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rnaseq-pipeline

Repository for the nf-core Hackathon demos

https://github.com/asacrea/rnaseq-pipeline

Science Score: 44.0%

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Repository

Repository for the nf-core Hackathon demos

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  • Host: GitHub
  • Owner: asacrea
  • License: mit
  • Language: Nextflow
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Created 10 months ago · Last pushed 10 months ago
Metadata Files
Readme Changelog License Code of conduct Citation

README.md

nf-core/rnaseq

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Introduction

nf-core/rnaseq is a bioinformatics pipeline that can be used to analyse RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs quality control (QC), trimming and (pseudo-)alignment, and produces a gene expression matrix and extensive QC report.

nf-core/rnaseq metro map

In case the image above is not loading, please have a look at the static version.

  1. Merge re-sequenced FastQ files (cat)
  2. Auto-infer strandedness by subsampling and pseudoalignment (fq, Salmon)
  3. Read QC (FastQC)
  4. UMI extraction (UMI-tools)
  5. Adapter and quality trimming (Trim Galore!)
  6. Removal of genome contaminants (BBSplit)
  7. Removal of ribosomal RNA (SortMeRNA)
  8. Choice of multiple alignment and quantification routes:
    1. STAR -> Salmon
    2. STAR -> RSEM
    3. HiSAT2 -> NO QUANTIFICATION
  9. Sort and index alignments (SAMtools)
  10. UMI-based deduplication (UMI-tools)
  11. Duplicate read marking (picard MarkDuplicates)
  12. Transcript assembly and quantification (StringTie)
  13. Create bigWig coverage files (BEDTools, bedGraphToBigWig)
  14. Extensive quality control:
    1. RSeQC
    2. Qualimap
    3. dupRadar
    4. Preseq
    5. DESeq2
    6. Kraken2 -> Bracken on unaligned sequences; optional
  15. Pseudoalignment and quantification (Salmon or 'Kallisto'; optional)
  16. Present QC for raw read, alignment, gene biotype, sample similarity, and strand-specificity checks (MultiQC, R)

Note The SRA download functionality has been removed from the pipeline (>=3.2) and ported to an independent workflow called nf-core/fetchngs. You can provide --nf_core_pipeline rnaseq when running nf-core/fetchngs to download and auto-create a samplesheet containing publicly available samples that can be accepted directly as input by this pipeline.

Warning Quantification isn't performed if using --aligner hisat2 due to the lack of an appropriate option to calculate accurate expression estimates from HISAT2 derived genomic alignments. However, you can use this route if you have a preference for the alignment, QC and other types of downstream analysis compatible with the output of HISAT2.

Usage

[!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

csv sample,fastq_1,fastq_2,strandedness CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,auto CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz,auto CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz,auto

Each row represents a fastq file (single-end) or a pair of fastq files (paired end). Rows with the same sample identifier are considered technical replicates and merged automatically. The strandedness refers to the library preparation and will be automatically inferred if set to auto.

Warning: Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Now, you can run the pipeline using:

bash nextflow run nf-core/rnaseq \ --input <SAMPLESHEET> \ --outdir <OUTDIR> \ --gtf <GTF> \ --fasta <GENOME FASTA> \ -profile <docker/singularity/.../institute>

[!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

This pipeline quantifies RNA-sequenced reads relative to genes/transcripts in the genome and normalizes the resulting data. It does not compare the samples statistically in order to assign significance in the form of FDR or P-values. For downstream analyses, the output files from this pipeline can be analysed directly in statistical environments like R, Julia or via the nf-core/differentialabundance pipeline.

Online videos

A short talk about the history, current status and functionality on offer in this pipeline was given by Harshil Patel (@drpatelh) on 8th February 2022 as part of the nf-core/bytesize series.

You can find numerous talks on the nf-core events page from various topics including writing pipelines/modules in Nextflow DSL2, using nf-core tooling, running nf-core pipelines as well as more generic content like contributing to Github. Please check them out!

