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GitHub / nf-core / rnavar

gatk4 RNA variant calling pipeline

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

Stars: 28
Forks: 29
Open Issues: 39

License: mit
Language: Nextflow
Repo Size: 3.64 MB
Dependencies: 15

Created: about 3 years ago
Updated: 2 months ago
Last pushed: 11 days ago
Last synced: 11 days ago

Commit Stats

Commits: 237
Authors: 7
Mean commits per author: 33.86
Development Distribution Score: 0.194
More commit stats: https://commits.ecosyste.ms/hosts/GitHub/repositories/nf-core/rnavar

Topics: gatk4, nextflow, nf-core, pipeline, rna, rnaseq, variant-calling, worflow, workflow

Files

Readme

Dependencies

.github/workflows/awsfulltest.yml actions

nf-core/tower-action v3 composite

.github/workflows/awstest.yml actions

nf-core/tower-action v3 composite

.github/workflows/branch.yml actions

mshick/add-pr-comment v1 composite

.github/workflows/ci.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/fix-linting.yml actions

actions/checkout v3 composite
actions/setup-node v2 composite

.github/workflows/linting.yml actions

actions/checkout v2 composite
actions/setup-node v2 composite
actions/setup-python v3 composite
actions/upload-artifact v2 composite

.github/workflows/linting_comment.yml actions

dawidd6/action-download-artifact v2 composite
marocchino/sticky-pull-request-comment v2 composite

modules/nf-core/modules/ensemblvep/Dockerfile docker

nfcore/base 1.14 build

modules/nf-core/modules/snpeff/Dockerfile docker

nfcore/base 1.14 build

modules/nf-core/modules/cat/fastq/meta.yml cpan

modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml cpan

modules/nf-core/modules/ensemblvep/meta.yml cpan

modules/nf-core/modules/fastqc/meta.yml cpan

modules/nf-core/modules/gatk4/applybqsr/meta.yml cpan

modules/nf-core/modules/gatk4/baserecalibrator/meta.yml cpan

modules/nf-core/modules/gatk4/bedtointervallist/meta.yml cpan

modules/nf-core/modules/gatk4/createsequencedictionary/meta.yml cpan

modules/nf-core/modules/gatk4/haplotypecaller/meta.yml cpan

modules/nf-core/modules/gatk4/indexfeaturefile/meta.yml cpan

modules/nf-core/modules/gatk4/intervallisttools/meta.yml cpan

modules/nf-core/modules/gatk4/markduplicates/meta.yml cpan

modules/nf-core/modules/gatk4/mergevcfs/meta.yml cpan

modules/nf-core/modules/gatk4/splitncigarreads/meta.yml cpan

modules/nf-core/modules/gatk4/variantfiltration/meta.yml cpan

modules/nf-core/modules/gffread/meta.yml cpan

modules/nf-core/modules/gunzip/meta.yml cpan

modules/nf-core/modules/multiqc/meta.yml cpan

modules/nf-core/modules/samtools/faidx/meta.yml cpan

modules/nf-core/modules/samtools/flagstat/meta.yml cpan

modules/nf-core/modules/samtools/idxstats/meta.yml cpan

modules/nf-core/modules/samtools/index/meta.yml cpan

modules/nf-core/modules/samtools/merge/meta.yml cpan

modules/nf-core/modules/samtools/sort/meta.yml cpan

modules/nf-core/modules/samtools/stats/meta.yml cpan

modules/nf-core/modules/snpeff/meta.yml cpan

modules/nf-core/modules/star/align/meta.yml cpan

modules/nf-core/modules/star/genomegenerate/meta.yml cpan

modules/nf-core/modules/tabix/bgziptabix/meta.yml cpan

modules/nf-core/modules/tabix/tabix/meta.yml cpan

modules/nf-core/modules/untar/meta.yml cpan

modules/nf-core/modules/ensemblvep/environment.yml pypi

modules/nf-core/modules/snpeff/environment.yml pypi