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callingcards

A pipeline for processing calling cards data

https://github.com/nf-core/callingcards

Science Score: 57.0%

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    Found 10 DOI reference(s) in README
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Keywords

nextflow nf-core pipeline workflow
Last synced: 6 months ago · JSON representation ·

Repository

A pipeline for processing calling cards data

Basic Info
Statistics
  • Stars: 5
  • Watchers: 170
  • Forks: 4
  • Open Issues: 5
  • Releases: 1
Topics
nextflow nf-core pipeline workflow
Created over 3 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

nf-core/callingcards

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Introduction

nf-core/callingcards is a bioinformatics pipeline that can be used to process raw Calling Cards data obtained from either mammals (human, mouse) or yeast. It takes a samplesheet, which describes the sample names, paths to the fastq files, and paths to the barcode details json files, a parameter which identifies the organism type (either mammals or yeast) and either the name of the reference genome on igenomes or paths to the fasta/gff. It then parses the reads, counts the number of calling cards insertions, and provides some QC metrics.

nf-core/rnaseq metro map

  1. Prepare the Genome
  2. Prepare the Reads
  3. Align
    • Any one of the aligners listed above in 'Prepare the Genome'
    • Alignment QC (samtools, picard,rseqc)))
  4. Count Hops (callingCardsTools)
  5. Present QC data (MultiQC)

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 according to your organism.

A Yeast samplesheet will look like:

yeast_samplesheet.csv:

csv sample,fastq_1,fastq_2,barcode_details run_6177,run_6177_sample_R1.fastq.gz,run_6177_sample_R2.fastq.gz,run_6177_barcode_details.json

Each row represents a multiplexed fastq file where the barcode_details.json file describes the barcodes which correspond to each transcription factor in the library.

A mammals (human, mouse) samplesheet will look like:

mammals_samplesheet.csv:

csv sample,fastq_1,fastq_2,barcode_details midbrain_rep3,midbrain_rep3_R1.fastq.gz,,barcode_details.json

Note that currently, the mammals workflow expects only R1 reads.

Now, you can run the pipeline using:

bash nextflow run nf-core/callingcards \ -profile <docker/singularity/.../institute>,<default_yeast/default_mammals> \ --input samplesheet.csv \ --genome <igenomes_name (only required for mammals)> \ --outdir <OUTDIR>

Note that the default_yeast and default_mammals profiles are provided for convenience. You should check the parameters which these set to ensure that they are what you need for your data.

:::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.

Credits

nf-core/callingcards is implemented in nextflow by Chase Mateusiak. It was adapted from scripts written by:

We thank the following people for their extensive assistance in the development of this pipeline:

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 #callingcards channel (you can join with this invite).

Citations

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: nf-core
  • Login: nf-core
  • Kind: organization
  • Email: core@nf-co.re

A community effort to collect a curated set of analysis pipelines built using Nextflow.

Citation (CITATIONS.md) 

# nf-core/callingcards: 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

- [bedtools](https://doi.org/10.1093/bioinformatics/btq033)

  > Aaron R. Quinlan, Ira M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, Volume 26, Issue 6, March 2010, Pages 841–842, https://doi.org/10.1093/bioinformatics/btq033

- [bowtie](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2009-10-3-r25)

  > Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.

- [bowtie2](https://www.nature.com/articles/nmeth.1923)

  > Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.

- [bwa](https://pubmed.ncbi.nlm.nih.gov/19451168/)

  > Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18. PMID: 19451168; PMCID: PMC2705234.

- [bwamem2](https://doi.org/10.1109/IPDPS.2019.00041)

  > Vasimuddin Md, Sanchit Misra, Heng Li, Srinivas Aluru. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IEEE Parallel and Distributed Processing Symposium (IPDPS), 2019. 10.1109/IPDPS.2019.00041

- [callingCardsTools](https://zenodo.org/records/10042067)

  > Chase Mateusiak. (2023). cmatKhan/callingCardsTools: v1.2.0 (v1.2.0). Zenodo. https://doi.org/10.5281/zenodo.10042067

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

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

- [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.

- [nf-core/rnaseq:GTF2BED](https://github.com/nf-core/rnaseq/blob/master/bin/gtf2bed)

  > Harshil Patel, Phil Ewels, Alexander Peltzer, Olga Botvinnik, Gregor Sturm, Denis Moreno, Pranathi Vemuri, Maxime U Garcia, silviamorins, Lorena Pantano, Mahesh Binzer-Panchal, nf-core bot, Robert Syme, Matthias Zepper, Gavin Kelly, Friederike Hanssen, James A. Fellows Yates, Chris Cheshire, rfenouil, … Paolo Di Tommaso. (2023). nf-core/rnaseq: nf-core/rnaseq v3.12.0 - Osmium Octopus (3.12.0). Zenodo. https://doi.org/10.5281/zenodo.7998767

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

  > “Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/; Broad Institute.

- [rseqc](https://rseqc.sourceforge.net/)

  > 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. PMID: 22743226.

- [samtools](https://doi.org/10.1093/gigascience/giab008)

  > Twelve years of SAMtools and BCFtools Petr Danecek, James K Bonfield, Jennifer Liddle, John Marshall, Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A McCarthy, Robert M Davies, Heng Li GigaScience, Volume 10, Issue 2, February 2021, giab008, https://doi.org/10.1093/gigascience/giab008

- [seqkit](https://doi.org/10.1371/journal.pone.0163962)

  > Shen W, Le S, Li Y, Hu F (2016) SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLoS ONE 11(10): e0163962. https://doi.org/10.1371/journal.pone.0163962

- [trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic)

  > Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170.

