blastn subworkflow #31
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muffato
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Sep 19, 2022
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| seqtk subseq \\ |
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seqtk/subseq is already in nf-core (https://github.com/nf-core/modules/blob/master/modules/seqtk/subseq/main.nf), don't make your own here
| def log = "${prefix}.log" | ||
| def output = "${prefix}.blastn.raw" | ||
| """ | ||
| if [ -s ${fasta} ]; then \\ |
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This (if really needed) should be in the subworkflow
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| blastn -task megablast \\ | ||
| $args \\ | ||
| -num_threads $task.cpus \\ | ||
| -query ${fasta} \\ | ||
| -db ${db} \\ | ||
| > $output 2> $log || \\ | ||
| sleep 30; \ | ||
| if [ -s $log ]; then \\ | ||
| echo "Restarting blastn without taxid filter" >> $log; \\ | ||
| > $output; \ | ||
| blastn -task megablast \\ | ||
| $args2 \\ | ||
| -num_threads $task.cpus \\ | ||
| -query ${fasta} \\ | ||
| -db ${db} \\ | ||
| > $output 2>> $log; \\ | ||
| fi \\ |
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I think you could do this in the subworkflow by calling the nfcore module https://github.com/nf-core/modules/blob/master/modules/blast/blastn/main.nf
| val evalue | ||
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| output: | ||
| path "*.nohit.txt" , emit: nohit_list |
removed prefix.log file Co-authored-by: Matthieu Muffato <[email protected]>
deleted args Co-authored-by: Matthieu Muffato <[email protected]>
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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).This PR is part of the Google Summer of Code 2022 project: Conversion of the BlobToolKit pipeline to Nextflow, GitHub repository: https://github.com/sanger-tol/blobtoolkit