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cellranger_mkfastq
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  • publish_2.2.0
    234c9659 · Merge branch 'develop' into 'master' ·
    Release publish_2.2.0

    v2.2.0

    UserFacing

    • Update cellranger to version 4.0.0

    Background

    • Add runtime info
    • Make standard (profile) be biohpc AND cluster

    Known Bugs

    • cellranger mkfastq will not accept spaces in path for run param even if quoted, issue raised on 10XGenomics/cellranger github issue #31
      • note: 10x doesn't check github issues, emailed instead
      • note: pipeline checks for spaces and exits prematurely if found
    • If multiple flowcells (tar'd) files are inputted then there will be multiple fastq's by the same name, currently dealing with that name conflict is not tractable
      • note: if multiple bcl files are detected then cellranger_count design file is not created
    • If too many (or too large) .tar(.gz) bcl files are placed in one run, aws runs appears to fail possibly due to timeout on staging
  • test_2.2.0rc5
    558b6410 · Update singularity version. ·
  • test_2.2.0rc4
    5086afef · add cache directory to current workdir. ·
  • test_2.2.0rc3
    46020e2c · Update default config to be astrocyte and include astrocyte config. ·
  • test_2.2.0rc2
    bb5c8d1b · remove track start. ·
  • test_2.2.0
    c82f7a6d · Add in change log. ·
  • publish_2.1.5
    ab04237e · Merge branch 'develop' into 'master' ·
    Release publish_2.1.5

    v2.1.5

    UserFacing

    • Check Design File for spaces in name and file contents
    • Update design example, README, and astrocyte.yml with current barcode IDs
    • Remove unnecessary intermediate process files
    • Add config option for running on AWS
    • Ignore dual index
    • Add parameter for base mask (not available in Astrocyte)
    • Output Nextflow version in QC report
    • Output pipeline version (manual) in QC report

    Background

    • Add Nextflow Tower integration into CI (GHH's profile)
    • Update to be runnable on cloud
    • Refactor configs

    Known Bugs

    • cellranger mkfastq will not accept spaces in path for run param even if quoted, issue raised on 10XGenomics/cellranger github issue #31
      • note: 10x doesn't check github issues, emailed instead
      • note: pipeline checks for spaces and exits prematurely if found
    • If multiple flowcells (tar'd) files are inputted then there will be multiple fastq's by the same name, currently dealing with that name conflict is not tractable
      • note: if multiple bcl files are detected then cellranger_count design file is not created
    • If too many (or too large) .tar(.gz) bcl files are placed in one run, aws runs appears to fail possibly due to timeout on staging
  • containerized   This is a fully containerized version of the pipeline
    fbf1a9f7 · Fix pipeline badges ·
  • publish_1.3.1
    6752c850 · Merge branch 'develop' into 'master' ·
    Release publish_1.3.1

    v1.3.1

    User Facing

    • Change Cellranger Version to 3.1.0
    • Fix countDesign to take multiple samples
    • Add MIT License
    • Check Design File for spaces in name and file contents
    • Update design example, README, and astrocyte.yml with current barcode IDs

    Background

    • Add CI artifacts
    • Add Nextflow Tower integration into CI (GHH's profile)

    Known Bugs

    • cellranger mkfastq will not accept spaces in path for run param even if quoted, issue raised on 10XGenomics/cellranger github issue #31
      • note: 10x doesn't check github issues, emailed instead
      • note: pipeline checks for spaces and exits prematurely if found
    • If multiple flowcells (tar'd) files are inputted then there will be multiple fastq's by the same name, currently dealing with that name conflict is not tractable
      • note: if multiple bcl files are detected then cellranger_count design file is not created
  • publish_1.2.0
    33e60071 · Merge branch 'develop' into 'master' ·
    Release publish_1.2.0

    v1.2.0

    User Facing

    • Add references to of tools to mutiQC report
    • Add BICF details to multiqc report
    • Create cellranger_count design file (if only 1 flowcell is inputted)

    Background

    • Add DOI (develop branch)
    • Add changelog as link to astrocyte docs (master branch)
    • Update example design file link in astrocyte docs (master branch)
    • Check tarballed bcl directory for spaces and exit if it contains one...cellranger mkfastq cannot handle spaces (develop branch)
    • Move untar (including space check) to bash script
    • Add Jeremy Mathews to author list
    • Apply style guide
    • Add pytests for ouptuts

    Known Bugs

    • cellranger mkfastq will not accept spaces in path for run param even if quoted, issue raised on 10XGenomics/cellranger github issue #31
      • note: 10x doesn't check github issues, emailed instead
      • note: pipeline checks for spaces and exits prematurely if found
    • If multiple flowcells (tar'd) files are inputted then there will be multiple fastq's by the same name, currently dealing with that name conflict is not tractable
      • note: if multiple bcl files are detected then cellranger_count design file is not created
  • publish_1.1.4
    4c37ee84 · Merge branch 'develop' into 'master' ·
    Release publish_1.1.4

    v1.1.4

    User Facing

    • Fix design file not visible in Astrocyte
    • Fix handling of multiple flowcells in 1 submission

    Background

    • Move multiqc config to conf folder
    • Add CI test for multiple flowcells
    • Add changelog
    • Quote design/tarball/$baseDir path in processes in case of spaces

    Known Bugs

    • cellranger mkfastq will not accept spaces in path for run param even if quoted, issue raised on 10XGenomics/cellranger github issue #31
  • publish_1.0.0
    45100352 · Merge branch 'develop' into 'master' ·
    Release publish_1.0.0

    Initial Astrocyte deployed version