DSL2 conversion #73
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DSL2 conversion #73
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PR for 1.0.0 release
PR for 1.1.0 release
Update to new file structure
…erge-template-update
…-template-update
Merge template update v2.1
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edmundmiller
requested changes
Oct 29, 2021
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
edmundmiller
approved these changes
Oct 29, 2021
grst
approved these changes
Oct 30, 2021
| The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible. | ||
| The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! | ||
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| <!-- TODO nf-core: Add full-sized test dataset and amend the paragraph below if applicable --> |
| mode: 'copy', | ||
| saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } | ||
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| container "streitlab/custom-nf-modules-cellranger:latest" |
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I thought we had that in the nf core namespace now?
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| if("${gtf}".endsWith('.gz')){ | ||
| name = "${gtf.baseName}" | ||
| unzip = "gunzip -f ${gtf}" | ||
| } else { | ||
| unzip = "" | ||
| name = "${gtf}" | ||
| } | ||
| """ | ||
| $unzip | ||
| cat $name | t2g.py --use_version > transcripts_to_genes.txt | ||
| """ |
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Suggested change
| if("${gtf}".endsWith('.gz')){ | |
| name = "${gtf.baseName}" | |
| unzip = "gunzip -f ${gtf}" | |
| } else { | |
| unzip = "" | |
| name = "${gtf}" | |
| } | |
| """ | |
| $unzip | |
| cat $name | t2g.py --use_version > transcripts_to_genes.txt | |
| """ | |
| """ | |
| gzip -cdf $gtf | t2g.py --use_version > transcripts_to_genes.txt | |
| """ |
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| if (meta.single_end) { | ||
| array = [ meta, [ file(row.fastq_1, checkIfExists: true) ] ] | ||
| } else { | ||
| array = [ meta, [ file(row.fastq_1, checkIfExists: true), file(row.fastq_2, checkIfExists: true) ] ] |
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We don't have single end in this pipeline, do we?
apeltzer
approved these changes
Nov 2, 2021
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
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Seems some tests have been renamed - Can someone with write access please update the required tests for this repo? |
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I'll be merging this and work on the next template update in a separate PR |
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PR checklist
scrape_software_versions.pynf-core lint .).nextflow run . -profile test,docker).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).