This repository was archived by the owner on Mar 10, 2023. It is now read-only.
PSEUDO PR - DO NOT MERGE#1
Draft
ewels wants to merge 13 commits into
Draft
Conversation
mashehu
suggested changes
Jan 3, 2022
mashehu
left a comment
mashehu
left a comment
There was a problem hiding this comment.
I had a first look through it. Good work! Some smaller things and then I'll give my 👍🏻. The output docs could use a bit more love (it is not so clear to me what the important files are, from where in the workflow they come, some more explanation of the SSDS plots in the multiqc report would be helpful).
|
|
||
| * [Trimgalore](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) | ||
|
|
||
| * [BWA](https://github.com/lh3/bwa) |
There was a problem hiding this comment.
Please check for these tools if there is really no citeable publication. BWA for example lists some in their readme.
| ## Introduction | ||
|
|
||
| <!-- TODO nf-core: Write a 1-2 sentence summary of what data the pipeline is for and what it does --> | ||
| **nf-core/ssds** is a bioinformatics best-practice analysis pipeline for Single-Stranded DNA Sequencing (SSDS) pipeline. |
There was a problem hiding this comment.
Suggested change
| **nf-core/ssds** is a bioinformatics best-practice analysis pipeline for Single-Stranded DNA Sequencing (SSDS) pipeline. | |
| **nf-core/ssds** is a bioinformatics best-practice analysis pipeline for Single-Stranded DNA Sequencing (SSDS). |
| } | ||
|
|
||
| withName:SAMPLESHEET_CHECK { | ||
| executor = 'local' |
| } | ||
|
|
||
| withName:PICARD_SORTSAM_QRY { | ||
| cpus = { check_max( 12 * task.attempt, 'cpus' ) } |
There was a problem hiding this comment.
why don't you use the cpu and memory specifications from the process_* labels?
| @@ -0,0 +1,121 @@ | |||
| /* | |||
There was a problem hiding this comment.
Is this a remnant of an older nf-core template? Should be merged with modules.config imo.
| }, | ||
| "parse_extra_types": { | ||
| "type": "boolean", | ||
| "description": "SSDS identifies ssDNA using the micro-homology structure at the 5' end of reads. When set to true, the SSDS pipeline also infers three additional, but low confidence fragment types; importantly, reads of these thress types are a best guess, but could be incorrect (i.e. fragments classified as dsDNA may instead come from ssDNA in a sufficiently enriched library).", |
There was a problem hiding this comment.
Suggested change
| "description": "SSDS identifies ssDNA using the micro-homology structure at the 5' end of reads. When set to true, the SSDS pipeline also infers three additional, but low confidence fragment types; importantly, reads of these thress types are a best guess, but could be incorrect (i.e. fragments classified as dsDNA may instead come from ssDNA in a sufficiently enriched library).", | |
| "description": "SSDS identifies ssDNA using the micro-homology structure at the 5' end of reads. When set to true, the SSDS pipeline also infers three additional, but low confidence fragment types; importantly, reads of these three types are a best guess, but could be incorrect (i.e. fragments classified as dsDNA may instead come from ssDNA in a sufficiently enriched library).", |
| "format": "file-path", | ||
| "mimetype": "text/plain", | ||
| "description": "Path to the BWA index folder.", | ||
| "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.", |
There was a problem hiding this comment.
I don't see the save_reference parameter implemented in your workflow. Either update this section (and the one for --fasta) or don't mention it here.
| @@ -0,0 +1,42 @@ | |||
| // | |||
There was a problem hiding this comment.
I guess this file a left over and can be deleted? 🙂
| ch_versions = ch_versions.mix(UCSC_BEDGRAPHTOBIGWIG.out.versions.first()) | ||
|
|
||
| emit: | ||
| bigwig = UCSC_BEDGRAPHTOBIGWIG.out.bigwig // channel: [ val(meta), [ bai ] ] |
There was a problem hiding this comment.
Suggested change
| bigwig = UCSC_BEDGRAPHTOBIGWIG.out.bigwig // channel: [ val(meta), [ bai ] ] | |
| bigwig = UCSC_BEDGRAPHTOBIGWIG.out.bigwig // channel: [ val(meta), [ bigwig ] ] |
| emit: | ||
| bam = PICARD_MARKDUPLICATES.out.bam // channel: [ val(meta), [ bam ] ] | ||
| bai = SAMTOOLS_INDEX.out.bai // channel: [ val(meta), [ bai ] ] | ||
| mdmetrics = PICARD_MARKDUPLICATES.out.metrics // channel: [ val(meta), [ bam ] ] |
There was a problem hiding this comment.
Suggested change
| mdmetrics = PICARD_MARKDUPLICATES.out.metrics // channel: [ val(meta), [ bam ] ] | |
| mdmetrics = PICARD_MARKDUPLICATES.out.metrics // channel: [ val(meta), [ metrics ] ] |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to subscribe to this conversation on GitHub.
Already have an account?
Sign in.
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
DO NOT MERGE THIS PULL REQUEST
This PR is a pseudo-PR designed to be used for a community review of the pipeline prior to first release. Feel free to add comments and review content here - as new commits are pushed to
devthe PR will update automatically.