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Co-authored-by: Jonathan Manning <[email protected]>
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@siddharthab @pinin4fjords
siddharthab and pinin4fjords committed Nov 6, 2024
1 parent e5d9d4b commit 05513ee
Showing 1 changed file with 25 additions and 25 deletions.
50 changes: 25 additions & 25 deletions workflows/rnaseq/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -222,28 +222,28 @@ workflow RNASEQ {
BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME (
ch_genome_bam.join(ch_genome_bam_index, by: [0])
)
umi_dedup_genome = BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME
ch_multiqc_files = ch_multiqc_files.mix(umi_dedup_genome.out.dedup_stats.collect{it[1]}.ifEmpty([]))
UMI_DEDUP_GENOME = BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME
ch_multiqc_files = ch_multiqc_files.mix(UMI_DEDUP_GENOME.out.dedup_stats.collect{it[1]}.ifEmpty([]))
} else if (params.umi_dedup_tool == "umitools") {
BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME (
ch_genome_bam.join(ch_genome_bam_index, by: [0]),
params.umitools_dedup_stats
)
umi_dedup_genome = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME
ch_multiqc_files = ch_multiqc_files.mix(umi_dedup_genome.out.deduplog.collect{it[1]})
UMI_DEDUP_GENOME = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME
ch_multiqc_files = ch_multiqc_files.mix(UMI_DEDUP_GENOME.out.deduplog.collect{it[1]})
} else {
error("Unknown umi_dedup_tool '${params.umi_dedup_tool}'")
}
ch_genome_bam = umi_dedup_genome.out.bam
ch_genome_bam_index = umi_dedup_genome.out.bai
ch_multiqc_files = ch_multiqc_files.mix(umi_dedup_genome.out.stats.collect{it[1]})
ch_multiqc_files = ch_multiqc_files.mix(umi_dedup_genome.out.flagstat.collect{it[1]})
ch_multiqc_files = ch_multiqc_files.mix(umi_dedup_genome.out.idxstats.collect{it[1]})
ch_genome_bam = UMI_DEDUP_GENOME.out.bam
ch_genome_bam_index = UMI_DEDUP_GENOME.out.bai
ch_multiqc_files = ch_multiqc_files.mix(UMI_DEDUP_GENOME.out.stats.collect{it[1]})
ch_multiqc_files = ch_multiqc_files.mix(UMI_DEDUP_GENOME.out.flagstat.collect{it[1]})
ch_multiqc_files = ch_multiqc_files.mix(UMI_DEDUP_GENOME.out.idxstats.collect{it[1]})

if (params.bam_csi_index) {
ch_genome_bam_index = umi_dedup_genome.out.csi
ch_genome_bam_index = UMI_DEDUP_GENOME.out.csi
}
ch_versions = ch_versions.mix(umi_dedup_genome.out.versions)
ch_versions = ch_versions.mix(UMI_DEDUP_GENOME.out.versions)

// Co-ordinate sort, index and run stats on transcriptome BAM
BAM_SORT_STATS_SAMTOOLS (
Expand All @@ -258,20 +258,20 @@ workflow RNASEQ {
BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_TRANSCRIPTOME (
ch_transcriptome_sorted_bam.join(ch_transcriptome_sorted_bai, by: [0])
)
umi_dedup_transcriptome = BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_TRANSCRIPTOME
UMI_DEDUP_TRANSCRIPTOME = BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_TRANSCRIPTOME
} else if (params.umi_dedup_tool == "umitools") {
BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME (
ch_transcriptome_sorted_bam.join(ch_transcriptome_sorted_bai, by: [0]),
params.umitools_dedup_stats
)
umi_dedup_transcriptome = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME
UMI_DEDUP_TRANSCRIPTOME = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME
} else {
error("Unknown umi_dedup_tool '${params.umi_dedup_tool}'")
}

// Name sort BAM before passing to Salmon
SAMTOOLS_SORT (
umi_dedup_transcriptome.out.bam,
UMI_DEDUP_TRANSCRIPTOME.out.bam,
ch_fasta.map { [ [:], it ] }
)

Expand Down Expand Up @@ -398,27 +398,27 @@ workflow RNASEQ {
BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME (
ch_genome_bam.join(ch_genome_bam_index, by: [0]),
)
umi_dedup_genome = BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME
ch_multiqc_files = ch_multiqc_files.mix(umi_dedup_genome.out.dedup_stats.collect{it[1]}.ifEmpty([]))
UMI_DEDUP_GENOME = BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME
ch_multiqc_files = ch_multiqc_files.mix(UMI_DEDUP_GENOME.out.dedup_stats.collect{it[1]}.ifEmpty([]))
} else if (params.umi_dedup_tool == "umitools") {
BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME (
ch_genome_bam.join(ch_genome_bam_index, by: [0]),
params.umitools_dedup_stats
)
umi_dedup_genome = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME
ch_multiqc_files = ch_multiqc_files.mix(umi_dedup_genome.out.deduplog.collect{it[1]})
UMI_DEDUP_GENOME = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME
ch_multiqc_files = ch_multiqc_files.mix(UMI_DEDUP_GENOME.out.deduplog.collect{it[1]})
} else {
error("Unknown umi_dedup_tool '${params.umi_dedup_tool}'")
}
ch_genome_bam = umi_dedup_genome.out.bam
ch_genome_bam_index = umi_dedup_genome.out.bai
ch_multiqc_files = ch_multiqc_files.mix(umi_dedup_genome.out.stats.collect{it[1]})
ch_multiqc_files = ch_multiqc_files.mix(umi_dedup_genome.out.flagstat.collect{it[1]})
ch_multiqc_files = ch_multiqc_files.mix(umi_dedup_genome.out.idxstats.collect{it[1]})
ch_genome_bam = UMI_DEDUP_GENOME.out.bam
ch_genome_bam_index = UMI_DEDUP_GENOME.out.bai
ch_multiqc_files = ch_multiqc_files.mix(UMI_DEDUP_GENOME.out.stats.collect{it[1]})
ch_multiqc_files = ch_multiqc_files.mix(UMI_DEDUP_GENOME.out.flagstat.collect{it[1]})
ch_multiqc_files = ch_multiqc_files.mix(UMI_DEDUP_GENOME.out.idxstats.collect{it[1]})
if (params.bam_csi_index) {
ch_genome_bam_index = umi_dedup_genome.out.csi
ch_genome_bam_index = UMI_DEDUP_GENOME.out.csi
}
ch_versions = ch_versions.mix(umi_dedup_genome.out.versions)
ch_versions = ch_versions.mix(UMI_DEDUP_GENOME.out.versions)
}
}

Expand Down

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