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Some fixes #339

Merged
merged 24 commits into from
Apr 18, 2023
Merged

Some fixes #339

merged 24 commits into from
Apr 18, 2023

Commits on Apr 17, 2023

  1. Add back skip_spp parameter

    @JoseEspinosa
    JoseEspinosa committed Apr 17, 2023
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  2. Install fastq_fastqc_umitools_trimgalore subworkflow

    @JoseEspinosa
    JoseEspinosa committed Apr 17, 2023
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  3. Install fastq_align_bwa subworkflow

    @JoseEspinosa
    JoseEspinosa committed Apr 17, 2023
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  4. Install fastq_align_bowtie2 subworkflow

    @JoseEspinosa
    JoseEspinosa committed Apr 17, 2023
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  5. Install fastq_align_chromap subworkflow

    @JoseEspinosa
    JoseEspinosa committed Apr 17, 2023
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  6. use the FASTQ_FASTQC_UMITOOLS_TRIMGALORE subworkflow insead of fastq_… 

    …trimgalore
    @JoseEspinosa
    JoseEspinosa committed Apr 17, 2023
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  7. Use FASTQ_ALIGN_BWA subworkflow

    @JoseEspinosa
    JoseEspinosa committed Apr 17, 2023
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Commits on Apr 18, 2023

  1. Use FASTQ_ALIGN_BOWTIE2 subworkflow

    @JoseEspinosa
    JoseEspinosa committed Apr 18, 2023
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  2. Install custom/getchromsizes and picard/collectmultiplemetrics

    @JoseEspinosa
    JoseEspinosa committed Apr 18, 2023
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  3. Remove substituted modules and subworkflows

    @JoseEspinosa
    JoseEspinosa committed Apr 18, 2023
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  4. Rename bamtools/filter

    @JoseEspinosa
    JoseEspinosa committed Apr 18, 2023
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  5. add align_star local subworkflow

    @JoseEspinosa
    JoseEspinosa committed Apr 18, 2023
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  6. Refactor and rename bam_filter_bamtools

    @JoseEspinosa
    JoseEspinosa committed Apr 18, 2023
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  7. Refactor code to use nf-core official subworkflows

    @JoseEspinosa
    JoseEspinosa committed Apr 18, 2023
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  8. Simplify code

    @JoseEspinosa
    JoseEspinosa committed Apr 18, 2023
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  9. changelog

    @JoseEspinosa
    JoseEspinosa committed Apr 18, 2023
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  10. Resolved arguments for bamtools_filteer

    @JoseEspinosa
    JoseEspinosa committed Apr 18, 2023
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  11. Update bowtie2/align to fix the container download

    @JoseEspinosa
    JoseEspinosa committed Apr 18, 2023
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  12. Remove code used for view

    @JoseEspinosa
    JoseEspinosa committed Apr 18, 2023
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  13. Feed missing arguments to star subworkflow

    @JoseEspinosa
    JoseEspinosa committed Apr 18, 2023
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  14. Update chromap/chromap

    @JoseEspinosa
    JoseEspinosa committed Apr 18, 2023
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  15. Update star_align

    @JoseEspinosa
    JoseEspinosa committed Apr 18, 2023
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  16. Update changelog

    @JoseEspinosa
    JoseEspinosa committed Apr 18, 2023
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  17. Update bowtie2/build

    @JoseEspinosa
    JoseEspinosa committed Apr 18, 2023
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