available_tools.md



Available tools


nf module: a working example of nextflow process is available in src/nf_modules/<tools>/<tool>.nf and src/nf_modules/<tools>/<tool>.config


docker module: you can create a docker with the src/docker_modules/<tool>/<version>/docker_init.sh


psmn module: you can use the tool in the PSMN

IN2P3 module: you can use the tool in the CCIN2P3


tool
nf module
docker module
psmn module
in2p3 module


BEDtools
ok
ok
ok
ok


BFCtools
no
ok
ok
ok


bioawk
no
ok
ok
ok


Bowtie
ok
ok
no
ok


Bowtie2
ok
ok
ok
ok


BWA
ok
ok
ok
ok


canu
ok
ok
ok
ok


cutadapt
ok
ok
ok
ok


deepTools
ok
ok
ok
ok


fastp
ok
ok
ok
ok


FastQC
ok
ok
ok
ok


file_handle
no
ok
ok
ok


GATK
no
ok
ok
ok


HISAT2
ok
ok
ok
ok


HTSeq
ok
ok
ok
ok


Kallisto
ok
ok
ok
ok


MACS2
ok
ok
ok
ok


MultiQC
ok
ok
ok
ok


MUSIC
ok
ok
ok
ok


picard
no
ok
ok
ok


pigz
no
ok
ok
ok


RSEM
ok
ok
ok
ok


Salmon
no
ok
ok
ok


sambamba
ok
ok
ok
ok


samblaster
ok
ok
ok
ok


SAMtools
ok
ok
ok
ok


SRAtoolkit
ok
ok
ok
ok


STAR
ok
ok
ok
ok


subread
no
ok
ok
ok


TopHat
no
ok
ok
ok


Trimmomatic
no
ok
ok
ok


UMItools
no
ok
ok
ok


UrQt
ok
ok
ok
ok