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GitHub / nf-core / rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

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

Stars: 795
Forks: 662
Open Issues: 77

License: mit
Language: Nextflow
Repo Size: 64.1 MB
Dependencies: 21

Created: about 6 years ago
Updated: 4 days ago
Last pushed: 6 days ago
Last synced: 5 days ago

Commit Stats

Commits: 3329
Authors: 97
Mean commits per author: 34.32
Development Distribution Score: 0.645
More commit stats: https://commits.ecosyste.ms/hosts/GitHub/repositories/nf-core/rnaseq

Topics: nextflow, nf-core, pipeline, rna, rna-seq, workflow

Files

Readme

Dependencies

.github/workflows/branch.yml actions

mshick/add-pr-comment v1 composite

.github/workflows/ci.yml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/checkout v2 composite
nf-core/setup-nextflow v1 composite

.github/workflows/clean-up.yml actions

actions/stale v7 composite

.github/workflows/cloud_tests_full.yml actions

actions/upload-artifact v3 composite
seqeralabs/action-tower-launch v1 composite

.github/workflows/cloud_tests_small.yml actions

actions/upload-artifact v3 composite
seqeralabs/action-tower-launch v1 composite

.github/workflows/fix-linting.yml actions

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

.github/workflows/linting.yml actions

actions/checkout v3 composite
actions/setup-node v3 composite
actions/setup-python v4 composite
actions/upload-artifact v3 composite
mshick/add-pr-comment v1 composite
nf-core/setup-nextflow v1 composite
psf/black stable composite

.github/workflows/linting_comment.yml actions

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

modules/nf-core/bbmap/bbsplit/meta.yml cpan

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

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

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

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

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

modules/nf-core/fq/subsample/meta.yml cpan

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

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

modules/nf-core/hisat2/align/meta.yml cpan

modules/nf-core/hisat2/build/meta.yml cpan

modules/nf-core/hisat2/extractsplicesites/meta.yml cpan

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

modules/nf-core/preseq/lcextrap/meta.yml cpan

modules/nf-core/rsem/calculateexpression/meta.yml cpan

modules/nf-core/rsem/preparereference/meta.yml cpan

modules/nf-core/rseqc/bamstat/meta.yml cpan

modules/nf-core/rseqc/inferexperiment/meta.yml cpan

modules/nf-core/rseqc/innerdistance/meta.yml cpan

modules/nf-core/rseqc/junctionannotation/meta.yml cpan

modules/nf-core/rseqc/junctionsaturation/meta.yml cpan

modules/nf-core/rseqc/readdistribution/meta.yml cpan

modules/nf-core/rseqc/readduplication/meta.yml cpan

modules/nf-core/rseqc/tin/meta.yml cpan

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

modules/nf-core/salmon/quant/meta.yml cpan

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

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

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

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

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

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

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

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

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

modules/nf-core/subread/featurecounts/meta.yml cpan

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

modules/nf-core/ucsc/bedclip/meta.yml cpan

modules/nf-core/ucsc/bedgraphtobigwig/meta.yml cpan

modules/nf-core/umitools/dedup/meta.yml cpan

modules/nf-core/umitools/extract/meta.yml cpan

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

subworkflows/nf-core/bam_dedup_stats_samtools_umitools/meta.yml cpan

subworkflows/nf-core/bam_markduplicates_picard/meta.yml cpan

subworkflows/nf-core/bam_rseqc/meta.yml cpan

subworkflows/nf-core/bam_sort_stats_samtools/meta.yml cpan

subworkflows/nf-core/bam_stats_samtools/meta.yml cpan

subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/meta.yml cpan

subworkflows/nf-core/fastq_align_hisat2/meta.yml cpan

subworkflows/nf-core/fastq_fastqc_umitools_fastp/meta.yml cpan

subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/meta.yml cpan

subworkflows/nf-core/fastq_subsample_fq_salmon/meta.yml cpan

pyproject.toml pypi