 2023
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  2. fix a bug in creating maps signal cooler file.

    @jianhong
    jianhong committed Aug 28, 2023
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Commits on Aug 30, 2023

  1. export the filtered pairs files.

    @jianhong
    jianhong committed Aug 30, 2023
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  2. add control for skip circos.

    @jianhong
    jianhong committed Aug 30, 2023
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Commits on Aug 31, 2023

  1. fix a bug that if genome fastq file can not be handled by the bwa index.

    @jianhong
    jianhong committed Aug 31, 2023
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Commits on Sep 12, 2023

  1. update the Channel of genome fasta.

    @jianhong
    jianhong committed Sep 12, 2023
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  2. add output controler for pairs file.

    @jianhong
    jianhong committed Sep 12, 2023
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Commits on Sep 13, 2023

  1. try to fix the github storage issue by free-dist-space.

    @jianhong
    jianhong committed Sep 13, 2023
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  2. try again.

    @jianhong
    jianhong committed Sep 13, 2023
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Commits on Sep 25, 2023

  1. Template update for nf-core/tools version 2.10

    @nf-core-bot
    nf-core-bot committed Sep 25, 2023
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Commits on Sep 28, 2023

  1. add parse2 module.

    @jianhong
    jianhong committed Sep 28, 2023
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Commits on Oct 2, 2023

  1. fix the sort memory issue (exit code 139 with fragment fault)

    @jianhong
    jianhong committed Oct 2, 2023
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Commits on Oct 3, 2023

  1. add tmpdir parameter for pairtools sort.

    @jianhong
    jianhong committed Oct 3, 2023
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Commits on Oct 4, 2023

  1. try to fix the pairtools sort memory issue.

    @jianhong
    jianhong committed Oct 4, 2023
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Commits on Oct 10, 2023

  1. add same fragement stats and change the TSSEscre calculation range.

    @jianhong
    jianhong committed Oct 10, 2023
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Commits on Oct 11, 2023

  1. fix the potential issue if the container can not download the source … 

    …code from github.
    @jianhong
    jianhong committed Oct 11, 2023
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Commits on Oct 13, 2023

  1. update pairtools/sort

    @jianhong
    jianhong committed Oct 13, 2023
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  2. Merge remote-tracking branch 'upstream/nf-core-template-merge-2.10' i… 

    …nto dev2rc
    @jianhong
    jianhong committed Oct 13, 2023
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  3. Merge remote-tracking branch 'origin/dev2rc' into ver2rc

    @jianhong
    jianhong committed Oct 13, 2023
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  4. fix the space issue.

    @jianhong
    jianhong committed Oct 13, 2023
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  5. update the citation in WorkflowHicar.groovy

    @jianhong
    jianhong committed Oct 13, 2023
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  6. Merge remote-tracking branch 'origin/dev2rc' into ver2rc

    @jianhong
    jianhong committed Oct 13, 2023
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  7. try to pass the linting.

    @jianhong
    jianhong committed Oct 13, 2023
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  8. add dev to the version number back.

    @jianhong
    jianhong committed Oct 13, 2023
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  9. remove the 'dev' for multiqc_config.yml

    @jianhong
    jianhong committed Oct 13, 2023
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  10. remove dev from multiqc_config.yml

    @jianhong
    jianhong committed Oct 13, 2023
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  11. Merge remote-tracking branch 'origin/dev2rc' into ver2rc

    @jianhong
    jianhong committed Oct 13, 2023
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  12. remove dev from nextflow.config.

    @jianhong
    jianhong committed Oct 13, 2023
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