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Starting complement for umi factor-out
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| // | ||
| // BAM deduplication with UMI processing | ||
| // | ||
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| include { BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE } from '../../../subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse' | ||
| include { BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS } from '../../../subworkflows/nf-core/bam_dedup_stats_samtools_umitools' | ||
| include { BAM_SORT_STATS_SAMTOOLS } from '../../../subworkflows/nf-core/bam_sort_stats_samtools' | ||
| include { UMITOOLS_PREPAREFORRSEM } from '../../../modules/nf-core/umitools/prepareforrsem' | ||
| include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' | ||
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| workflow BAM_DEDUP_UMI { | ||
| take: | ||
| ch_genome_bam // channel: [ val(meta), path(bam), path(bai) ] | ||
| ch_fasta // channel: [ path(fasta) ] | ||
| umi_dedup_tool // string: 'umicollapse' or 'umitools' | ||
| umitools_dedup_stats // boolean: whether to generate UMI-tools dedup stats | ||
| bam_csi_index // boolean: whether to generate CSI index | ||
| ch_transcriptome_bam // | ||
| ch_transcript_fasta | ||
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| main: | ||
| ch_versions = Channel.empty() | ||
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| if (umi_dedup_tool == "umicollapse" && umi_dedup_tool != "umitools"){ | ||
| error("Unknown umi_dedup_tool '${umi_dedup_tool}'") | ||
| } | ||
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| // Genome BAM deduplication | ||
| if (umi_dedup_tool == "umicollapse") { | ||
| BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE ( | ||
| ch_genome_bam | ||
| ) | ||
| UMI_DEDUP_GENOME = BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE | ||
| ch_dedup_log = UMI_DEDUP_GENOME.out.dedup_stats | ||
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| } else if (umi_dedup_tool == "umitools") { | ||
| BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS ( | ||
| ch_genome_bam, | ||
| umitools_dedup_stats | ||
| ) | ||
| UMI_DEDUP_GENOME = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS | ||
| ch_dedup_log = UMI_DEDUP_GENOME.out.deduplog | ||
| } | ||
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| // Co-ordinate sort, index and run stats on transcriptome BAM. This takes | ||
| // some preparation- we have to coordinate sort the BAM, run the | ||
| // deduplication, then restore name sorting and run a script from umitools | ||
| // to prepare for rsem or salmon | ||
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| // 1. Coordinate sort | ||
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| BAM_SORT_STATS_SAMTOOLS ( | ||
| ch_transcriptome_bam, | ||
| ch_transcript_fasta.map { [ [:], it ] } | ||
| ) | ||
| ch_sorted_transcriptome_bam = BAM_SORT_STATS_SAMTOOLS.out.bam | ||
| .join(BAM_SORT_STATS_SAMTOOLS.out.bai) | ||
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| // 2. Transcriptome BAM deduplication | ||
| if (umi_dedup_tool == "umicollapse") { | ||
| BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE ( | ||
| ch_sorted_transcriptome_bam | ||
| ) | ||
| UMI_DEDUP_GENOME = BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE | ||
| ch_dedup_log = UMI_DEDUP_GENOME.out.dedup_stats | ||
|
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||
| } else if (umi_dedup_tool == "umitools") { | ||
| BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS ( | ||
| ch_sorted_transcriptome_bam, | ||
| umitools_dedup_stats | ||
| ) | ||
| UMI_DEDUP_GENOME = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS | ||
| ch_dedup_log = UMI_DEDUP_GENOME.out.deduplog | ||
| } | ||
|
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||
| // 3. Restore name sorting | ||
| SAMTOOLS_SORT ( | ||
| UMI_DEDUP_TRANSCRIPTOME.out.bam, | ||
| ch_fasta.map { [ [:], it ] } | ||
| ) | ||
|
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| // 4. Run prepare_for_rsem.py on paired-end BAM files | ||
| // This fixes paired-end reads in name sorted BAM files | ||
| // See: https://github.com/nf-core/rnaseq/issues/828 | ||
| ended_transcriptome_dedup_bam = SAMTOOLS_SORT.out.bam | ||
| .branch { | ||
| meta, bam -> | ||
| single_end: meta.single_end | ||
| return [ meta, bam ] | ||
| paired_end: !meta.single_end | ||
| return [ meta, bam ] | ||
| } | ||
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| UMITOOLS_PREPAREFORSALMON ( | ||
| ended_transcriptome_dedup_bam.paired_end | ||
| .map { meta, bam -> [ meta, bam, [] ] } | ||
| ) | ||
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| ch_dedup_transcriptome_bam = ch_transcriptome_bam | ||
| .single_end | ||
| .mix(UMITOOLS_PREPAREFORSALMON.out.bam) | ||
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| // Record versions | ||
|
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| ch_versions = UMI_DEDUP_GENOME.out.versions | ||
| .mix(BAM_SORT_STATS_SAMTOOLS.out.versions) | ||
| .mix(UMITOOLS_PREPAREFORSALMON.out.versions) | ||
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| emit: | ||
| bam = UMI_DEDUP_GENOME.out.bam // channel: [ val(meta), path(bam) ] | ||
| bam_index = bam_csi_index ? UMI_DEDUP_GENOME.out.csi : UMI_DEDUP_GENOME.out.bai // channel: [ val(meta), path(bai) ] | ||
| dedup_log = ch_dedup_log // channel: [ val(meta), path(log) ] | ||
| stats = UMI_DEDUP_GENOME.out.stats | ||
| flagstat = UMI_DEDUP_GENOME.out.flagstat | ||
| idxstats = UMI_DEDUP_GENOME.out.idxstats | ||
| transcriptome_bam = ch_dedup_transcriptome_bam // channel: [ val(meta), path(bam) ] | ||
| versions = ch_versions // channel: [ path(versions.yml) ] | ||
| } |
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