Containers for the OmniNeo workflow publication: OmniNeo: A Multi-Omics Pipeline Incorporating Proteomics and AI Selection for Neoantigen Optimization in Tumor Immunotherapy Details of software installed in the containers can be found below: category function software version container name 1 Quality control fastp 0.23.4 fastp_0.23.4.sif 2 SAM/BAM manipulation samtools 1.3.1 samtools_1.3.1--h60f3df9_12.sif 3 Read alignment bwa 0.7.19 bwa_0.7.19--h577a1d6_0.sif 4 Variant calling and processing gatk4 4.6.1.0 gatk4_4.6.1.0--py310hdfd78af_0.sif 5 BAM file processing picard 3.4.0 picard_3.4.0--hdfd78af_0.sif 6 RNA quantification kallisto 0.51.1 kallisto_0.51.1--ha4fb952_1.sif 7 Proteomics analysis maxquant 2.0.3.0 maxquant_2.0.3.0--py310hdfd78af_1.sif 8 Fusion detection star-fusion 1.14.0 star-fusion_1.14.0--hdfd78af_2.sif 9 HLA Class I typing optitype 1.3.3 optitype_latest.sif 10 VCF manipulation bcftools 1.21 bcftools_1.21--h3a4d415_1.sif 11 downstream analysis Python 3.6 python_3.6_bio.sif 12 AI Selection for Neoantigen Optimization Pytorch 2.7.0 pytorch_latest.sif