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Initial release review [DO NOT MERGE] #29

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Closed

Initial release review [DO NOT MERGE] #29

wants to merge 609 commits into from
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Commits on Feb 29, 2024

  1. Adjust, fix bwa-mem2 index handling

    @scwatts
    scwatts committed Feb 29, 2024
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  2. Remove deprecated MarkDups -multi_bam argument

    @scwatts
    scwatts committed Feb 29, 2024
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  3. Template update for nf-core/tools version 2.13.1

    @nf-core-bot
    nf-core-bot committed Feb 29, 2024
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  4. Fix AMBER subworkflow TN mode

    @scwatts
    scwatts committed Feb 29, 2024
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  5. Fix COBALT subworkflow TN mode

    @scwatts
    scwatts committed Feb 29, 2024
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  6. Adjust indentation

    @scwatts
    scwatts committed Feb 29, 2024
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  7. Fix SAGE calling subworkflow TN mode

    @scwatts
    scwatts committed Feb 29, 2024
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  8. Improving handling of 'no merge' RNA BAM scenarios

    @scwatts
    scwatts committed Feb 29, 2024
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  9. Set outputs for alignment workflows

    @scwatts
    scwatts committed Feb 29, 2024
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  10. Add missing channel docs

    @scwatts
    scwatts committed Feb 29, 2024
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  11. Further work on RNA BAM handling

    @scwatts
    scwatts committed Feb 29, 2024
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  12. Use explicit returns in .branch ops

    @scwatts
    scwatts committed Feb 29, 2024
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  13. Do not index RNA BAMs prior to merge

    @scwatts
    scwatts committed Feb 29, 2024
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Commits on Mar 2, 2024

  1. Update acknowledgements

    @scwatts
    scwatts committed Mar 2, 2024
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  2. Bump PURPLE to 4.0.2

    @scwatts
    scwatts committed Mar 2, 2024
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  3. Correct comment capitalisation

    @scwatts
    scwatts committed Mar 2, 2024
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Commits on Mar 3, 2024

  1. Handle backslashes in linxreport more consistently

    @scwatts
    scwatts committed Mar 3, 2024
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  2. Correct typo in PAVE somatic module

    @scwatts
    scwatts committed Mar 3, 2024
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Commits on Mar 4, 2024

  1. Bump version: 0.3.0 → 0.3.1

    @scwatts
    scwatts committed Mar 4, 2024
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Commits on Mar 5, 2024

  1. Remove obsolete TODOs

    @mkcmkc
    mkcmkc committed Mar 5, 2024
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Commits on Mar 7, 2024

  1. Fix Isofox singularity container URL

    @scwatts
    scwatts committed Mar 7, 2024
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  2. Bump TSO500 data bundle version 

    * restrict target regions to canonical Ensembl transcripts
    @scwatts
    scwatts committed Mar 7, 2024
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  3. Remove -force_pathogenic_pass in PAVE somatic

    @scwatts
    scwatts committed Mar 7, 2024
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Commits on Mar 14, 2024

  1. Merge branch 'nf-core-template-merge-2.13.1' into dev

    @scwatts
    scwatts committed Mar 14, 2024
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  2. Apply prettier linting

    @scwatts
    scwatts committed Mar 14, 2024
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  3. Fix indenting

    @scwatts
    scwatts committed Mar 14, 2024
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  4. Fix more linting failures

    @scwatts
    scwatts committed Mar 14, 2024
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  5. More indenting fixes

    @scwatts
    scwatts committed Mar 14, 2024
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Commits on Mar 15, 2024

  1. Update pipeline description

    @scwatts
    scwatts committed Mar 15, 2024
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  2. Update test config, adjust relevant arg schema

    @scwatts
    scwatts committed Mar 15, 2024
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  3. Reorganise reference data and params

    @scwatts
    scwatts committed Mar 15, 2024
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  4. Fix creation of stub placeholders

    @scwatts
    scwatts committed Mar 15, 2024
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  5. Change ordering of HMF data config loading

    @scwatts
    scwatts committed Mar 15, 2024
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  6. Add test_stub profile

    @scwatts
    scwatts committed Mar 15, 2024
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  7. Run only stubs in CI job 