Credits

These scripts were originally written for use at the National Genomics Infrastructure, part of SciLifeLab in Stockholm, Sweden, by Phil Ewels (@ewels) and Rickard Hammarén (@Hammarn).

The pipeline was re-written in Nextflow DSL2 and is primarily maintained by Harshil Patel (@drpatelh) from Seqera Labs, Spain.

The pipeline workflow diagram was initially designed by Sarah Guinchard (@G-Sarah) and James Fellows Yates (@jfy133), further modifications where made by Harshil Patel (@drpatelh) and Maxime Garcia (@maxulysse).

Many thanks to other who have helped out along the way too, including (but not limited to):

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on the Slack #rnaseq channel (you can join with this invite).

Citations

If you use nf-core/rnaseq for your analysis, please cite it using the following doi: 10.5281/zenodo.1400710

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.

Owner

  • Name: Andres Sacré
  • Login: asacrea
  • Kind: user

Computer Scientist and Computational biologist with strong background in technology, science, math and statistics. 6+ years experience in Data Engineering & DS

Citation (CITATIONS.md) 

# nf-core/rnaseq: Citations

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

## Pipeline tools

- [BBMap](https://sourceforge.net/projects/bbmap/)

- [BEDTools](https://pubmed.ncbi.nlm.nih.gov/20110278/)

  > Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824.

- [Bracken](https://doi.org/10.7717/peerj-cs.104)

  > Lu, J., Breitwieser, F. P., Thielen, P., & Salzberg, S. L. (2017). Bracken: estimating species abundance in metagenomics data. PeerJ. Computer Science, 3(e104), e104. https://doi.org/10.7717/peerj-cs.104

- [fastp](https://www.ncbi.nlm.nih.gov/pubmed/30423086/)

  > Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560. PubMed PMID: 30423086; PubMed Central PMCID: PMC6129281.

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

- [featureCounts](https://pubmed.ncbi.nlm.nih.gov/24227677/)

  > Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014 Apr 1;30(7):923-30. doi: 10.1093/bioinformatics/btt656. Epub 2013 Nov 13. PubMed PMID: 24227677.

- [fq](https://github.com/stjude-rust-labs/fq)

- [GffRead](https://pubmed.ncbi.nlm.nih.gov/32489650/)

  > Pertea G, Pertea M. GFF Utilities: GffRead and GffCompare. F1000Res. 2020 Apr 28;9:ISCB Comm J-304. doi: 10.12688/f1000research.23297.2. eCollection 2020. PubMed PMID: 32489650; PubMed Central PMCID: PMC7222033.

- [HISAT2](https://pubmed.ncbi.nlm.nih.gov/31375807/)

  > Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4. Epub 2019 Aug 2. PubMed PMID: 31375807.

- [Kraken2](https://doi.org/10.1186/s13059-019-1891-0)

  > Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 257. https://doi.org/10.1186/s13059-019-1891-0

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

- [picard-tools](http://broadinstitute.github.io/picard)

- [preseq](https://pubmed.ncbi.nlm.nih.gov/23435259/)

  > Daley T, Smith AD. Predicting the molecular complexity of sequencing libraries. Nat Methods. 2013 Apr;10(4):325-7. doi: 10.1038/nmeth.2375. Epub 2013 Feb 24. PubMed PMID: 23435259; PubMed Central PMCID: PMC3612374.

- [Qualimap 2](https://pubmed.ncbi.nlm.nih.gov/26428292/)

  > Okonechnikov K, Conesa A, García-Alcalde F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data Bioinformatics. 2016 Jan 15;32(2):292-4. doi: 10.1093/bioinformatics/btv566. Epub 2015 Oct 1. PubMed PMID: 26428292; PubMed Central PMCID: PMC4708105.

