1.1.0 Updates #42
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1.1.0 Updates #42
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Updating dev versions to 1.1.0dev
…all na values are correctly set to 0
1.1.0 Updates
…run on just the genome, jsut the transcriptome, or both
Add in oarfish as additional quantification method
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@atrull314 : one thing I did just now catch is that we should disable |
itrujnara
reviewed
Jan 8, 2025
| ext.args = { | ||
| [ | ||
| "--threads 30", | ||
| params.barcode_format == "10X_3v3" ? "--kit-version 3v3" : params.barcode_format == "10X_5v2" ? "--kit-version 5v2" : "" |
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Is this information not required anymore?
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Correct, we had modified the blaze module to base threads off task.cpus as is the case with other modules, which resulted in this piece of the documentation being invalidated. This specific change was to resolve an error in documentation that we had put in before the change to the blaze module.
| task.ext.when == null || task.ext.when | ||
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| script: | ||
| def args = task.ext.args ?: '' |
| "${task.process}": | ||
| python: \$(python --version | sed 's/Python //g') | ||
| END_VERSIONS | ||
| """ |
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Consider adding a stub, might be handy later
| "${task.process}": | ||
| oarfish: \$(oarfish --version | sed 's#oarfish ##g') | ||
| END_VERSIONS | ||
| """ |
| def args = task.ext.args ?: '' | ||
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| """ | ||
| awk '/^>/{chrom=(split(substr(\$0,2), a, " ")); filename=( a[1] ".split.fa"); print > filename; next}{print >> filename}' $fasta |
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Does this have to be a new module? Looks like the same result could be achieved with the gawk nf-core module
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So the issue is the gawk nf-core module outputs as a single file, this awk statement is splitting a fasta into all of the chromosomes that compose it, so we need all the individual chromosome fastas as outputs. I'm not sure the module currently supports this behavior
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| ch_gene_qc_stats = Channel.empty() | ||
| ch_transcript_qc_stats = Channel.empty() | ||
| if (quantifier.equals("oarfish")) { |
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Is the "both" option handled correctly here?
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Yep! Its handled in a separate file to make sure they are able to run in parallel.
| ch_transcript_qc_stats = QUANTIFY_SCRNA_ISOQUANT.out.transcript_qc_stats | ||
| } | ||
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| emit: |
| // | ||
| // MODULE: Samtools Merge | ||
| // | ||
| SAMTOOLS_MERGE ( |
| // | ||
| // MODULE: Samtools Index | ||
| // | ||
| SAMTOOLS_INDEX_MERGED( ch_dedup_single_bam ) |
| validate_params, | ||
| "nextflow_schema.json" | ||
| null |
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PR Checklist
This PR contains the following updates for v1.1.0 of the pipeline: