refactor: nf-core subworkflows install bam_markduplicates_picard

Author: edmundmiller

conf/modules.config

@@ -333,7 +333,7 @@ if (!params.skip_alignment) {
 
     if (!params.skip_markduplicates) {
         process {
-            withName: '.*:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES' {
+            withName: '.*:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES' {
                 ext.args   = '--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp'
                 ext.prefix = { "${meta.id}.markdup.sorted" }
                 publishDir = [
@@ -350,7 +350,7 @@ if (!params.skip_alignment) {
                 ]
             }
 
-            withName: '.*:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX' {
+            withName: '.*:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX' {
                 ext.args   = params.bam_csi_index ? '-c' : ''
                 ext.prefix = { "${meta.id}.markdup.sorted" }
                 publishDir = [
@@ -360,7 +360,7 @@ if (!params.skip_alignment) {
                 ]
             }
 
-            withName: '.*:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*' {
+            withName: '.*:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*' {
                 ext.prefix = { "${meta.id}.markdup.sorted.bam" }
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/samtools_stats" },

modules.json

@@ -48,7 +48,7 @@
                     },
                     "picard/markduplicates": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "eca65aa4a5e2e192ac44d6962c8f9260f314ffb8"
                     },
                     "preseq/lcextrap": {
                         "branch": "master",
@@ -174,6 +174,10 @@
             },
             "subworkflows": {
                 "nf-core": {
+                    "bam_markduplicates_picard": {
+                        "branch": "master",
+                        "git_sha": "c9083a16a9a6c5e5beea40a88939b6e1138926f7"
+                    },
                     "bam_sort_stats_samtools": {
                         "branch": "master",
                         "git_sha": "3911652a6b24249358f79e8b8466338d63efb2a2"

modules/nf-core/picard/markduplicates/main.nf

@@ -146,7 +146,7 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoft
 include { FASTQC_UMITOOLS_TRIMGALORE } from '../subworkflows/nf-core/fastqc_umitools_trimgalore'
 include { FASTQ_ALIGN_HISAT2         } from '../subworkflows/nf-core/fastq_align_hisat2/main'
 include { BAM_SORT_STATS_SAMTOOLS    } from '../subworkflows/nf-core/bam_sort_stats_samtools/main'
-include { MARK_DUPLICATES_PICARD     } from '../subworkflows/nf-core/mark_duplicates_picard'
+include { BAM_MARKDUPLICATES_PICARD  } from '../subworkflows/nf-core/bam_markduplicates_picard/main'
 include { RSEQC                      } from '../subworkflows/nf-core/rseqc'
 include { DEDUP_UMI_UMITOOLS as DEDUP_UMI_UMITOOLS_GENOME        } from '../subworkflows/nf-core/dedup_umi_umitools'
 include { DEDUP_UMI_UMITOOLS as DEDUP_UMI_UMITOOLS_TRANSCRIPTOME } from '../subworkflows/nf-core/dedup_umi_umitools'
@@ -565,19 +565,21 @@ workflow RNASEQ {
     //
     ch_markduplicates_multiqc = Channel.empty()
     if (!params.skip_alignment && !params.skip_markduplicates) {
-        MARK_DUPLICATES_PICARD (
-            ch_genome_bam
+        BAM_MARKDUPLICATES_PICARD (
+            ch_genome_bam,
+            PREPARE_GENOME.out.fasta,
+            PREPARE_GENOME.out.fai
         )
-        ch_genome_bam             = MARK_DUPLICATES_PICARD.out.bam
-        ch_genome_bam_index       = MARK_DUPLICATES_PICARD.out.bai
-        ch_samtools_stats         = MARK_DUPLICATES_PICARD.out.stats
-        ch_samtools_flagstat      = MARK_DUPLICATES_PICARD.out.flagstat
-        ch_samtools_idxstats      = MARK_DUPLICATES_PICARD.out.idxstats
-        ch_markduplicates_multiqc = MARK_DUPLICATES_PICARD.out.metrics
+        ch_genome_bam             = BAM_MARKDUPLICATES_PICARD.out.bam
+        ch_genome_bam_index       = BAM_MARKDUPLICATES_PICARD.out.bai
+        ch_samtools_stats         = BAM_MARKDUPLICATES_PICARD.out.stats
+        ch_samtools_flagstat      = BAM_MARKDUPLICATES_PICARD.out.flagstat
+        ch_samtools_idxstats      = BAM_MARKDUPLICATES_PICARD.out.idxstats
+        ch_markduplicates_multiqc = BAM_MARKDUPLICATES_PICARD.out.metrics
         if (params.bam_csi_index) {
-            ch_genome_bam_index = MARK_DUPLICATES_PICARD.out.csi
+            ch_genome_bam_index = BAM_MARKDUPLICATES_PICARD.out.csi
         }
-        ch_versions = ch_versions.mix(MARK_DUPLICATES_PICARD.out.versions)
+        ch_versions = ch_versions.mix(BAM_MARKDUPLICATES_PICARD.out.versions)
     }
 
     //