    GHA executing instances do not have sufficient space to run the
COLO829_mini test.
    @scwatts
    scwatts committed Mar 15, 2024
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  8. Merge pull request #3 from nf-core/nf-core-template-merge-2.13.1

    @scwatts
    scwatts authored Mar 15, 2024
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Commits on Mar 16, 2024

  1. Correct prepare reference panel data path lookup

    @scwatts
    scwatts committed Mar 16, 2024
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  2. Merge branch 'dev' into alignment-subworkflow

    @scwatts
    scwatts committed Mar 16, 2024
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  3. Fix optional channel placeholders

    @scwatts
    scwatts committed Mar 16, 2024
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  4. Update modules.json

    @scwatts
    scwatts committed Mar 16, 2024
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  5. Adjust indenting

    @scwatts
    scwatts committed Mar 16, 2024
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Commits on Mar 18, 2024

  1. Use standard container directive format for STAR

    @scwatts
    scwatts committed Mar 18, 2024
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  2. Add missing imports and subworkflow descriptions

    @scwatts
    scwatts committed Mar 18, 2024
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Commits on Mar 19, 2024

  1. Use Bioconda/BioContainers for bwa-mem2 module

    @scwatts
    scwatts committed Mar 19, 2024
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Commits on Mar 25, 2024

  1. Use fixed GRIDSS container for VIRUSBreakend 

    The BioContainers Docker image only provides BusyBox grep, which has
poor performance compared to GNU grep and increases runtime by up to an
hour. The current Bioconda CI infrastructure is unable to build a
patched GRIDSS image at the moment, so I've made a temporary fix here
instead to restore expected performance.
    @scwatts
    scwatts committed Mar 25, 2024
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Commits on Mar 26, 2024

  1. Apply linting

    @scwatts
    scwatts committed Mar 26, 2024
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  2. Use standard BioContainers base for VIRUSBreakend 

    Having distroless as the base Docker image for the VIRUSBreakend
container was causing RepeatMasker to crash without an error/traceback
when executing a system process. Switching to
`quay.io/bioconda/base-glibc-busybox-bash:2.1.0` (the standard
BioContainers base image) resolves the problem.
    @scwatts
    scwatts committed Mar 26, 2024
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  3. Lint modules/local/virusbreakend/Dockerfile

    @scwatts
    scwatts committed Mar 26, 2024
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Commits on Mar 27, 2024

  1. Improve naming for bwa-mem2 output BAMs

    @scwatts
    scwatts committed Mar 27, 2024
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Commits on Apr 3, 2024

  1. Apply @maxulysse recommendations 

    Co-authored-by: Maxime U Garcia <[email protected]>
    @scwatts @maxulysse
    scwatts and maxulysse authored Apr 3, 2024
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  2. Update VIRUSBreakend process container directive

    @scwatts
    scwatts committed Apr 3, 2024
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  3. Do not qualify nf-core quay.io Docker URI

    @scwatts
    scwatts committed Apr 3, 2024
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  4. Merge pull request #12 from nf-core/nf-core-gridss-docker-image 

    Use fixed GRIDSS container for VIRUSBreakend
    @scwatts
    scwatts authored Apr 3, 2024
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Commits on Apr 15, 2024

  1. Use BAM index created during alignment

    @scwatts
    scwatts committed Apr 15, 2024
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Commits on Apr 22, 2024

  1. Improve BAM index selection

    @scwatts
    scwatts committed Apr 22, 2024
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  2. Include BAI in bwa-mem2/align stub

    @scwatts
    scwatts committed Apr 22, 2024
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  3. Adjust input selection logic

    @scwatts
    scwatts committed Apr 22, 2024
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Commits on Apr 23, 2024

  1. Bump MarkDups to 1.1.5

    @scwatts
    scwatts committed Apr 23, 2024
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  2. Remove Sambamba index module file

    @scwatts
    scwatts committed Apr 23, 2024
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  3. Add new meta.yaml

    @scwatts
    scwatts committed Apr 23, 2024
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Commits on Apr 24, 2024

  1. Merge pull request #6 from nf-core/alignment-subworkflow 

    Implement alignment subworkflow
    @scwatts
    scwatts authored Apr 24, 2024
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  2. Adjust Hartwig genome data URLs

    @scwatts
    scwatts committed Apr 24, 2024
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  3. Adjust other reference data URLs

    @scwatts
    scwatts committed Apr 24, 2024
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Commits on Apr 26, 2024

  1. Give GHA CI workflow step more accurate name

    @scwatts
    scwatts committed Apr 26, 2024
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Commits on Apr 28, 2024

  1. Implement reference data writing

    @scwatts
    scwatts committed Apr 28, 2024
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Commits on Apr 30, 2024

  1. Merge pull request #14 from nf-core/update-reference-genome-urls 

    Update reference data URLs
    @scwatts
    scwatts authored Apr 30, 2024
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  2. Merge pull request #15 from nf-core/rename-ci-job-step 

    Improve GHA CI workflow step name
    @scwatts
    scwatts authored Apr 30, 2024
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  3. Refactor reference data parameters

    @scwatts
    scwatts committed Apr 30, 2024
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  4. Fix variable names and config load order

    @scwatts
    scwatts committed Apr 30, 2024
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  5. Correct malformed variable name

    @scwatts
    scwatts committed Apr 30, 2024
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  6. Merge pull request #16 from nf-core/refdata-param-refactor 

    Refactor reference data parameters
    @scwatts
    scwatts authored Apr 30, 2024
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  7. Update default bwa-mem2 and GRIDSS index URLs

    @scwatts
    scwatts committed Apr 30, 2024
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  8. Add container and label to write refdata process

    @scwatts
    scwatts committed Apr 30, 2024
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  9. Ensure ref_data_panel_data_path is defined

    @scwatts
    scwatts committed Apr 30, 2024
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  10. Improve names for decompressed refdata output dirs

    @scwatts
    scwatts committed Apr 30, 2024
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  11. Add index name to decompressed refdata output dirs

    @scwatts
    scwatts committed Apr 30, 2024
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  12. Correct mistake in assets/samplesheet.csv 

    Resolves #17.
    @scwatts
    scwatts committed Apr 30, 2024
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  13. Ensure ref_data_virusbreakenddb_path is defined

    @scwatts
    scwatts committed Apr 30, 2024
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  14. Only write reference data require for analysis

    @scwatts
    scwatts committed Apr 30, 2024
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  15. Fix panel data path default assignment

    @scwatts
    scwatts committed Apr 30, 2024
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  16. Use consistent spacing in prepare_reference.nf

    @scwatts
    scwatts committed Apr 30, 2024
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  17. Set 'process_high_memory' label for bwa-mem2 index

    @scwatts
    scwatts committed Apr 30, 2024
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Commits on May 1, 2024

  1. Use bwa-mem2 for HLA read realignment

    @scwatts
    scwatts committed May 1, 2024
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  2. Create bwa-mem1 index prior to GRIDSS indexing

    @scwatts
    scwatts committed May 1, 2024
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  3. Update GRIDSS index module 

    - add BWA index as input
- update arguments for bioconda package
    @scwatts
    scwatts committed May 1, 2024
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  4. Fix GRIDSS index output

    @scwatts
    scwatts committed May 1, 2024
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  5. Include optional ALT file input for bwa-mem1

    @scwatts
    scwatts committed May 1, 2024
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  6. Do not add ALT file during GRIDSS indexing 

    This file should now be added upstream in the bwa-mem1 indexing process
    @scwatts
    scwatts committed May 1, 2024
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  7. Merge pull request #18 from nf-core/fix-samplesheet-asset 

    Correct mistake in assets/samplesheet.csv
    @scwatts
    scwatts authored May 1, 2024
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Commits on May 2, 2024

  1. Increase allocated memory for GRIDSS index process 

    Pulled the process_medium_memory from metapep and applied to GRIDSS
index.
    @scwatts
    scwatts committed May 2, 2024
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  2. Output ALT file in GRIDSS index if present

    @scwatts
    scwatts committed May 2, 2024
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  3. Rename STAR index output directory

    @scwatts
    scwatts committed May 2, 2024
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  4. Rename bwa-mem2 index output directory

    @scwatts
    scwatts committed May 2, 2024
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  5. Make PAVE genome version comparison more robust

    @scwatts
    scwatts committed May 2, 2024
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  6. Use STAR 2.7.3a for indexing

    @scwatts
    scwatts committed May 2, 2024
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  7. Use bwa-mem2 to realign HLA reads

    @scwatts
    scwatts committed May 2, 2024
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Commits on May 3, 2024

