New release 1.1.0 #362
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New release 1.1.0 #362
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Review of the MetaPhlAn4
Change falco process into medium, solve memory issue
Remove meta clone everywhere for improved resume stability
Fix CENTRIFUGE header modification when --out-fmt turned on
The placement of the function is debatable, but to have its definition evaluated by nextflow, rather than pure Groovy makes it work.
Updated Bracken and Kraken2 database description to reflect the current contents on @BenLangmead database indexes. Also, required *.kraken from the expected files list for Bracken since they are no longer needed.
Updated Change Log to mention the usage update in PR #342
minor corrections based on reviews
Co-authored-by: Sofia Stamouli <[email protected]>
jfy133
reviewed
Sep 12, 2023
| - `<sample_id>.centrifuge.report.txt`: A classification report that summarises the taxonomic ID, the taxonomic rank, length of genome sequence, number of classified and uniquely classified reads | ||
| - `<sample_id>.centrifuge.results.txt`: A file that summarises the classification assignment for a read, i.e read ID, sequence ID, score for the classification, score for the next best classification, number of classifications for this read | ||
| - `<sample_id>.centrifuge.txt`: A Kraken2-style report that summarises the fraction abundance, taxonomic ID, number of k-mers, taxonomic path of all the hits in the centrifuge run for a given sample | ||
| - `<sample_id>.centrifuge.unmapped.fastq.gz`: FASTQ file containing all unmapped reads | ||
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This was referenced Sep 14, 2023
Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
Update modules
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@maxulysse Could you approve the merge if you don't have any comments or reviews? |
maxulysse
approved these changes
Sep 18, 2023
| pattern: '*.fastq.gz', | ||
| enabled: params.save_analysis_ready_fastqs, | ||
| // Don't know why `!` doesn't work here, but `== false` makes it work... | ||
| saveAs: { ( params.perform_runmerging == false || ( params.perform_runmerging && !meta.is_multirun ) ) && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs ? it : null } |
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I know I know... I'll refactor in the future™️
| withName: MALT_RUN { | ||
| tag = {"${meta.db_name}|${meta.id}"} |
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| // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") | ||
| // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ | ||
| // ! There is currently no tooling to help you write a sample sheet schema |
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seems like template leftovers, but no big deal
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Yes, leaving that as a reminder for the next release
FriederikeHanssen
approved these changes
Sep 18, 2023
Correct the release date
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PR checklist
nf-core lint).nextflow run . -profile 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).