├── .circ ├── .github └── workflows │ └── ci.yml ├── .gitignore ├── CHANGELOG.md ├── CITATION.cff ├── LICENSE ├── Makefile ├── README.md ├── TODO.md ├── VERSION ├── bin ├── TrtoGn_RPKM.sh ├── contigsNew.py ├── gff2gff.awk └── grape_infer_experiment.py ├── config └── resources │ └── ihec.config ├── data ├── annotation.gtf ├── gemflux.md5 ├── genome.fa ├── ihec.md5 ├── markdup.md5 ├── rmdup.md5 ├── sample3_m4_n10_toGenome.bam ├── sample3_m4_n10_toTranscriptome.bam ├── starflux.md5 ├── starrsem.md5 ├── test1_1.fastq.gz ├── test1_2.fastq.gz ├── test2_1.fastq.gz ├── test2_2.fastq.gz ├── test3_1.fastq.gz └── test3_2.fastq.gz ├── docker ├── Makefile ├── Readme.md ├── base │ └── Dockerfile ├── common.mk ├── conda │ └── Dockerfile ├── ihec │ └── Dockerfile ├── java │ └── Dockerfile ├── process │ ├── bigwig │ │ ├── Rules.mk │ │ ├── rgcrg │ │ │ ├── Dockerfile │ │ │ └── Rules.mk │ │ └── star │ │ │ ├── Dockerfile │ │ │ └── Rules.mk │ ├── contig │ │ ├── Rules.mk │ │ └── rgcrg │ │ │ ├── Dockerfile │ │ │ └── Rules.mk │ ├── inferexp │ │ ├── Rules.mk │ │ └── rseqc │ │ │ ├── Dockerfile │ │ │ └── Rules.mk │ ├── mapping │ │ ├── Rules.mk │ │ ├── gem │ │ │ ├── Dockerfile │ │ │ └── Rules.mk │ │ └── star │ │ │ ├── Dockerfile │ │ │ └── Rules.mk │ └── quantification │ │ ├── Rules.mk │ │ ├── flux │ │ ├── Dockerfile │ │ └── Rules.mk │ │ └── rsem │ │ ├── Dockerfile │ │ ├── Rules.mk │ │ └── static.txt ├── python │ └── Dockerfile └── tool │ ├── bamstats │ └── Dockerfile │ ├── bedtools │ └── Dockerfile │ ├── flux-capacitor │ └── Dockerfile │ ├── gemtools │ ├── Dockerfile │ └── Dockerfile.alpine │ ├── kentutils │ └── Dockerfile │ ├── rsem │ └── Dockerfile │ ├── rseqc │ └── Dockerfile │ ├── sambamba │ ├── Dockerfile │ └── Dockerfile.compile │ ├── samtools │ └── Dockerfile │ └── star │ └── Dockerfile ├── docs ├── Gemfile ├── Gemfile.lock ├── Makefile ├── css │ └── crg.css └── src │ ├── header.php │ ├── password.php │ ├── quickstart.adoc │ └── workflow.adoc ├── grape-pipeline.nf ├── ihec-index.txt ├── ihec-setup.md ├── modules ├── bamStats │ └── bamstats │ │ └── main.nf ├── bigwig │ ├── rgcrg │ │ └── main.nf │ └── star │ │ └── main.nf ├── contig │ └── rgcrg │ │ └── main.nf ├── fastaIndex │ └── samtools │ │ └── main.nf ├── functions.nf ├── inferExp │ └── rseqc │ │ └── main.nf ├── mapping │ ├── gem │ │ └── main.nf │ └── star │ │ └── main.nf ├── markdup │ └── sambamba │ │ └── main.nf ├── mergeBam │ ├── sambamba │ │ └── main.nf │ └── samtools │ │ └── main.nf ├── quantification │ ├── flux │ │ └── main.nf │ └── rsem │ │ └── main.nf └── sortBam │ ├── sambamba │ └── main.nf │ └── samtools │ └── main.nf ├── nextflow.config ├── scripts ├── changelog ├── prepare_input.sh └── singularity-prefetch.sh ├── test-index.txt └── workflows ├── mapping.nf ├── merging.nf ├── qc.nf ├── quantification ├── flux.nf └── rsem.nf └── signal.nf /.circ: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guigolab/grape-nf/HEAD/.circ 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