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dockerImages.yml
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dockerImages.yml
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# Copyright (c) 2018 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
# This file contains the docker images used in the pipeline.
# The containers used by default are biocontainers uploaded on quay.io.
# https://quay.io/organization/biocontainers
# The string should be formatted in the same way as utilized in a 'docker pull'
# command.
# Tools are sorted alphabetically for ease of use.
bcftools: "quay.io/biocontainers/bcftools:1.10.2--h4f4756c_2"
bedtools: "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
biowdl-input-converter: "quay.io/biocontainers/biowdl-input-converter:0.2.1--py_0"
chunked-scatter: "quay.io/biocontainers/chunked-scatter:1.0.0--py_0"
cutadapt: "quay.io/biocontainers/cutadapt:2.10--py37hf01694f_1"
cpat: "quay.io/biocontainers/cpat:3.0.4--py39hcbe4a3b_0"
collect-columns: "quay.io/biocontainers/collect-columns:1.0.0--py_0"
fastqc: "quay.io/biocontainers/fastqc:0.11.9--0"
gatk4: "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
gffcompare: "quay.io/biocontainers/gffcompare:0.10.6--h2d50403_0"
gffread: "quay.io/biocontainers/gffread:0.9.12--0"
# "hisat2" uses a combined container that has both hisat2 and samtools
# quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1
# hisat2=2.2.0, samtools=1.10.
hisat2: "quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0"
htseq: "quay.io/biocontainers/htseq:0.12.4--py37h0498b6d_2"
multiqc: "quay.io/biocontainers/multiqc:1.9--pyh9f0ad1d_0"
picard: "quay.io/biocontainers/picard:2.23.2--0"
predex: "quay.io/biocontainers/predex:0.9.2--pyh3252c3a_0"
samtools: "quay.io/biocontainers/samtools:1.10--h9402c20_2"
star: "quay.io/biocontainers/star:2.7.5a--0"
stringtie: "quay.io/biocontainers/stringtie:1.3.6--h92e31bf_0"
tabix: "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
# "UMI-tools" uses a combined container that has both UMI-tools and samtools
# quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:3067b520386698317fd507c413baf7f901666fd4-0
# this particular tag has versions umi_tools=1.1.1,samtools=1.10
umi-tools: "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:3067b520386698317fd507c413baf7f901666fd4-0"