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freerkvandijk
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In general, [modules/local/umi_consensus/main.nf is a mess. Almost everything there has a matching nf-core module, so we should switch to those. Local models should be limited to preprocessing workflow specific implementation that we can’t be found/pushed upstream in nf-core modules.
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Don't forget to remove the unnecessary tests for the now deleted local modules. |
| include { SAMTOOLS_CONVERT as SAMTOOLS_CONVERT_UMI } from "../../../modules/nf-core/samtools/convert/main" | ||
| include { SAMTOOLS_SORMADUP } from "../../../modules/nf-core/samtools/sormadup/main.nf" | ||
| include { SAMTOOLS_SORT } from "../../../modules/nf-core/samtools/sort/main" | ||
| include { UMI_CONSENSUS_KAPA } from '../../local/umi_consensus/main' |
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Could it be that you forgotten git add the now separated UMI_CONSENSUS_KAPA subworkflow file?
docs/README.md
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| - [Usage](usage.md) | ||
| - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags. | ||
| - [Technical map](technical_map.md) |
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Where does this change originate from? Since there’s no technical_map.md introduced in this PR, is this a merge/rebase conflict resolution artifact?
samplesheet.minimal.yml
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Test samplesheet should go in the tests/inputs/test.yml Amend test samplesheet and retain per sample configurability
tests/config/nf-test.config
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| params { | ||
| disable_pipeline_plugins = true |
modules/local/umi_consensus/main.nf
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| // Local lightweight filtering step used before module-based UMI processing. | ||
| // Keeps primary mapped reads and removes unmapped/secondary/supplementary records. | ||
| process UMI_LOCAL_SAMTOOLS_VIEW { |
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No need for this to be an extra process. You can just alias the nf-core samtools_view module and configure in modules.config
docs/umi_consensus.md
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Integrate relevant (global) info in existing markdown files, amend the metro map and then remove this file
docs/usage.md
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| When `umi_consensus` is enabled, the `UMI_CONSENSUS_KAPA` workflow runs multiple `samtools`/`fgbio` processes plus remapping through `FASTQ_ALIGN_DNA`. | ||
| With container-based execution (`docker`, `singularity`, etc.), default per-process containers are already configured. | ||
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| Example custom config snippet: |
modules/local/umi_consensus/main.nf
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| } | ||
| .set { ch_umi_bam_bai_fasta_fai } | ||
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| SAMTOOLS_CONVERT_UMI(ch_umi_bam_bai_fasta_fai) |
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No need for extra import, just mix the output bams in the bam channel and pipe to the regular samtools view
| .set { ch_cram_crai } | ||
| ch_cram_crai.dump(tag: "FASTQ_TO_CRAM: cram and crai", pretty: true) | ||
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| ch_sormadup_metrics = ch_sormadup_metrics.mix(UMI_CONSENSUS_KAPA.out.family_sizes) |
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| main: | ||
| // 1) Initial mapping of raw reads with the configured aligner/index. | ||
| FASTQ_ALIGN_DNA(ch_meta_reads_aligner_index_fasta, false) |
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Should be handled by the parent workflow, use pre-aligned bam as input
| } | ||
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| // 3) Prepare read-pair metadata and UMI tags before consensus calling. | ||
| UMI_SAMTOOLS_VIEW( |
| // 3) Prepare read-pair metadata and UMI tags before consensus calling. | ||
| UMI_SAMTOOLS_VIEW( | ||
| FASTQ_ALIGN_DNA.out.bam | ||
| .map { meta, bam -> [meta, bam, file('/etc/hosts')] }, |
tests/inputs/zipper_ref2.txt
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remove this and add to test-datasets if needed
…s named UMI_SAMTOOLS_PREP_TEMPLATE
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| -o ${prefix}.bam \\ | ||
| -t ${task.cpus} \\ | ||
| snap-aligner ${subcmd} \ | ||
| \$INDEX \ |
| SAMTOOLS_STATS(ch_bam_bai_fasta_fai) | ||
| SAMTOOLS_FLAGSTAT(ch_bam_bai_fasta_fai) | ||
| SAMTOOLS_IDXSTATS(ch_bam_bai_fasta_fai) | ||
| SAMTOOLS_FLAGSTAT(ch_bam_bai) |
| // FUNCTIONS | ||
| include { getGenomeAttribute } from '../../local/utils_nfcore_preprocessing_pipeline' | ||
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| workflow FASTQ_ALIGN_DNA { |
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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).