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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"
# Contains bwa 0.7.17 bwakit 0.7.17.dev1 and samtools 1.10.
bwakit+samtools: "quay.io/biocontainers/mulled-v2-ad317f19f5881324e963f6a6d464d696a2825ab6:c59b7a73c87a9fe81737d5d628e10a3b5807f453-0"
# Contains bwa-mem2 bwakit 0.7.17.dev1 and samtools 1.10.
bwamem2+kit+samtools: "quay.io/biocontainers/mulled-v2-6a15c99309c82b345497d24489bee67bbb76c2f6:1c9c3227b9bf825a8dc9726a25701aa23c0b1f12-0"
chunked-scatter: "quay.io/biocontainers/chunked-scatter:1.0.0--py_0"
clever: "quay.io/biowdl/clever-toolkit:2.4"
cutadapt: "quay.io/biocontainers/cutadapt:4.4--py310h1425a21_0"
delly: "quay.io/biocontainers/delly:0.8.1--h4037b6b_1"
duphold: "quay.io/biocontainers/duphold:0.2.1--h516909a_1"
fastqc: "quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0"
gatk4: "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
gatk-broad: "docker.io/broadinstitute/gatk:4.1.8.0"
gridss: "quay.io/biowdl/gridss:2.12.2"
manta: "quay.io/biocontainers/manta:1.4.0--py27_1"
multiqc: "quay.io/biocontainers/multiqc:1.9--pyh9f0ad1d_0"
picard: "quay.io/biocontainers/picard:2.23.2--0"
# Python 3.7-slim on buster.
python: "docker.io/python@sha256:e0f6a4df17d5707637fa3557ab266f44dddc46ebfc82b0f1dbe725103961da4e"
sambamba: "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
samtools: "quay.io/biocontainers/samtools:1.10--h9402c20_2"
strelka: "quay.io/biocontainers/strelka:2.9.7--0"
smoove: quay.io/biocontainers/smoove:0.2.5--0
somaticseq: "docker.io/lethalfang/somaticseq:3.1.0"
survivor: "quay.io/biocontainers/survivor:1.0.7--hd03093a_2"
tabix: "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
umi-tools: "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:3067b520386698317fd507c413baf7f901666fd4-0"
vardict-java: "quay.io/biocontainers/vardict-java:1.5.8--1"