2 # This file contains the docker images used in the pipeline.
3 # The containers used by default are biocontainers uploaded on quay.io.
4 # https://quay.io/organization/biocontainers
6 # The string should be formatted in the same way as utilized in a 'docker pull'
9 # Tools are sorted alphabetically for ease of use.
10 bcftools: "quay.io/biocontainers/bcftools:1.10.2--h4f4756c_2"
11 bedtools: "quay.io/biocontainers/bedtools:2.23.0--hdbcaa40_3"
12 biowdl-input-converter: "quay.io/biocontainers/biowdl-input-converter:0.2.1--py_0"
13 # A mulled container is needed to have both samtools and bwa in one container.
14 # This container contains: samtools (1.10), bwa (0.7.17-r1188)
15 bwa+samtools: "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0"
16 # Contains bwa 0.7.17 bwakit 0.7.17.dev1 and samtools 1.10
17 bwakit+samtools: "quay.io/biocontainers/mulled-v2-ad317f19f5881324e963f6a6d464d696a2825ab6:c59b7a73c87a9fe81737d5d628e10a3b5807f453-0"
18 chunked-scatter: "quay.io/biocontainers/chunked-scatter:1.0.0--py_0"
19 clever: "quay.io/biocontainers/clever-toolkit:2.4--py36hcfe0e84_6"
20 cutadapt: "quay.io/biocontainers/cutadapt:2.10--py37hf01694f_1"
21 delly: "quay.io/biocontainers/delly:0.8.1--h4037b6b_1"
22 fastqc: "quay.io/biocontainers/fastqc:0.11.9--0"
23 gatk4: "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
24 gatk-broad: "broadinstitute/gatk:4.1.8.0"
25 manta: "quay.io/biocontainers/manta:1.4.0--py27_1"
26 multiqc: "quay.io/biocontainers/multiqc:1.9--pyh9f0ad1d_0"
27 picard: "quay.io/biocontainers/picard:2.23.2--0"
28 # Python 3.7-slim on buster
29 python: "python@sha256:e0f6a4df17d5707637fa3557ab266f44dddc46ebfc82b0f1dbe725103961da4e"
30 sambamba: "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
31 samtools: "quay.io/biocontainers/samtools:1.10--h9402c20_2"
32 strelka: "quay.io/biocontainers/strelka:2.9.7--0"
33 smoove: quay.io/biocontainers/smoove:0.2.5--0
34 somaticseq: "lethalfang/somaticseq:3.1.0"
35 survivor: "quay.io/biocontainers/survivor:1.0.6--h6bb024c_0"
36 tabix: "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
37 vardict-java: "quay.io/biocontainers/vardict-java:1.5.8--1"