config.yaml

versoin: 1.0
containers:
  registry: quay.io/hisplan
  images:
    - name: seqc
      version: 0.2.11
      project_url: https://github.com/hisplan/seqc-docker
      download_url: https://github.com/hisplan/seqc-docker/archive/refs/tags/v0.2.11.tar.gz
    - name: seqc-basic-analysis
      version: 0.0.11
      project_url: https://github.com/hisplan/seqc-ada
      download_url: https://github.com/hisplan/seqc-ada/archive/refs/tags/v0.0.4.tar.gz
      directory: dockers/seqc-basic-analysis
    - name: seqc-utils
      version: 0.5.2
      project_url: https://github.com/hisplan/seqc-utils
      download_url: https://github.com/hisplan/seqc-utils/archive/refs/tags/v0.5.2.tar.gz
    - name: samtools
      version: 1.9
      project_url: https://github.com/hisplan/docker-samtools
      download_url: https://github.com/hisplan/docker-samtools/archive/refs/tags/v1.9.tar.gz
    - name: velocyto
      version: 0.17.17
      project_url: https://github.com/hisplan/docker-velocyto
      download_url: https://github.com/hisplan/docker-velocyto/archive/refs/tags/v0.17.17.tar.gz
    - name: fastqc
      version: 0.11.9
      project_url: https://github.com/hisplan/docker-fastqc
      download_url: https://github.com/hisplan/docker-fastqc/archive/refs/tags/v0.11.9.tar.gz
    - name: asap2kite
      version: 0.0.1
      project_url: https://github.com/hisplan/docker-asap2kite
      download_url: https://github.com/hisplan/docker-asap2kite/archive/refs/tags/v0.0.1.tar.gz
    - name: star
      version: 2.5.3a
      project_url: https://github.com/hisplan/docker-star
      download_url: https://github.com/hisplan/docker-star/archive/refs/tags/v2.5.3a.tar.gz
    - name: star
      version: 2.7.6a
      project_url: https://github.com/hisplan/docker-star
      download_url: https://github.com/hisplan/docker-star/archive/refs/tags/v2.7.6a.tar.gz
    - name: cutadapt
      version: 2.5
      project_url: https://github.com/hisplan/docker-cutadapt
      download_url: https://github.com/hisplan/docker-cutadapt/archive/refs/tags/v2.5.tar.gz
    - name: seqkit
      version: 0.16.1
      project_url: https://github.com/hisplan/sharp/tree/master/dockers/seqkit
      download_url: https://github.com/hisplan/sharp/archive/refs/tags/v0.1.1.tar.gz
      directory: dockers/seqkit
    - name: hto-demux-kmeans
      version: 0.5.0
      project_url: https://github.com/hisplan/sharp/tree/master/dockers/hto-demux-kmeans
      download_url: https://github.com/hisplan/sharp/archive/refs/tags/v0.1.1.tar.gz
      directory: dockers/hto-demux-kmeans
    - name: hto-demux-seurat
      version: 0.6.0
      project_url: https://github.com/hisplan/sharp/tree/master/dockers/hto-demux-seurat
      download_url: https://github.com/hisplan/sharp/archive/refs/tags/v0.1.1.tar.gz
      directory: dockers/hto-demux-seurat
    - name: hto-adt-postprocess
      version: 0.3.4
      project_url: https://github.com/hisplan/sharp/tree/master/dockers/hto-adt-postprocess
      download_url: https://github.com/hisplan/sharp/archive/refs/tags/v0.1.1.tar.gz
      directory: dockers/hto-adt-postprocess
    - name: cut-indrop-spacer
      version: 0.2.0
      project_url: https://github.com/hisplan/sharp/tree/master/dockers/cut-indrop-spacer
      download_url: https://github.com/hisplan/sharp/archive/refs/tags/v0.1.1.tar.gz
      directory: dockers/cut-indrop-spacer
    - name: basic-qc
      version: 0.2.1
      project_url: https://github.com/hisplan/sharp/tree/master/dockers/basic-qc
      download_url: https://github.com/hisplan/sharp/archive/refs/tags/v0.1.1.tar.gz
      directory: dockers/cut-indrop-spacer
    - name: cite-seq-count
      version: 1.4.2-develop
      project_url: https://github.com/hisplan/sharp/tree/master/dockers/cite-seq-count
      download_url: https://github.com/hisplan/sharp/archive/refs/tags/v0.1.1.tar.gz
      directory: dockers/cite-seq-count
    - name: pigz
      version: 2.4
      project_url: https://github.com/hisplan/docker-pigz
      download_url: https://github.com/hisplan/docker-pigz/archive/refs/tags/v2.4.tar.gz
    - name: htslib
      version: 1.9
      project_url: https://github.com/hisplan/docker-htslib
      download_url: https://github.com/hisplan/docker-htslib/archive/refs/tags/v1.9.tar.gz
    - name: fai2gtf
      version: 0.2.0
      project_url: https://github.com/hisplan/wdl-transgenes