- [RSEM](https://pubmed.ncbi.nlm.nih.gov/21816040/)

  > Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome BMC Bioinformatics. 2011 Aug 4;12:323. doi: 10.1186/1471-2105-12-323. PubMed PMID: 21816040; PubMed Central PMCID: PMC3163565.

- [RSeQC](https://pubmed.ncbi.nlm.nih.gov/22743226/)

  > Wang L, Wang S, Li W. RSeQC: quality control of RNA-seq experiments Bioinformatics. 2012 Aug 15;28(16):2184-5. doi: 10.1093/bioinformatics/bts356. Epub 2012 Jun 27. PubMed PMID: 22743226.

- [Salmon](https://pubmed.ncbi.nlm.nih.gov/28263959/)

  > Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression Nat Methods. 2017 Apr;14(4):417-419. doi: 10.1038/nmeth.4197. Epub 2017 Mar 6. PubMed PMID: 28263959; PubMed Central PMCID: PMC5600148.

- [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/)

  > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.

- [SortMeRNA](https://pubmed.ncbi.nlm.nih.gov/23071270/)

  > Kopylova E, Noé L, Touzet H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data Bioinformatics. 2012 Dec 15;28(24):3211-7. doi: 10.1093/bioinformatics/bts611. Epub 2012 Oct 15. PubMed PMID: 23071270.

- [STAR](https://pubmed.ncbi.nlm.nih.gov/23104886/)

  > Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905.

- [StringTie2](https://pubmed.ncbi.nlm.nih.gov/31842956/)

  > Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly from long-read RNA-seq alignments with StringTie2 Genome Biol. 2019 Dec 16;20(1):278. doi: 10.1186/s13059-019-1910-1. PubMed PMID: 31842956; PubMed Central PMCID: PMC6912988.

- [Trim Galore!](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)

- [UMI-tools](https://pubmed.ncbi.nlm.nih.gov/28100584/)

  > Smith T, Heger A, Sudbery I. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy Genome Res. 2017 Mar;27(3):491-499. doi: 10.1101/gr.209601.116. Epub 2017 Jan 18. PubMed PMID: 28100584; PubMed Central PMCID: PMC5340976.

- [UCSC tools](https://pubmed.ncbi.nlm.nih.gov/20639541/)
  > Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010 Sep 1;26(17):2204-7. doi: 10.1093/bioinformatics/btq351. Epub 2010 Jul 17. PubMed PMID: 20639541; PubMed Central PMCID: PMC2922891.

## R packages

- [R](https://www.R-project.org/)

  > R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.

- [DESeq2](https://pubmed.ncbi.nlm.nih.gov/25516281/)

  > Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. PubMed PMID: 25516281; PubMed Central PMCID: PMC4302049.

- [dupRadar](https://pubmed.ncbi.nlm.nih.gov/27769170/)

  > Sayols S, Scherzinger D, Klein H. dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data BMC Bioinformatics. 2016 Oct 21;17(1):428. doi: 10.1186/s12859-016-1276-2. PubMed PMID: 27769170; PubMed Central PMCID: PMC5073875.

- [ggplot2](https://cran.r-project.org/web/packages/ggplot2/index.html)

  > H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.

- [optparse](https://CRAN.R-project.org/package=optparse)

  > Trevor L Davis (2018). optparse: Command Line Option Parser.

- [pheatmap](https://CRAN.R-project.org/package=pheatmap)

  > Raivo Kolde (2018). pheatmap: Pretty Heatmaps.

- [RColorBrewer](https://CRAN.R-project.org/package=RColorBrewer)

  > Erich Neuwirth (2014). RColorBrewer: ColorBrewer Palettes.

- [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html)

  > Morgan M, Obenchain V, Hester J and Pagès H (2020). SummarizedExperiment: SummarizedExperiment container.

- [Tximeta](https://pubmed.ncbi.nlm.nih.gov/32097405/)
  > Love MI, Soneson C, Hickey PF, Johnson LK, Pierce NT, Shepherd L, Morgan M, Patro R. Tximeta: Reference sequence checksums for provenance identification in RNA-seq PLoS Comput Biol. 2020 Feb 25;16(2):e1007664. doi: 10.1371/journal.pcbi.1007664. eCollection 2020 Feb. PubMed PMID: 32097405; PubMed Central PMCID: PMC7059966.

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

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Dependencies

modules/nf-core/bbmap/bbsplit/meta.yml cpan
modules/nf-core/bedtools/genomecov/meta.yml cpan
modules/nf-core/bracken/bracken/meta.yml cpan
modules/nf-core/cat/fastq/meta.yml cpan
modules/nf-core/custom/catadditionalfasta/meta.yml cpan
modules/nf-core/custom/getchromsizes/meta.yml cpan
modules/nf-core/custom/tx2gene/meta.yml cpan
modules/nf-core/dupradar/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/extractsplicesites/meta.yml cpan
modules/nf-core/kallisto/index/meta.yml cpan
modules/nf-core/kallisto/quant/meta.yml cpan
modules/nf-core/kraken2/kraken2/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
modules/nf-core/picard/markduplicates/meta.yml cpan
modules/nf-core/preseq/lcextrap/meta.yml cpan
modules/nf-core/qualimap/rnaseq/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/summarizedexperiment/summarizedexperiment/meta.yml cpan
modules/nf-core/trimgalore/meta.yml cpan
modules/nf-core/tximeta/tximport/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/umitools/prepareforrsem/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_qc_trim_filter_setstrandedness/meta.yml cpan
subworkflows/nf-core/fastq_subsample_fq_salmon/meta.yml cpan
subworkflows/nf-core/quantify_pseudo_alignment/meta.yml cpan
subworkflows/nf-core/utils_nextflow_pipeline/meta.yml cpan
subworkflows/nf-core/utils_nfcore_pipeline/meta.yml cpan
subworkflows/nf-core/utils_nfschema_plugin/meta.yml cpan
modules/local/deseq2_qc/environment.yml pypi
modules/local/gtf2bed/environment.yml pypi
modules/local/gtf_filter/environment.yml pypi
modules/local/multiqc_custom_biotype/environment.yml pypi
modules/local/preprocess_transcripts_fasta_gencode/environment.yml pypi
modules/local/rsem_merge_counts/environment.yml pypi
modules/local/star_align_igenomes/environment.yml pypi
modules/local/star_genomegenerate_igenomes/environment.yml pypi
modules/nf-core/bbmap/bbsplit/environment.yml pypi
modules/nf-core/bedtools/genomecov/environment.yml pypi
modules/nf-core/bracken/bracken/environment.yml pypi
modules/nf-core/cat/fastq/environment.yml pypi
modules/nf-core/custom/catadditionalfasta/environment.yml pypi
modules/nf-core/custom/getchromsizes/environment.yml pypi
modules/nf-core/custom/tx2gene/environment.yml pypi
modules/nf-core/dupradar/environment.yml pypi
modules/nf-core/fastp/environment.yml pypi
modules/nf-core/fastqc/environment.yml pypi
modules/nf-core/fq/subsample/environment.yml pypi
modules/nf-core/gffread/environment.yml pypi
modules/nf-core/gunzip/environment.yml pypi
modules/nf-core/hisat2/align/environment.yml pypi
modules/nf-core/hisat2/extractsplicesites/environment.yml pypi
modules/nf-core/kallisto/index/environment.yml pypi
modules/nf-core/kallisto/quant/environment.yml pypi
modules/nf-core/kraken2/kraken2/environment.yml pypi
modules/nf-core/multiqc/environment.yml pypi
modules/nf-core/picard/markduplicates/environment.yml pypi
modules/nf-core/preseq/lcextrap/environment.yml pypi
modules/nf-core/qualimap/rnaseq/environment.yml pypi
modules/nf-core/rsem/calculateexpression/environment.yml pypi
modules/nf-core/rsem/preparereference/environment.yml pypi