Dockers

On Biowulf, this pipeline is executed by first loading the Singularity and Nextflow modules. The pipeline itself utilizes Docker containers for processing data across its various subworkflows and processes.

Docker Containers Used in the Pipeline¶

NCI Docker Containers¶

Tool/Process	Container Path
Cutadapt	`nciccbr/ncigb_cutadapt_v1.18:latest`
Fastqc	`nciccbr/ccrgb_qctools:latest`
Star., Rsem., Arriba, Starfusion	`nciccbr/ccrgb_starplus:latest`
Fusioncatcher	`nciccbr/ccrgb_fusioncatcher:v2.0`
Multiqc.*	`nciccbr/ccbr_multiqc_1.9:v0.0.1`
Picard.*, HSMetrics, Hotspot_Coverage, Hotspot_Boxplot, Flagstat, Bamutils, Merge_new_HLA, MergeHLA, Read_depth, FailedExons_Genes, Combine_variants, Merge_Pvacseq_vcf	`nciccbr/ccrgb_qctools:latest`
GATK.*, RNAseq_HaplotypeCaller, Exome_HaplotypeCaller	`nciccbr/ccrgb_gatk_3.8-1:v1.0`
Genotyping, HotspotPileup, Mutect_order, MutationalSignature, CoveragePlot, Exome_QC, CircosPlot, CircosPlot_lib, Mergefusion, Allstepscomplete, RNAlibrary_customQC, RNAqc_TrancriptCoverage, CoveragePlot, Coverage, Lib2_RNAqc_TrancriptCoverage, TargetIntervals, CNVkit_png, Strelka_vcf_processing	`nciccbr/ccrgb_qctools:latest`
AddAnnotation., Split_vcf, UnionSomaticCalls, Actionable., DBinput.*, Sequenza_annot, MutationBurden, Expressed	`nciccbr/ccrgb_qctools:latest`
Mixcr	`nciccbr/ccrgb_mixcr:v1.1`
VDJtools	`nciccbr/ccrgb_vdjtools:latest`
Bamutil	`nciccbr/ccrgb_bamutil:latest`
SnpEff	`nciccbr/ccrgb_snpeff:1.0`
Vcf2txt, FormatInput.*, Annovar, Custom_annotation, Combine_annotation	`nciccbr/ccrgb_annovar:v1.0`
RNAseQC	`nciccbr/ccrgb_rnaseqc_v1.1.8:latest`
Strandedness	`nciccbr/ccbr_ngsderive:v1.0`
BWA	`nciccbr/ccbr_ubuntu_base_20.04:v2.0`
Sequenza	`nciccbr/ccrgb_qctools:v3.2`
Cosmic3Signature	`nciccbr/ccrgb_qctools:v4.0`
Fastq_screen	`nciccbr/ccbr_fastq_screen_0.14.1:latest`
TcellExtrect.*	`hsienchao/tcell_extrect:v1`
HLA_HD	`vinegang/ccrgb_hlahd_1.7.0:v1.0`
Conpair.*	`nciccbr/ccrgb_conpair:latest`
Fusion_Annotation, Merge_fusion_annotation	`hsienchao/fusion_tools:v1`
VEP	`dnousome/ccbr_vcf2maf:v102.0.0`
Pvacseq	`vinegang/pvactools_1.3.5_ps:1.0`
Mantis_MSI	`vinegang/mantis:v1.0.5`

Non-NCI Docker Containers¶

Tool/Process	Container Path
Kraken	`staphb/kraken:1.1.1-no-db`
Krona	`pbelmann/krona:latest`
Bam2tdf	`quay.io/biocontainers/igvtools:2.3.93--0`
Optitype	`fred2/optitype:release-v1.3.1`
VerifyBamID	`ottov/verifybamid-aws:latest`
CNVkitP.*	`zlskidmore/cnvkit:0.9.6`
Mutect	`dinglab2/mutect-tool:20190313`
Manta	`szarate/manta:v1.6.0`
Strelka	`davelabhub/strelka:2.9.10--0`
Sequenza_utils	`nkrumm/sequenza-nf:latest`
CUSTOM_DUMPSOFTWAREVERSIONS	`quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0`