  1. Clean up comments, whitespace, needed config

    @scwatts
    scwatts committed May 3, 2024
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  2. Apply linting

    @scwatts
    scwatts committed May 3, 2024
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  3. Merge pull request #19 from nf-core/improve-prepare-reference-workflow 

    Improve the prepare reference workflow
    @scwatts
    scwatts authored May 3, 2024
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  4. Use nf-core indenting for subworkflows

    @scwatts
    scwatts committed May 3, 2024
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  5. Remove quay.io qualifier from container URLs

    @scwatts
    scwatts committed May 3, 2024
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  6. Remove MRD/longitudinal subworkflow placeholder

    @scwatts
    scwatts committed May 3, 2024
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  7. Improve consistency of local modules

    @scwatts
    scwatts committed May 3, 2024
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  8. Rename local STAR module

    @scwatts
    scwatts committed May 3, 2024
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  9. Merge pull request #20 from nf-core/nfcore-style-adjustments 

    Adjustments to better match nf-core standards
    @scwatts
    scwatts authored May 3, 2024
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  10. Set bwa-mem2 batch size for reproducibility 

    Parameter value set to match Sarek default configuration.
    @scwatts
    scwatts committed May 3, 2024
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Commits on May 8, 2024

  1. Template update for nf-core/tools version 2.14.0

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  2. Merge remote-tracking branch 'origin/dev' into nf-core-template-merge… 

    …-2.14.0
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  3. Fix template-introduced linting breakage 

    A template fix is discussed here: https://nfcore.slack.com/archives/CE5LG7WMB/p1715182664778019
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  4. Do not apply linting fix manually 

    Doing so introduces another linting error indicating that the
linting.yml GHA workflow has been modified. Instead, use a placeholder
pyproject.toml file to avoid original issue.
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  5. Merge pull request #23 from nf-core/nf-core-template-merge-2.14.0

    @scwatts
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Commits on May 9, 2024

  1. Template update for nf-core/tools version 2.14.1

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  2. Merge remote-tracking branch 'nf-core/dev' into nf-core-template-merg… 

    …e-2.14.1
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Commits on May 10, 2024

  1. Merge pull request #24 from nf-core/nf-core-template-merge-2.14.1

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  2. Bump SAGE to 3.4.3

    @scwatts
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  3. Apply formatting fixes and other minor fixes

    @scwatts
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  4. Merge pull request #26 from nf-core/bump-sage-version 

    Bump SAGE to 3.4.3
    @scwatts
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  5. Merge pull request #25 from nf-core/further-formatting-improvements 

    Apply formatting fixes and other minor fixes
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  6. First full pass of nf-core documentation

    @scwatts
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  7. Fix Cloudflare R2 base URL

    @scwatts
    scwatts committed May 10, 2024
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  8. Apply prettier to docs

    @scwatts
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  9. Link typo in docs/output.md

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  10. Improve docs/usage.md

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  11. Correct and clarify development/stable branches

    @scwatts
    scwatts committed May 10, 2024
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  12. Update release parity versions

    @scwatts
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  13. Update prepare reference data docs

    @scwatts
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  14. Various documentation edits

    @scwatts
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  15. Update pipeline tests

    @scwatts
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  16. Remove schema ignore param from test profiles

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Commits on May 11, 2024

  1. Adjust pipeline test config, comments

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Commits on May 12, 2024

  1. Merge branch 'master' into fix-dev-root-commit

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Commits on May 13, 2024

  1. Add tool entries to CITATIONS.md

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  2. Merge pull request #28 from nf-core/fix-dev-root-commit

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Commits on May 14, 2024

  1. Merge pull request #27 from nf-core/update-pipeline-tests 

    Use simulated data for pipeline tests
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Commits on May 15, 2024

  1. Merge pull request #31 from nf-core/update-citations 

    Update CITATIONS.md
    @scwatts
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  2. Remove unused ref params from test_stub profile

    @scwatts
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  3. Use test_stub profile in download_pipline GHA wfl

    @scwatts
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  4. Remove non-stub run from download_pipeline CI

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  5. Merge pull request #32 from nf-core/fix-download-pipeline-ci 

    Fix 'download_pipeline.yml' GHA workflow
    @scwatts
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  6. Merge pull request #33 from nf-core/update-test-stub-genome-parameters 

