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edmundmilleredmundmiller
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refactor: nf-core subworkflows install bam_dedup_stats_samtools_umitools
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5 files changed

+94
-31
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‎conf/modules.config‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -373,7 +373,7 @@ if (!params.skip_alignment) {
373373

374374
if (params.with_umi && ['star_salmon','hisat2'].contains(params.aligner)) {
375375
process {
376-
withName: '.*:DEDUP_UMI_UMITOOLS_GENOME:UMITOOLS_DEDUP' {
376+
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:UMITOOLS_DEDUP' {
377377
ext.args = { [
378378
meta.single_end ? '' : '--unpaired-reads=discard --chimeric-pairs=discard',
379379
params.umitools_grouping_method ? "--method='${params.umitools_grouping_method}'" : '',
@@ -399,7 +399,7 @@ if (!params.skip_alignment) {
399399
]
400400
}
401401

402-
withName: '.*:DEDUP_UMI_UMITOOLS_GENOME:SAMTOOLS_INDEX' {
402+
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:SAMTOOLS_INDEX' {
403403
ext.args = params.bam_csi_index ? '-c' : ''
404404
ext.prefix = { "${meta.id}.umi_dedup.sorted" }
405405
publishDir = [
@@ -414,7 +414,7 @@ if (!params.skip_alignment) {
414414
]
415415
}
416416

417-
withName: '.*:DEDUP_UMI_UMITOOLS_GENOME:BAM_STATS_SAMTOOLS:.*' {
417+
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:BAM_STATS_SAMTOOLS:.*' {
418418
ext.prefix = { "${meta.id}.umi_dedup.sorted.bam" }
419419
publishDir = [
420420
path: { "${params.outdir}/${params.aligner}/samtools_stats" },
@@ -616,7 +616,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
616616
]
617617
}
618618

619-
withName: '.*:DEDUP_UMI_UMITOOLS_TRANSCRIPTOME:UMITOOLS_DEDUP' {
619+
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:UMITOOLS_DEDUP' {
620620
ext.args = { [
621621
meta.single_end ? '' : '--unpaired-reads=discard --chimeric-pairs=discard',
622622
params.umitools_grouping_method ? "--method='${params.umitools_grouping_method}'" : '',
@@ -630,14 +630,14 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
630630
]
631631
}
632632

633-
withName: '.*:DEDUP_UMI_UMITOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX' {
633+
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX' {
634634
publishDir = [
635635
path: { "${params.outdir}/${params.aligner}" },
636636
enabled: false
637637
]
638638
}
639639

640-
withName: '.*:DEDUP_UMI_UMITOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:.*' {
640+
withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:.*' {
641641
ext.prefix = { "${meta.id}.umi_dedup.transcriptome.sorted.bam" }
642642
publishDir = [
643643
path: { "${params.outdir}/${params.aligner}/samtools_stats" },

‎modules.json‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -174,6 +174,10 @@
174174
},
175175
"subworkflows": {
176176
"nf-core": {
177+
"bam_dedup_stats_samtools_umitools": {
178+
"branch": "master",
179+
"git_sha": "41891ec2c3704911cd68b9317f26545b95a1c48d"
180+
},
177181
"bam_markduplicates_picard": {
178182
"branch": "master",
179183
"git_sha": "c9083a16a9a6c5e5beea40a88939b6e1138926f7"

‎subworkflows/nf-core/dedup_umi_umitools.nf‎ renamed to ‎subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf‎

Lines changed: 4 additions & 4 deletions
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‎subworkflows/nf-core/bam_dedup_stats_samtools_umitools/meta.yml‎

Lines changed: 56 additions & 0 deletions
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‎workflows/rnaseq.nf‎

Lines changed: 24 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -148,8 +148,10 @@ include { FASTQ_ALIGN_HISAT2 } from '../subworkflows/nf-core/fastq_align
148148
include { BAM_SORT_STATS_SAMTOOLS } from '../subworkflows/nf-core/bam_sort_stats_samtools/main'
149149
include { BAM_MARKDUPLICATES_PICARD } from '../subworkflows/nf-core/bam_markduplicates_picard/main'
150150
include { BAM_RSEQC } from '../subworkflows/nf-core/bam_rseqc/main'
151-
include { DEDUP_UMI_UMITOOLS as DEDUP_UMI_UMITOOLS_GENOME } from '../subworkflows/nf-core/dedup_umi_umitools'
152-
include { DEDUP_UMI_UMITOOLS as DEDUP_UMI_UMITOOLS_TRANSCRIPTOME } from '../subworkflows/nf-core/dedup_umi_umitools'
151+
include {
152+
BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS as BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME
153+
BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS as BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME
154+
} from '../subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main'
153155
include { BEDGRAPH_TO_BIGWIG as BEDGRAPH_TO_BIGWIG_FORWARD } from '../subworkflows/nf-core/bedgraph_to_bigwig'
154156
include { BEDGRAPH_TO_BIGWIG as BEDGRAPH_TO_BIGWIG_REVERSE } from '../subworkflows/nf-core/bedgraph_to_bigwig'
155157

