v0.3 - Pipeline now validated on five real genomes #88
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only run BLAST_BLASTN if BLASTN_TAXON has an empty output
muffato
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With the `-0` option, the output file ("interleaved") is empty for PacBio
because all the reads go to the "other" file. Whereas paired-reads all go to
the "interleaved" file and none to the "other" file.
The simplest is to not use the `-0` option. Then, `samtools fasta` simply sends
all the reads to the standard output.
(waiting for nf-core approval)
This simplifies connecting to the fetchngs pipeline
…uses some problems
Python linting (
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This means that .fastq.gz will remain .fastq.gz and can then match the condition to bypass the SAMTOOLS_FASTA process. There is a pull-request for this, nf-core/modules#4230
muffato
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Ignore the prettier error for now. |
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To run on the farm, use these arguments: (there isn't a central NT database with taxonomy information yet. It's still in progress) |
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Prettier error fixed, thanks to @BethYates |
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The code looks good but the images aren't being published to the results directory |
Since the blobdir is incrementally built, only the last version needs to be published
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BethYates
approved these changes
Feb 9, 2024
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I've now tested the pipeline on five real, complete, genomes (though all under 100 Mbp). This PR is to fix all the issues I've found along the way:
nf-core/fetchngs pipeline by passing the
--fetchngs_samplesheet trueoption.I want to release this as the version 0.3.
The following is still needed for the version 1.0:
which may require another 0.* release.
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).