    Remove unused reference parameters from the test_stub profile
    @scwatts
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Commits on May 16, 2024

  1. Remove duplicate tests

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  2. Do not split FASTQs during tests

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  3. Update docs/usage.md 

    Co-authored-by: Cassie Litchfield <[email protected]>
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    scwatts and casslitch authored May 16, 2024
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  4. Update docs/usage.md 

    Co-authored-by: Cassie Litchfield <[email protected]>
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    scwatts and casslitch authored May 16, 2024
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Commits on May 17, 2024

  1. Further clarify MarkDups function, requirements

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  2. Merge pull request #9 from nf-core/nf-core-documentation 

    Add basic nf-core documentation
    @scwatts
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  3. Rename bwa-mem2 index variables

    @scwatts
    scwatts committed May 17, 2024
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  4. Use correct bwa-mem2 pointers in usage.md

    @scwatts
    scwatts committed May 17, 2024
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  5. Correct typo usage.md

    @scwatts
    scwatts committed May 17, 2024
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  6. Merge pull request #34 from nf-core/improve-bwa-mem2-index-name 

    Rename bwa-mem2 index variables
    @scwatts
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  7. Merge pull request #35 from nf-core/remove-nf-test-tests 

    Remove duplicate tests
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  8. Merge pull request #36 from nf-core/avoid-fastq-splitting-in-tests 

    Do not split FASTQs during tests
    @scwatts
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Commits on May 18, 2024

  1. Change admonition style to fix rendering

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  2. Add known issue section to README.md

    @scwatts
    scwatts committed May 18, 2024
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  3. Apply Prettier linting to usage.md

    @scwatts
    scwatts committed May 18, 2024
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  4. Improve wording for known issue entry in README.md

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Commits on May 20, 2024

  1. Merge pull request #39 from nf-core/fix-usage-docs-rendering 

    Change admonition style to fix usage docs rendering
    @scwatts
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  2. Merge pull request #38 from nf-core/add-known-issues 

    Add known issue section to README.md
    @scwatts
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  3. Fix display of ORANGE report screencap on website

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  4. Merge pull request #40 from nf-core/fix-website-image-rendering 

    Fix display of the ORANGE report screencap on the nf-core website
    @scwatts
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  5. Make README.md adminitions compatible with website

    @scwatts
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  6. Merge pull request #41 from nf-core/adjust-readme-admonition 

    Make README.md admonition compatible with website
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Commits on May 21, 2024

  1. Only create bwa-mem2 index if FASTQ inputs present

    @scwatts
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  2. Merge pull request #42 from nf-core/fix-conditional-bwamem2-index-cre… 

    …ation

Fix conditional creation of bwa-mem2 index
    @scwatts
    scwatts authored May 21, 2024
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Commits on May 22, 2024

  1. Use all available threads for fastp process

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  2. Merge pull request #43 from nf-core/set-fastp-threads 

    Use all available threads for fastp process
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Commits on May 27, 2024

  1. Adjust test_stub.config usage comment

    @scwatts
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  2. Update .nf-core.yml lint rule skip list

    @scwatts
    scwatts committed May 27, 2024
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  3. Correct typo in docs/output.md

    @scwatts
    scwatts committed May 27, 2024
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  4. Replace System.exit with Nextflow.exit

    @scwatts
    scwatts committed May 27, 2024
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  5. Further standardise variable naming

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  6. Make output tarball channel name more descriptive

    @scwatts
    scwatts committed May 27, 2024
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  7. Bump MarkDups 1.1.5 to Bioconda build hdfd78af_1

    @scwatts
    scwatts committed May 27, 2024
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  8. Bump SvPrep to 1.2.4

    @scwatts
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  9. Bump bwa-mem2 container build and update Conda env 

    - update Conda environments to use fixed Sambamba Bioconda package
- new container build also uses fixed Sambamba package
    @scwatts
    scwatts committed May 27, 2024
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  10. Bump Sambamba to 1.0.1

    @scwatts
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Commits on May 29, 2024

  1. Bump version to 1.0.0 for initial release

    @scwatts
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  2. Fix usage.md MarkDups link

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  3. Merge pull request #49 from nf-core/initial-release-review-changes 

    Apply the first set of reviewer recommendations
    @scwatts
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  4. Merge pull request #47 from nf-core/bump-svprep-version 

    Bump SvPrep to 1.2.4
    @scwatts
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  5. Merge pull request #46 from nf-core/bump-sambamba-version 

    Bump Sambamba to 1.0.1
    @scwatts
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  6. Merge pull request #45 from nf-core/bump-markdups-package-build 

    Bump MarkDups 1.1.5 to Bioconda build hdfd78af_1
    @scwatts
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  7. Merge pull request #48 from nf-core/bump-bwa_mem2-container-build 

    Bump bwa-mem2 container build
    @scwatts
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Commits on May 31, 2024

  1. Merge pull request #21 from nf-core/bwamem2-input-batch-size 

    Set bwa-mem2 batch size for reproducibility
    @scwatts
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  2. Bump MarkDups to 1.1.7

    @scwatts
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  3. Update README.md known issues section

    @scwatts
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  4. Merge pull request #52 from nf-core/bump-markdups-version 

    Bump MarkDups to 1.1.7
    @scwatts
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Commits on Jun 4, 2024

  1. Quote absolute paths used in directory shadowing

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  2. Merge pull request #53 from nf-core/fix-directory-shadowing-symlinks 

    Fix directory shadowing symlinks
    @scwatts
    scwatts authored Jun 4, 2024
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  3. symlink specific gridss index files 

    genome_gridss_index folder may contain additional files that are staged by nextflow if they are part of the inputs (e.g. someone might have the .dict file in this folder if they created it via gridss.PrepareReference). This causes an error when we try to symlink the entire contents of the folder. Could we change this line to symlink the specific files of interest?
    @casslitch
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Commits on Jun 5, 2024

  1. Explicitly define all gridss index files to be symlinked 

    Accomodates users using externally created GRIDSS indexes that may contain clashing file names.
    @casslitch
    casslitch committed Jun 5, 2024
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  2. Fixed typo in find command

    @casslitch
    casslitch committed Jun 5, 2024
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  3. Fixed regex string in find command 

    Escaped back-slashes.
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Commits on Jun 6, 2024

  1. Add BAI placeholder in read processing out channel

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  2. Merge pull request #56 from nf-core/fix-read-processing-optional-channel 

    Correct read processing subworkflow optional output channel
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  3. Merge pull request #54 from nf-core/casslitch-patch-1

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Commits on Jun 7, 2024

  1. Bump AMBER to 4.0.1

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  2. Merge pull request #57 from nf-core/bump-amber-version 

    Bump AMBER to 4.0.1
    @scwatts
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Commits on Jun 12, 2024

  1. Bump SAGE to 3.4.4

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  2. Merge pull request #58 from nf-core/bump-sage-version 

    Bump SAGE to 3.4.4
    @scwatts
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Commits on Jun 13, 2024

  1. Correct MarkDups version in Conda env and docs URL

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  2. Merge pull request #59 from nf-core/fix-markdups-version 

    Use correct MarkDups version in Conda env and documentation URL
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Commits on Jun 19, 2024

  1. Add type for isofox_read_length in schema

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  2. Merge pull request #61 from nf-core/fix-nextflow-schema 

    Correct Nextflow schema entry for Isofox read length
    @scwatts
    scwatts authored Jun 19, 2024
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Commits on Jul 5, 2024

  1. Include 1.0.0 version in release parity table

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    scwatts committed Jul 5, 2024
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  2. Remove TODO in methods_description_template.yml

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    scwatts committed Jul 5, 2024
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  3. Adjust filepaths in assets/samplesheet.csv

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    scwatts committed Jul 5, 2024
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  4. Simplify target parameter definitions

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    scwatts committed Jul 5, 2024
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  5. Fix templated version in usage.md

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    scwatts committed Jul 5, 2024
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  6. Fix grammar and clarify usage.md

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    scwatts committed Jul 5, 2024
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  7. Add backticks to in text usage of oncoanalyser

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    scwatts committed Jul 5, 2024
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  8. Update .bumpversion.cfg

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    scwatts committed Jul 5, 2024
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  9. Merge pull request #62 from nf-core/initial-release-review-changes 

    Apply the second set of reviewer recommendations
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    scwatts authored Jul 5, 2024
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Commits on Jul 11, 2024

