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edmundmilleredmundmiller
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refactor: nf-core subworkflows install bam_rseqc
1 parent 0688de7 commit f5c6ad7

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‎conf/modules.config‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -862,7 +862,7 @@ if (!params.skip_alignment && !params.skip_qc) {
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863863
if (!params.skip_rseqc && 'bam_stat' in rseqc_modules) {
864864
process {
865-
withName: '.*:RSEQC:RSEQC_BAMSTAT' {
865+
withName: '.*:BAM_RSEQC:RSEQC_BAMSTAT' {
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publishDir = [
867867
path: { "${params.outdir}/${params.aligner}/rseqc/bam_stat" },
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mode: params.publish_dir_mode,
@@ -874,7 +874,7 @@ if (!params.skip_alignment && !params.skip_qc) {
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if (!params.skip_rseqc && 'infer_experiment' in rseqc_modules) {
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process {
877-
withName: '.*:RSEQC:RSEQC_INFEREXPERIMENT' {
877+
withName: '.*:BAM_RSEQC:RSEQC_INFEREXPERIMENT' {
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publishDir = [
879879
path: { "${params.outdir}/${params.aligner}/rseqc/infer_experiment" },
880880
mode: params.publish_dir_mode,
@@ -886,7 +886,7 @@ if (!params.skip_alignment && !params.skip_qc) {
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if (!params.skip_rseqc && 'junction_annotation' in rseqc_modules) {
888888
process {
889-
withName: '.*:RSEQC:RSEQC_JUNCTIONANNOTATION' {
889+
withName: '.*:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION' {
890890
publishDir = [
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[
892892
path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/pdf" },
@@ -920,7 +920,7 @@ if (!params.skip_alignment && !params.skip_qc) {
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if (!params.skip_rseqc && 'junction_saturation' in rseqc_modules) {
922922
process {
923-
withName: '.*:RSEQC:RSEQC_JUNCTIONSATURATION' {
923+
withName: '.*:BAM_RSEQC:RSEQC_JUNCTIONSATURATION' {
924924
publishDir = [
925925
[
926926
path: { "${params.outdir}/${params.aligner}/rseqc/junction_saturation/pdf" },
@@ -939,7 +939,7 @@ if (!params.skip_alignment && !params.skip_qc) {
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940940
if (!params.skip_rseqc && 'read_duplication' in rseqc_modules) {
941941
process {
942-
withName: '.*:RSEQC:RSEQC_READDUPLICATION' {
942+
withName: '.*:BAM_RSEQC:RSEQC_READDUPLICATION' {
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publishDir = [
944944
[
945945
path: { "${params.outdir}/${params.aligner}/rseqc/read_duplication/pdf" },
@@ -963,7 +963,7 @@ if (!params.skip_alignment && !params.skip_qc) {
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964964
if (!params.skip_rseqc && 'read_distribution' in rseqc_modules && !params.bam_csi_index) {
965965
process {
966-
withName: '.*:RSEQC:RSEQC_READDISTRIBUTION' {
966+
withName: '.*:BAM_RSEQC:RSEQC_READDISTRIBUTION' {
967967
publishDir = [
968968
path: { "${params.outdir}/${params.aligner}/rseqc/read_distribution" },
969969
mode: params.publish_dir_mode,
@@ -975,7 +975,7 @@ if (!params.skip_alignment && !params.skip_qc) {
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976976
if (!params.skip_rseqc && 'inner_distance' in rseqc_modules && !params.bam_csi_index) {
977977
process {
978-
withName: '.*:RSEQC:RSEQC_INNERDISTANCE' {
978+
withName: '.*:BAM_RSEQC:RSEQC_INNERDISTANCE' {
979979
publishDir = [
980980
[
981981
path: { "${params.outdir}/${params.aligner}/rseqc/inner_distance/txt" },
@@ -1000,7 +1000,7 @@ if (!params.skip_alignment && !params.skip_qc) {
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10011001
if (!params.skip_rseqc && 'tin' in rseqc_modules && !params.bam_csi_index) {
10021002
process {
1003-
withName: '.*:RSEQC:RSEQC_TIN' {
1003+
withName: '.*:BAM_RSEQC:RSEQC_TIN' {
10041004
publishDir = [
10051005
path: { "${params.outdir}/${params.aligner}/rseqc/tin" },
10061006
mode: params.publish_dir_mode,