- [UMITools](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. PMID: 28100584; PMCID: PMC5340976.

## 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.

GitHub Events

Total
  • Issues event: 2
  • Watch event: 2
  • Delete event: 13
  • Issue comment event: 10
  • Push event: 12
  • Pull request review event: 1
  • Pull request event: 12
  • Create event: 7
Last Year
  • Issues event: 2
  • Watch event: 2
  • Delete event: 13
  • Issue comment event: 10
  • Push event: 12
  • Pull request review event: 1
  • Pull request event: 12
  • Create event: 7

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 37
  • Total Committers: 1
  • Avg Commits per committer: 37.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 37
  • Committers: 1
  • Avg Commits per committer: 37.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
chase mateusiak c****k@g****m 37

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 9
  • Total pull requests: 12
  • Average time to close issues: 3 months
  • Average time to close pull requests: 2 months
  • Total issue authors: 3
  • Total pull request authors: 3
  • Average comments per issue: 1.56
  • Average comments per pull request: 0.75
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 4
  • Average time to close issues: about 2 months
  • Average time to close pull requests: about 2 months
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 2.0
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • cmatKhan (8)
  • allenyen (3)
  • jen-reeve (1)
Pull Request Authors
  • nf-core-bot (17)
  • cmatKhan (5)
  • adamrtalbot (1)
Top Labels
Issue Labels
enhancement (6) bug (3) question (1) documentation (1)
Pull Request Labels

Dependencies

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modules/nf-core/bedtools/maskfasta/meta.yml cpan
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modules/nf-core/bowtie/build/meta.yml cpan
modules/nf-core/bowtie2/align/meta.yml cpan
modules/nf-core/bowtie2/build/meta.yml cpan
modules/nf-core/bwa/aln/meta.yml cpan
modules/nf-core/bwa/index/meta.yml cpan
modules/nf-core/bwa/sampe/meta.yml cpan
modules/nf-core/bwa/samse/meta.yml cpan
modules/nf-core/bwamem2/index/meta.yml cpan
modules/nf-core/bwamem2/mem/meta.yml cpan
modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan
modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
modules/nf-core/picard/collectmultiplemetrics/meta.yml cpan
modules/nf-core/preseq/ccurve/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/samtools/faidx/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/merge/meta.yml cpan
modules/nf-core/samtools/sort/meta.yml cpan
modules/nf-core/samtools/stats/meta.yml cpan
modules/nf-core/seqkit/split2/meta.yml cpan
modules/nf-core/subread/featurecounts/meta.yml cpan
modules/nf-core/trimmomatic/meta.yml cpan
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modules/local/concatFasta/environment.yml conda
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modules/local/concatFastq/environment.yml conda
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modules/local/gtf2bed/environment.yml conda
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modules/local/callingcardstools/mammals/concatQC/environment.yml pypi
modules/local/callingcardstools/mammals/count_hops/environment.yml pypi
modules/local/callingcardstools/yeast/concatQC/environment.yml pypi
modules/local/callingcardstools/yeast/count_hops/environment.yml pypi
modules/local/callingcardstools/yeast/demultiplex/environment.yml pypi
modules/nf-core/bedtools/maskfasta/environment.yml pypi
modules/nf-core/bowtie/align/environment.yml pypi
modules/nf-core/bowtie/build/environment.yml pypi
modules/nf-core/bowtie2/align/environment.yml pypi
modules/nf-core/bowtie2/build/environment.yml pypi
modules/nf-core/bwa/aln/environment.yml pypi
modules/nf-core/bwa/index/environment.yml pypi
modules/nf-core/bwa/sampe/environment.yml pypi
modules/nf-core/bwa/samse/environment.yml pypi
modules/nf-core/bwamem2/index/environment.yml pypi
modules/nf-core/bwamem2/mem/environment.yml pypi
modules/nf-core/custom/dumpsoftwareversions/environment.yml pypi
modules/nf-core/fastqc/environment.yml pypi
modules/nf-core/multiqc/environment.yml pypi
modules/nf-core/picard/collectmultiplemetrics/environment.yml pypi
modules/nf-core/preseq/ccurve/environment.yml pypi
modules/nf-core/rseqc/bamstat/environment.yml pypi
modules/nf-core/rseqc/inferexperiment/environment.yml pypi
modules/nf-core/rseqc/innerdistance/environment.yml pypi
modules/nf-core/rseqc/junctionannotation/environment.yml pypi
modules/nf-core/rseqc/junctionsaturation/environment.yml pypi
modules/nf-core/rseqc/readdistribution/environment.yml pypi
modules/nf-core/rseqc/readduplication/environment.yml pypi
modules/nf-core/rseqc/tin/environment.yml pypi
modules/nf-core/samtools/faidx/environment.yml pypi
modules/nf-core/samtools/flagstat/environment.yml pypi
modules/nf-core/samtools/idxstats/environment.yml pypi
modules/nf-core/samtools/index/environment.yml pypi
modules/nf-core/samtools/merge/environment.yml pypi
modules/nf-core/samtools/sort/environment.yml pypi
modules/nf-core/samtools/stats/environment.yml pypi
modules/nf-core/seqkit/split2/environment.yml pypi
modules/nf-core/subread/featurecounts/environment.yml pypi
modules/nf-core/trimmomatic/environment.yml pypi
modules/nf-core/umitools/extract/environment.yml pypi