feat: samclip module #8999
feat: samclip module #8999
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emmcauley
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…Seqera container, update tests
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Other things to consider:
- I think it would be good to add args to the samtools commands, which would allow for e.g. sorting ready for tools that require name-sorted or template-coordinate sorted, or filtering via that first samtools view.
- Do we want to support making cram files?
- Do we want to support index creation inside the final samtools sort?
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| samtools view -h --output-fmt sam ${bam} | \\ | ||
| samclip ${args} --ref ${ref_filename} | \\ | ||
| samtools sort -n -O BAM -T /tmp | \\ |
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Do you need to make this output a bam, or would an uncompressed sam be faster?
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1', single_end:false ]` |
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I know it is in the template, but we don't need to mention single_end here.
| e.g. `[ id:'sample1', single_end:false ]` | |
| e.g. `[ id:'sample1' ]` |
| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "samclip" | ||
| tag "samtools/view" |
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| tag "samtools/view" |
| tag "samtools/view" | ||
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| test("test-data - NA12878.chr22.bam") { | ||
| config "./nextflow.config" |
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| config "./nextflow.config" |
| name "Test Process SAMCLIP" | ||
| script "../main.nf" | ||
| process "SAMCLIP" | ||
| config "./nextflow.config" |
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| config "./nextflow.config" |
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Can delete this now you are not using samtools_view
| def ref_filename = reference.getName().replaceAll(/\.gz$/, "") | ||
| """ | ||
| # decompress reference if gzipped | ||
| ${is_compressed ? "gzip -c -d ${reference} > ${ref_filename}" : ""} |
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Can we remove this decompressed reference at the end if it is made please.
| def prefix = task.ext.prefix ?: "${meta.id}.samclip" | ||
| def is_compressed = reference.getName().endsWith(".gz") | ||
| def ref_filename = reference.getName().replaceAll(/\.gz$/, "") | ||
| """ |
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https://nf-co.re/docs/guidelines/components/modules#command-file-output-naming
| """ | |
| if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!" | |
| """ |
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| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}.samclip" |
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I think underscores is how most modules set the extra part of prefix:
| def prefix = task.ext.prefix ?: "${meta.id}.samclip" | |
| def prefix = task.ext.prefix ?: "${meta.id}_samclip" |
| """ | ||
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| stub: | ||
| def prefix = task.ext.prefix ?: "${meta.id}.samclip" |
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I think underscores is how most modules set the extra part of prefix:
| def prefix = task.ext.prefix ?: "${meta.id}.samclip" | |
| def prefix = task.ext.prefix ?: "${meta.id}_samclip" |
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This PR adds a new module,
samclip, and corresponding tests.samclipis used to filter SAM files for soft and hard clipped alignments. Test data is derived from nf-coretest-datasets.PR checklist
Closes #8342
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda