Adding single-read functionality to RAW and CLEAN#80

Merged

willbradshaw merged 108 commits intodevfrom single-read-raw-clean

Dec 20, 2024

+451-70

Commits on Oct 21, 2024

Adding single read option to raw/main.nf
simonleandergrimm
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Adding WIP version of run.nf to enable testing raw and clean versions for single read analyses.
simonleandergrimm
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Commits on Oct 22, 2024

Created separate versions of summarize-multiqc-single.R and summarize-multiqc-paired.R
simonleandergrimm
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Split processes in fastp to a single read and paired-end read version.
simonleandergrimm
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Split processes in MultiQC to a single read and paired-end read version. Renamed Multiqc to not be confusing regardings its naming as "Single"
simonleandergrimm
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Deleted summarizeMultiqcSingle, which was superseded by summarizeMultiqc
simonleandergrimm
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Split processes in truncateConcat to a single read and paired-end read version
simonleandergrimm
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Created a single_end if clause in Clean to either use the single read or paired-end read version of fastp
simonleandergrimm
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Created a single_end if clause in hv_screen to either use the single read or paired-end read version of fastp
simonleandergrimm
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Created a single_end if clause in qc to either use the single read or paired-end read version of SUMMARIZE_MULTIQC
simonleandergrimm
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Renamed test dir to test-paired-end. Added clause in nextflow.config for paired-end vs single read runs.
simonleandergrimm
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Edited gitignore to leave out test-paired-end and test-single-read run outputs
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Fixed name of test-single-end dir to test-single-read
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Created a version of test dir that allows the run of single-read data.
simonleandergrimm
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Commits on Oct 23, 2024

Commits on Oct 24, 2024

Amended qmd somewhat so data imports work.
simonleandergrimm
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Commits on Oct 25, 2024

Commits on Oct 26, 2024

Commits on Oct 28, 2024

Commits on Nov 12, 2024

Extended generate_samplesheet.sh so it also takes in single-read data.
Your Name
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Commits on Nov 19, 2024

Commits on Dec 3, 2024

Commits on Dec 5, 2024

Commits on Dec 10, 2024

Commits on Dec 11, 2024

Commits on Dec 16, 2024

Commits on Dec 19, 2024

Amended CHANGELOG.md with changes suggested by Will
simonleandergrimm
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