‎modules.json‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -178,6 +178,10 @@
178178
"branch": "master",
179179
"git_sha": "c9083a16a9a6c5e5beea40a88939b6e1138926f7"
180180
},
181+
"bam_rseqc": {
182+
"branch": "master",
183+
"git_sha": "36a77f7c6decf2d1fb9f639ae982bc148d6828aa"
184+
},
181185
"bam_sort_stats_samtools": {
182186
"branch": "master",
183187
"git_sha": "3911652a6b24249358f79e8b8466338d63efb2a2"

‎subworkflows/nf-core/rseqc.nf‎ renamed to ‎subworkflows/nf-core/bam_rseqc/main.nf‎

Lines changed: 24 additions & 21 deletions
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‎subworkflows/nf-core/bam_rseqc/meta.yml‎

Lines changed: 141 additions & 0 deletions
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‎workflows/rnaseq.nf‎

Lines changed: 12 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -147,7 +147,7 @@ include { FASTQC_UMITOOLS_TRIMGALORE } from '../subworkflows/nf-core/fastqc_umit
147147
include { FASTQ_ALIGN_HISAT2 } from '../subworkflows/nf-core/fastq_align_hisat2/main'
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'
150-
include { RSEQC } from '../subworkflows/nf-core/rseqc'
150+
include { BAM_RSEQC } from '../subworkflows/nf-core/bam_rseqc/main'
151151
include { DEDUP_UMI_UMITOOLS as DEDUP_UMI_UMITOOLS_GENOME } from '../subworkflows/nf-core/dedup_umi_umitools'
152152
include { DEDUP_UMI_UMITOOLS as DEDUP_UMI_UMITOOLS_TRANSCRIPTOME } from '../subworkflows/nf-core/dedup_umi_umitools'
153153
include { BEDGRAPH_TO_BIGWIG as BEDGRAPH_TO_BIGWIG_FORWARD } from '../subworkflows/nf-core/bedgraph_to_bigwig'
@@ -685,21 +685,20 @@ workflow RNASEQ {
685685
}
686686

687687
if (!params.skip_rseqc && rseqc_modules.size() > 0) {
688-
RSEQC (
689-
ch_genome_bam,
690-
ch_genome_bam_index,
688+
BAM_RSEQC (
689+
ch_genome_bam.join(ch_genome_bam_index, by: [0]),
691690
PREPARE_GENOME.out.gene_bed,
692691
rseqc_modules
693692
)
694-
ch_bamstat_multiqc = RSEQC.out.bamstat_txt
695-
ch_inferexperiment_multiqc = RSEQC.out.inferexperiment_txt
696-
ch_innerdistance_multiqc = RSEQC.out.innerdistance_freq
697-
ch_junctionannotation_multiqc = RSEQC.out.junctionannotation_log
698-
ch_junctionsaturation_multiqc = RSEQC.out.junctionsaturation_rscript
699-
ch_readdistribution_multiqc = RSEQC.out.readdistribution_txt
700-
ch_readduplication_multiqc = RSEQC.out.readduplication_pos_xls
701-
ch_tin_multiqc = RSEQC.out.tin_txt
702-
ch_versions = ch_versions.mix(RSEQC.out.versions)
693+
ch_bamstat_multiqc = BAM_RSEQC.out.bamstat_txt
694+
ch_inferexperiment_multiqc = BAM_RSEQC.out.inferexperiment_txt
695+
ch_innerdistance_multiqc = BAM_RSEQC.out.innerdistance_freq
696+
ch_junctionannotation_multiqc = BAM_RSEQC.out.junctionannotation_log
697+
ch_junctionsaturation_multiqc = BAM_RSEQC.out.junctionsaturation_rscript
698+
ch_readdistribution_multiqc = BAM_RSEQC.out.readdistribution_txt
699+
ch_readduplication_multiqc = BAM_RSEQC.out.readduplication_pos_xls
700+
ch_tin_multiqc = BAM_RSEQC.out.tin_txt
701+
ch_versions = ch_versions.mix(BAM_RSEQC.out.versions)
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704703
ch_inferexperiment_multiqc
705704
.map { meta, strand_log -> [ meta ] + WorkflowRnaseq.getInferexperimentStrandedness(strand_log, 30) }

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