Add nanoq to the pipeline #508
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The summary report from ERR3201952_ERR3201952_filtered.stats: |
jfy133
requested changes
Jul 12, 2024
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Great! That looks like a perfect log file for MultiQC!
For the newly designed 1.2, should we include pychopper as an alterantive adapterermoval tool? Particuarly given as it's an official nanopore tool.
In addition to comments below, also missing:
- Output docs descriptions for
nanoq - Missing auto-method-description update in the
local/utils_nfcore_taxprofiler<....>thingy - Missing listing of tool on main README in the various points
- Missing metromap update (let me know if yo uwant me to add dthat)
| @@ -270,6 +284,13 @@ | |||
| "description": "Specify the number of high-quality bases in the library to be retained", | |||
| "fa_icon": "fas fa-bullseye", | |||
| "help_text": "Removes the worst reads until only the specified value of bases remain, useful for very large read sets. If the input read set is less than the specified value, this setting will have no effect. _Modified from [Filtlong documentation](https://github.com/rrwick/Filtlong)_\n\n> Modifies tool parameter(s):\n> - Filtlong: `--keep_percent`" | |||
| }, | |||
| "longread_qc_qualityfilter_minquality": { | |||
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Given this only applies to nanoq, maybe we should indicate this... I guess we could change the name of the parmaeter but this would require a major bump e.g. 1.1 -> 2 (rather than 1.2)
Alternatively for the help descriptions we prepend for this and the other tools in this section if it's a tool-specific parameter
So here we could have maybe: Nanoq only: specify minimum average read quality filter, and above, longread_qc_qualityfilter_keeppercent could be Filtlong only: specify the percent of high-quality bases to be retained?
| @@ -17,31 +17,22 @@ workflow LONGREAD_PREPROCESSING { | |||
| ch_multiqc_files = Channel.empty() | |||
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| if ( !params.longread_qc_skipadaptertrim && params.longread_qc_skipqualityfilter) { | |||
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Missing MultiQC mixing from the adapterrermoval subworkflow
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
As Sofia mentioned in this issue, Pychopper was designed for cDNA reads. But I guess the principles for identifying and removing adapter sequences should be the same for both cDNA and DNA reads. Another thing is If you think it's proper, we could add it to 1.2 version. |
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@jfy133 It would be great if you could update metromap. I guess metromap could be updated in the end after adding all preprocessing tools for long reads. |
Ok if it's old and porechop_Abi is more recent we can stick with that
Yes lets update it right at the end, so I don't have to move everythign around every time :) |
jfy133
approved these changes
Jul 18, 2024
nextflow_schema.json
Outdated
| "default": "filtlong", | ||
| "enum": ["filtlong", "nanoq"], | ||
| "fa_icon": "fas fa-hammer", | ||
| "description": "Specify which tool to use for long reads filtering" |
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Can you give any guidance in teh long-form help text which to use when?
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Done! I also set the default as nanoq
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Add
nanoqfor nanopore reads filtering and nanopore reads summary statistics.Fix #415
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).