Important! Template update for nf-core/tools v3.0.1 #502
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fellen31
reviewed
Oct 11, 2024
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Should this be here? If so, does it need to be added to nextflow.config?
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There's also a files_exist - File not found: conf/igenomes.config warning in the linting - should it be added to the ignore list?
| @@ -129,7 +129,6 @@ process { | |||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, | |||
| ] | |||
| } | |||
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| ```yaml | ||
| ```yaml title="params.yaml" |
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Maybe it's just my browser, but how do you see this title?
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I don't see it, I think that is intentional, but indeed a bit weird
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| // | ||
| // Function to generate an error if contigs in genome fasta file > 512 Mbp | ||
| // | ||
| def checkMaxContigSize(fai_file) { | ||
| def max_size = 512000000 | ||
| fai_file.eachLine { line -> | ||
| def lspl = line.split('\t') | ||
| def chrom = lspl[0] | ||
| def size = lspl[1] | ||
| if (size.toInteger() > max_size) { | ||
| def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + | ||
| " Contig longer than ${max_size}bp found in reference genome!\n\n" + | ||
| " ${chrom}: ${size}\n\n" + | ||
| " Provide the '--bam_csi_index' parameter to use a CSI instead of BAI index.\n\n" + | ||
| " Please see:\n" + | ||
| " https://github.com/nf-core/rnaseq/issues/744\n" + | ||
| "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" | ||
| error(error_string) | ||
| } | ||
| } | ||
| } | ||
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Is this not needed anymore?
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Version Please use #504 to merge in the new changes from the nf-core template as soon as possible. |
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Version
3.0.1of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the
nf-core-template-merge-3.0.1branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.
For more information about this release of nf-core/tools, please see the
v3.0.1release page.