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Fixes #65 #67

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Fixes #65 #67

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0f4190e
Fixes missing BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS imports
evancofer Aug 5, 2024
e02b0d8
Cleaned up code from prior commit
evancofer Aug 5, 2024
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18 changes: 15 additions & 3 deletions workflows/riboseq/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -49,8 +49,11 @@ def filterGtf =
// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
//
include { BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS } from '../../subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main'
include { BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS as BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME } from '../../subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main'
include { BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS as BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME } from '../../subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main'
include { PREPROCESS_RNASEQ } from '../../subworkflows/nf-core/preprocess_rnaseq'
include { FASTQ_ALIGN_STAR } from '../../subworkflows/nf-core/fastq_align_star'
include { BAM_SORT_STATS_SAMTOOLS } from '../../subworkflows/nf-core/bam_sort_stats_samtools'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -178,7 +181,8 @@ workflow RIBOSEQ {

ch_genome_bam = FASTQ_ALIGN_STAR.out.bam
ch_genome_bam_index = FASTQ_ALIGN_STAR.out.bai
ch_transcriptome_bam = FASTQ_ALIGN_STAR.out.orig_bam_transcript
ch_transcriptome_bam = FASTQ_ALIGN_STAR.out.bam_transcript
ch_transcriptome_bai = FASTQ_ALIGN_STAR.out.bai_transcript
ch_versions = ch_versions.mix(FASTQ_ALIGN_STAR.out.versions)

ch_multiqc_files = ch_multiqc_files
Expand Down Expand Up @@ -207,13 +211,21 @@ workflow RIBOSEQ {
.mix(BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.flagstat.collect{it[1]})
.mix(BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.idxstats.collect{it[1]})

// Deduplicate transcriptome BAM file before downstream analysis

BAM_SORT_STATS_SAMTOOLS (
ch_transcriptome_bam,
ch_fasta.map { [ [:], it ] }
)
ch_transcriptome_bam = BAM_SORT_STATS_SAMTOOLS.out.bam
ch_transcriptome_bai = BAM_SORT_STATS_SAMTOOLS.out.bai
Comment on lines +219 to +220
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Suggested change
ch_transcriptome_bam = BAM_SORT_STATS_SAMTOOLS.out.bam
ch_transcriptome_bai = BAM_SORT_STATS_SAMTOOLS.out.bai
ch_transcriptome_sorted_bam = BAM_SORT_STATS_SAMTOOLS.out.bam
ch_transcriptome_sorted_bai = BAM_SORT_STATS_SAMTOOLS.out.bai

rnaseq does this (also rename the input to the function below), so that the unsorted bam is not over-written. Maybe try this first?


// Deduplicate transcriptome BAM file before read counting with Salmon
BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME (
ch_transcriptome_bam.join(ch_transcriptome_bai, by: [0]),
params.umitools_dedup_stats
)
ch_transcriptome_bam = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME.out.bam
ch_transcriptome_bam = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME.out.bam
ch_transcriptome_bai = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME.out.bai

ch_multiqc_files = ch_multiqc_files
.mix(BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME.out.stats.collect{it[1]})
Expand Down