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[Do not merge!] Pseudo PR for first release #69
base: first-commit-for-pseudo-pr
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Overall looks pretty good, main things are:
- Add license to ALL scripts in
bin/
(particularly for the package) - Make sure all version numbers are defined for all tools in the
conda
declaration of local modules with mulled containers,and these are exported.
workflows/circrna.nf
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ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) | ||
ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) | ||
ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) | ||
ch_multiqc_files = ch_multiqc_files.mix(FASTQC_TRIMGALORE.out.fastqc_zip.collect{it[1]}.ifEmpty([])) |
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Is it correct only FastQC goes into MultiQC?
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I'll look into generating BAM stats
README.md
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**workflow for the quantification, differential expression analysis and miRNA target prediction analysis of circRNAs in RNA-Seq data**. | ||
[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/circrna/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) |
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README.md
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4. circRNA annotation | ||
5. Export mature spliced length as FASTA file | ||
6. Annotate parent gene, underlying transcripts. | ||
7. circRNA count matrix |
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Are these the custom R scripts? Otherwise maybe also link the tools here in a similar fashion to above
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Nope, vanilla python and bash.
section_name: "nf-core/circrna Methods Description" | ||
section_href: "https://github.com/nf-core/circrna" | ||
plot_type: "html" | ||
## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline |
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you might want to add your paper here
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I'll give it a go! I went to the Sarek one to copy but... ;)
bin/ensembl_database_map.txt
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species command | |||
cel useMart(biomart = "ensembl", dataset = "celegans_gene_ensembl", host="https://www.ensembl.org", archive=FALSE) |
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This fetches the newest version every time, right? I am a bit worried about reproducibility and compatibility in the long run. Would there be a way to cache it?
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Think I'll deprecate this code, its only going to cause trouble
} | ||
} | ||
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// PREPARE GENOME |
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I suspect you will get WARN messages if the indices already exist
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I'll test this. I have a hard time resolving WARN messages
conf/modules.config
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// PREPARE GENOME | ||
withName: BOWTIE_BUILD { | ||
ext.when = { params.fasta && !params.bowtie && params.tool.split(',').contains('mapsplice') && params.module.split(',').contains('circrna_discovery') } |
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what happens if params.tools doesn't exist? Or does it always have to have a value?
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similar for params.module
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must have a value, a la --tool 'mutect2'
, --step 'mapping'
..
conf/test_full.config
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// Input data for full size test | ||
// TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA) | ||
// TODO nf-core: Give any required params for the test so that command line flags are not needed | ||
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' |
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is this the right input?
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nope, I was hoping for some help in getting my full test dataset up and running.
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# nf-core/circrna: Output | |||
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## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/circrna/output](https://nf-co.re/circrna/output) |
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is this line removed in the template @jfy133 ?
Co-authored-by: Nico Trummer <52698566+nictru@users.noreply.github.com>
Co-authored-by: Nico Trummer <52698566+nictru@users.noreply.github.com>
Improve circRNA-miRNA interaction analysis
Add credits for mweyrich
Add output containing per-tool quantification
Do not merge! This is a PR of dev compared to first release for whole-pipeline reviewing purposes.
Comments can be copied over to #66 for safety if necessary and changes made there. Changes should be made to
dev
and this PR should not be merged intofirst-commit-for-pseudo-pr
!