      download_url: https://github.com/hisplan/wdl-transgenes/archive/refs/tags/v0.0.8.tar.gz
      directory: dockers/fai2gtf
    - name: gtf-utils
      version: 0.0.6
      project_url: https://github.com/hisplan/gtf-utils
      download_url: https://github.com/hisplan/gtf-utils/archive/refs/tags/v0.0.6.tar.gz
    - name: cellranger
      version: 6.1.2
      project_url: https://github.com/hisplan/docker-cellranger
      download_url: https://github.com/hisplan/docker-cellranger/archive/refs/tags/v6.1.2.tar.gz
    - name: cellranger-arc
      version: 2.0.0
      project_url: https://github.com/hisplan/docker-cellranger-arc
      download_url: https://github.com/hisplan/docker-cellranger-arc/archive/refs/tags/v2.0.0.tar.gz
    - name: cellranger-atac
      version: 2.1.0
      project_url: https://github.com/hisplan/docker-cellranger-atac
      download_url: https://github.com/hisplan/docker-cellranger-atac/archive/refs/tags/v2.1.0.tar.gz
    - name: spaceranger
      version: 1.3.1
      project_url: https://github.com/hisplan/docker-spaceranger
      download_url: https://github.com/hisplan/docker-spaceranger/archive/refs/tags/v1.3.1.tar.gz
    - name: archr
      version: 0.9.x-snapshot-20200922b
      project_url: https://github.com/hisplan/docker-archr
      download_url: https://github.com/hisplan/docker-archr/archive/refs/tags/v0.9.x-snapshot-20200922b.tar.gz
    - name: archr2adata
      version: 0.0.3
      project_url: https://github.com/hisplan/archr2adata
      download_url: https://github.com/hisplan/archr2adata/archive/refs/tags/v0.0.3.tar.gz

pipelines:
  packages:
    - name: seqc
      version: 0.2.11
      project_url: https://github.com/hisplan/seqc-docker
      download_url: https://github.com/hisplan/seqc-docker/archive/refs/tags/v0.2.11.tar.gz
    - name: seqc-ada
      version: 0.0.4
      project_url: https://github.com/hisplan/seqc-ada
      download_url: https://github.com/hisplan/seqc-ada/archive/refs/tags/v0.0.4.tar.gz
    - name: sharp
      version: 0.1.1
      project_url: https://github.com/hisplan/sharp
      download_url: https://github.com/hisplan/sharp/archive/refs/tags/v0.1.1.tar.gz
    - name: velopipe
      version: 0.0.9
      project_url: https://github.com/hisplan/velopipe
      download_url: https://github.com/hisplan/velopipe/archive/refs/tags/v0.0.9.tar.gz
    - name: fastqc
      version: 0.11.9
      project_url: https://github.com/hisplan/wdl-fastqc
      download_url: https://github.com/hisplan/wdl-fastqc/archive/refs/tags/v0.11.9.tar.gz
    - name: transgenes
      version: 0.0.8
      project_url: https://github.com/hisplan/wdl-transgenes
      download_url: https://github.com/hisplan/wdl-transgenes/archive/refs/tags/v0.0.8.tar.gz
    - name: cellranger-gex
      version: 6.1.2
      project_url: https://github.com/hisplan/wdl-cellranger-gex
      download_url: https://github.com/hisplan/wdl-cellranger-gex/archive/refs/tags/v6.1.2.tar.gz
    - name: cellranger-vdj
      version: 6.1.2
      project_url: https://github.com/hisplan/wdl-cellranger-vdj
      download_url: https://github.com/hisplan/wdl-cellranger-vdj/archive/refs/tags/v6.1.2.tar.gz
    - name: cellranger-cellplex
      version: 6.1.2
      project_url: https://github.com/hisplan/wdl-cellranger-cellplex
      download_url: https://github.com/hisplan/wdl-cellranger-cellplex/archive/refs/tags/v6.1.2.tar.gz
    - name: cellranger-arc
      version: 2.0.0
      project_url: https://github.com/hisplan/wdl-cellranger-arc
      download_url: https://github.com/hisplan/wdl-cellranger-arc/archive/refs/tags/v2.0.0.tar.gz
    - name: cellranger-atac
      version: 2.1.0
      project_url: https://github.com/hisplan/wdl-cellranger-atac
      download_url: https://github.com/hisplan/wdl-cellranger-atac/archive/refs/tags/v2.1.0.tar.gz
    - name: spaceranger
      version: 1.3.1
      project_url: https://github.com/hisplan/wdl-spaceranger
      download_url: https://github.com/hisplan/wdl-spaceranger/archive/refs/tags/v1.3.1.tar.gz
    - name: mkref
      version: 0.0.6
      project_url: https://github.com/hisplan/wdl-mkref
      download_url: https://github.com/hisplan/wdl-mkref/archive/refs/tags/v0.0.6.tar.gz
    - name: archr
      version: 0.1.0
      project_url: https://github.com/hisplan/wdl-ArchR
      download_url: https://github.com/hisplan/wdl-ArchR/archive/refs/tags/v0.1.0.tar.gz