@@ -348,19 +350,19 @@ workflow RNASEQ {
348350
//
349351
if (params.with_umi) {
350352
// Deduplicate genome BAM file before downstream analysis
351-
DEDUP_UMI_UMITOOLS_GENOME (
353+
BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME (
352354
ch_genome_bam.join(ch_genome_bam_index, by: [0]),
353355
params.umitools_dedup_stats
354356
)
355-
ch_genome_bam = DEDUP_UMI_UMITOOLS_GENOME.out.bam
356-
ch_genome_bam_index = DEDUP_UMI_UMITOOLS_GENOME.out.bai
357-
ch_samtools_stats = DEDUP_UMI_UMITOOLS_GENOME.out.stats
358-
ch_samtools_flagstat = DEDUP_UMI_UMITOOLS_GENOME.out.flagstat
359-
ch_samtools_idxstats = DEDUP_UMI_UMITOOLS_GENOME.out.idxstats
357+
ch_genome_bam = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.bam
358+
ch_genome_bam_index = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.bai
359+
ch_samtools_stats = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.stats
360+
ch_samtools_flagstat = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.flagstat
361+
ch_samtools_idxstats = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.idxstats
360362
if (params.bam_csi_index) {
361-
ch_genome_bam_index = DEDUP_UMI_UMITOOLS_GENOME.out.csi
363+
ch_genome_bam_index = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.csi
362364
}
363-
ch_versions = ch_versions.mix(DEDUP_UMI_UMITOOLS_GENOME.out.versions)
365+
ch_versions = ch_versions.mix(BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.versions)
364366

365367
// Co-ordinate sort, index and run stats on transcriptome BAM
366368
BAM_SORT_STATS_SAMTOOLS (
@@ -371,14 +373,14 @@ workflow RNASEQ {
371373
ch_transcriptome_sorted_bai = BAM_SORT_STATS_SAMTOOLS.out.bai
372374

373375
// Deduplicate transcriptome BAM file before read counting with Salmon
374-
DEDUP_UMI_UMITOOLS_TRANSCRIPTOME (
376+
BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME (
375377
ch_transcriptome_sorted_bam.join(ch_transcriptome_sorted_bai, by: [0]),
376378
params.umitools_dedup_stats
377379
)
378380

379381
// Name sort BAM before passing to Salmon
380382
SAMTOOLS_SORT (
381-
DEDUP_UMI_UMITOOLS_TRANSCRIPTOME.out.bam
383+
BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME.out.bam
382384
)
383385

384386
// Only run prepare_for_rsem.py on paired-end BAM files
@@ -491,18 +493,19 @@ workflow RNASEQ {
491493
// SUBWORKFLOW: Remove duplicate reads from BAM file based on UMIs
492494
//
493495
if (params.with_umi) {
494-
DEDUP_UMI_UMITOOLS_GENOME (
495-
ch_genome_bam.join(ch_genome_bam_index, by: [0])
496+
BAM_DEDUP_STATS_SAMTOOLS_UMI_UMITOOLS_GENOME (
497+
ch_genome_bam.join(ch_genome_bam_index, by: [0]),
498+
params.umitools_dedup_stats
496499
)
497-
ch_genome_bam = DEDUP_UMI_UMITOOLS_GENOME.out.bam
498-
ch_genome_bam_index = DEDUP_UMI_UMITOOLS_GENOME.out.bai
499-
ch_samtools_stats = DEDUP_UMI_UMITOOLS_GENOME.out.stats
500-
ch_samtools_flagstat = DEDUP_UMI_UMITOOLS_GENOME.out.flagstat
501-
ch_samtools_idxstats = DEDUP_UMI_UMITOOLS_GENOME.out.idxstats
500+
ch_genome_bam = BAM_DEDUP_STATS_SAMTOOLS_UMI_UMITOOLS_GENOME.out.bam
501+
ch_genome_bam_index = BAM_DEDUP_STATS_SAMTOOLS_UMI_UMITOOLS_GENOME.out.bai
502+
ch_samtools_stats = BAM_DEDUP_STATS_SAMTOOLS_UMI_UMITOOLS_GENOME.out.stats
503+
ch_samtools_flagstat = BAM_DEDUP_STATS_SAMTOOLS_UMI_UMITOOLS_GENOME.out.flagstat
504+
ch_samtools_idxstats = BAM_DEDUP_STATS_SAMTOOLS_UMI_UMITOOLS_GENOME.out.idxstats
502505
if (params.bam_csi_index) {
503-
ch_genome_bam_index = DEDUP_UMI_UMITOOLS_GENOME.out.csi
506+
ch_genome_bam_index = BAM_DEDUP_STATS_SAMTOOLS_UMI_UMITOOLS_GENOME.out.csi
504507
}
505-
ch_versions = ch_versions.mix(DEDUP_UMI_UMITOOLS_GENOME.out.versions)
508+
ch_versions = ch_versions.mix(BAM_DEDUP_STATS_SAMTOOLS_UMI_UMITOOLS_GENOME.out.versions)
506509
}
507510
}
508511

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