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GitHub / guigolab / grape-nf

An automated RNA-seq pipeline using Nextflow

JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/guigolab%2Fgrape-nf

Stars: 35
Forks: 10
Open Issues: 32

License: gpl-3.0
Language: Nextflow
Repo Size: 5.43 MB
Dependencies: 77

Created: almost 9 years ago
Updated: about 2 months ago
Last pushed: 3 months ago
Last synced: 3 months ago

Topics: crg, guigo, nextflow, ngs, pipeline, rna-seq

Files

Readme

Dependencies

docker/tool/star/Dockerfile docker

alpine ${ALPINE_VER} build
grapenf/base latest build

docs/Gemfile rubygems

asciidoctor = 1.5.4
asciidoctor-pdf >= 1.0.0.alpha

.github/workflows/ci.yml actions

actions/checkout v2 composite
actions/setup-java v1 composite

docker/base/Dockerfile docker

alpine ${ALPINE_VER} build

docker/conda/Dockerfile docker

frolvlad/alpine-miniconda3 latest build

docker/ihec/Dockerfile docker

grapenf/bamstats ${BAMSTATS_VER} build
grapenf/bedtools ${BEDTOOLS_VER} build
grapenf/kentutils ${KENTUTILS_VER} build
grapenf/rsem ${RSEM_VER} build
grapenf/rseqc ${RSEQC_VER} build
grapenf/sambamba ${SAMBAMBA_VER} build
grapenf/samtools ${SAMTOOLS_VER} build
grapenf/star ${STAR_VER} build

docker/java/Dockerfile docker

frolvlad/alpine-oraclejre8 latest build

docker/process/bigwig/rgcrg/Dockerfile docker

grapenf/bedtools ${BEDTOOLS_VER} build
grapenf/kentutils ${KENTUTILS_VER} build
grapenf/python latest build
grapenf/sambamba ${SAMBAMBA_VER} build

docker/process/bigwig/star/Dockerfile docker

grapenf/base latest build
grapenf/kentutils ${KENTUTILS_VER} build
grapenf/sambamba ${SAMBAMBA_VER} build
grapenf/star ${STAR_VER} build

docker/process/contig/rgcrg/Dockerfile docker

grapenf/bedtools ${BEDTOOLS_VER} build
grapenf/python latest build
grapenf/sambamba ${SAMBAMBA_VER} build

docker/process/inferexp/rseqc/Dockerfile docker

grapenf/kentutils ${KENTUTILS_VER} build
grapenf/rseqc ${RSEQC_VER} build

docker/process/mapping/gem/Dockerfile docker

grapenf/gemtools ${GEMTOOLS_VER} build
grapenf/samtools ${SAMTOOLS_VER} build

docker/process/mapping/star/Dockerfile docker

grapenf/base latest build
grapenf/sambamba ${SAMBAMBA_VER} build
grapenf/star ${STAR_VER} build

docker/process/quantification/flux/Dockerfile docker

grapenf/flux-capacitor ${FLUX_VER} build
grapenf/samtools ${SAMTOOLS_VER} build

docker/process/quantification/rsem/Dockerfile docker

grapenf/base latest build
grapenf/rsem ${RSEM_VER} build
grapenf/sambamba ${SAMBAMBA_VER} build

docker/python/Dockerfile docker

grapenf/base latest build

docker/tool/bamstats/Dockerfile docker

golang alpine${ALPINE_VER} build
grapenf/base latest build

docker/tool/bedtools/Dockerfile docker

alpine ${ALPINE_VER} build
grapenf/base latest build

docker/tool/flux-capacitor/Dockerfile docker

grapenf/java latest build

docker/tool/gemtools/Dockerfile docker

grapenf/python latest build

docker/tool/kentutils/Dockerfile docker

alpine ${ALPINE_VER} build
grapenf/base latest build

docker/tool/rsem/Dockerfile docker

alpine ${ALPINE_VER} build
grapenf/base latest build

docker/tool/rseqc/Dockerfile docker

grapenf/python latest build

docker/tool/sambamba/Dockerfile docker

alpine ${ALPINE_VER} build
grapenf/base latest build

docker/tool/samtools/Dockerfile docker

alpine ${ALPINE_VER} build
grapenf/base latest build

docs/Gemfile.lock rubygems

Ascii85 1.0.2
addressable 2.8.0
afm 0.2.2
asciidoctor 1.5.4
asciidoctor-pdf 1.5.0.alpha.11
css_parser 1.4.1
hashery 2.1.1
pdf-core 0.6.1
pdf-reader 1.4.0
polyglot 0.3.5
prawn 2.1.0
prawn-icon 1.0.0
prawn-svg 0.21.0
prawn-table 0.2.2
prawn-templates 0.0.3
public_suffix 4.0.6
ruby-rc4 0.1.5
safe_yaml 1.0.4
thread_safe 0.3.5
treetop 1.5.3
ttfunk 1.4.0