  1. Do not use hardcoded absolute path for ref genomes

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    scwatts committed Jul 11, 2024
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  2. Remove obsolete NOTE

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    scwatts committed Jul 11, 2024
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  3. Use more consistent SAGE calling subworkflow args

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    scwatts committed Jul 11, 2024
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  4. Use more readable format in targeted params config

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    scwatts committed Jul 11, 2024
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  5. Merge pull request #64 from nf-core/initial-release-review-changes 

    Apply the third set of reviewer recommendations
    @scwatts
    scwatts authored Jul 11, 2024
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Commits on Jul 17, 2024

  1. Move GRIDSS config input to last process input pos

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    scwatts committed Jul 17, 2024
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  2. Correct typo

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    scwatts committed Jul 17, 2024
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  3. Indicate NOTE author

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    scwatts committed Jul 17, 2024
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  4. Provide more informative error for bad run mode

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    scwatts committed Jul 17, 2024
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  5. Remove obsolete TODOs

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    scwatts committed Jul 17, 2024
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  6. Apply typo correction 

    Co-authored-by: Simon Pearce <[email protected]>
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    scwatts and SPPearce authored Jul 17, 2024
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  7. Merge pull request #67 from nf-core/initial-release-review-changes 

    Apply the fourth set of reviewer recommendations
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    scwatts authored Jul 17, 2024
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Commits on Jul 18, 2024

  1. Demote double underscores to single underscores

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    scwatts committed Jul 18, 2024
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  2. Use better halt/error in PAVE process

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    scwatts committed Jul 18, 2024
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  3. Update params YAML example in usage.md

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    scwatts committed Jul 18, 2024
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  4. Update indicated location of software versions

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    scwatts committed Jul 18, 2024
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  5. Minor improvements to nextflow_schema.json

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    scwatts committed Jul 18, 2024
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  6. Merge pull request #68 from nf-core/initial-release-review-changes 

    Apply the fifth set of reviewer recommendations
    @scwatts
    scwatts authored Jul 18, 2024
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  7. Fix grammar in usage.md

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    scwatts committed Jul 18, 2024
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  8. Add note on sequencing depth to usage.md

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    scwatts committed Jul 18, 2024
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  9. Merge pull request #69 from nf-core/update-usage 

    Update documentation in usage.md
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    scwatts authored Jul 18, 2024
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Commits on Jul 19, 2024

  1. Improve fenced codeblock syntax highlight

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    scwatts committed Jul 19, 2024
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  2. Use correct AMBER version in conda env file

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    scwatts committed Jul 19, 2024
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  3. Pin Tar version in extracttarball conda env

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    scwatts committed Jul 19, 2024
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Commits on Jul 24, 2024

  1. Merge pull request #70 from nf-core/initial-release-review-changes 

    Apply the sixth set of reviewer recommendations
    @scwatts
    scwatts authored Jul 24, 2024
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Commits on Jul 31, 2024

  1. Add summary note on pipeline function in README.md

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    scwatts committed Jul 31, 2024
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  2. Correct Conda GRIDSS build version

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    scwatts committed Jul 31, 2024
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  3. Correct Conda SAGE version

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    scwatts committed Jul 31, 2024
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  4. Comment out any hint of citations

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    scwatts committed Jul 31, 2024
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  5. Use the HMF abbreviation more in README.md

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    scwatts committed Jul 31, 2024
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  6. Update input samplesheet URL for tests

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    scwatts committed Jul 31, 2024
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  7. Fix MarkDups URLs

    @scwatts
    scwatts committed Jul 31, 2024
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  8. Use stub samplesheet for test_stub profile

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    scwatts committed Jul 31, 2024
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  9. Switch to BAM inputs for test_stub samplesheet

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    scwatts committed Jul 31, 2024
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Commits on Aug 1, 2024

  1. Merge pull request #72 from nf-core/initial-release-review-changes 

    Apply the seventh set of reviewer recommendations
    @scwatts
    scwatts authored Aug 1, 2024
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Commits on Aug 6, 2024

  1. Allow RNA BAM from samplesheet as input to LILAC

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    scwatts committed Aug 6, 2024
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  2. Merge pull request #76 from nf-core/lilac-samplesheet-bam-input 

    Allow RNA BAM from samplesheet as LILAC input
    @scwatts
    scwatts authored Aug 6, 2024
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