move gatk preprocessing to sbwf #1812
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famosab
requested review from
FriederikeHanssen and
maxulysse
as code owners
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.0.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
maxulysse
reviewed
Feb 26, 2025
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| FASTQ_ALIGN_GATK( |
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I think I would have kept the spring and convert part out of it
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What do you mean? 🤔
famosab
commented
Feb 27, 2025
Comment on lines
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| one_fastq_gz_spring: it[0].data_type == "one_fastq_gz_spring" | ||
| two_fastq_gz_spring: it[0].data_type == "two_fastq_gz_spring" | ||
| } | ||
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| // Two fastq.gz-files | ||
| fastq_gz = input_sample_type.fastq_gz.map { meta, files -> addReadgroupToMeta(meta, files) } | ||
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| // Just one fastq.gz.spring-file with both R1 and R2 | ||
| fastq_gz_pair_from_spring = SPRING_DECOMPRESS_TO_FQ_PAIR(input_sample_type.one_fastq_gz_spring, false) | ||
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| one_fastq_gz_from_spring = fastq_gz_pair_from_spring.fastq.map { meta, files -> addReadgroupToMeta(meta, files) } | ||
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| // Two fastq.gz.spring-files - one for R1 and one for R2 | ||
| r1_fastq_gz_from_spring = SPRING_DECOMPRESS_TO_R1_FQ(input_sample_type.two_fastq_gz_spring.map{ meta, files -> | ||
| [meta, files[0] ]}, | ||
| true // write_one_fastq_gz | ||
| ) | ||
| r2_fastq_gz_from_spring = SPRING_DECOMPRESS_TO_R2_FQ(input_sample_type.two_fastq_gz_spring.map{ meta, files -> | ||
| [meta, files[1] ]}, | ||
| true // write_one_fastq_gz | ||
| ) | ||
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| two_fastq_gz_from_spring = r1_fastq_gz_from_spring.fastq.join(r2_fastq_gz_from_spring.fastq).map{ meta, fastq_1, fastq_2 -> [meta, [fastq_1, fastq_2]]} | ||
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| two_fastq_gz_from_spring = two_fastq_gz_from_spring.map { meta, files -> addReadgroupToMeta(meta, files) } |
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@maxulysse do you mean moving this part back to the main.nf?
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PR checklist
nf-core pipelines 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).