gtgraham

nim compiler and utils image (aarch64, x86_64)

clear linux container for methylation tools

clear linux build of strelka2, manta

clear linux with python 2.7.18, in path as python/pip

clear linux build of ataqv (requires python)

seqtools (fastp,bwa,bowtie2,picard,preseq,fastqc,seqtk,sambamba,samblaster,samtools+htslib,bamtools)

clear linux build of R, including Picard (and runner script) for output metrics steps

general bedtools (bedtools, deepTools, pysam, pyBigWig, MACS, bedGraphToBigWig,samtools)

python3_7 with sambamba, samtools

clear linux build of R packages up to ggplot2, tibble, tidyr, dplyr (and dep)

clear linux build of multiqc, pymdown-extensions (and dep) on gtgraham/clear-python3_7

clear linux build of perl+HOMER (only req for annotatePeaks.pl)

clear linux build of subread (featureCounts)

clear linux build of preseq (and htslib)

clear linux build of samtools, htslib

fastp (0.23.2), libdeflate, and isa-l built on clearlinux image (for nextflow)

builder image for bowtie2

clear linux with python 3.7.9, in path as python/pip (not python3/pip3)

clear linux container for wgs tools

collection of atacseq tools built from source from clear linux

extension of nfcore to use fastp instead of TrimGalore