Merge pull request #1101 from FriederikeHanssen/issue_1065

Remove redundant index computation for MD & version for MD Spark

CHANGELOG.md

@@ -27,6 +27,8 @@ Vuoinesluobbalah is a lake close to Bierikjávrre.
 - [#1093](https://github.com/nf-core/sarek/pull/1093) - Fixing Ascat by reverting meta.id in channels allele_files, loci_files, gc_file and rt_file to baseName.
 - [#1098](https://github.com/nf-core/sarek/pull/1098) - Fix Channel issue in Mutect2 subworkflow [#1094](https://github.com/nf-core/sarek/pull/1094)
 - [#1100](https://github.com/nf-core/sarek/pull/1100) - Remove duplicate index with deepvariant when no_intervals [#1069](https://github.com/nf-core/sarek/pull/1069)
+- [#1101](https://github.com/nf-core/sarek/pull/1101) - Remove duplicate index computation for GATK4 Markduplicates & [#1065](https://github.com/nf-core/sarek/issues/1065)
+- [#1101](https://github.com/nf-core/sarek/pull/1101) - Fix GATK4 version for GATK4 MarkduplicatesSpark [#1068](https://github.com/nf-core/sarek/issues/1068)
 - [#1105](https://github.com/nf-core/sarek/pull/1105) - Remove `params.tracedir`
 
 ## [3.2.1](https://github.com/nf-core/sarek/releases/tag/3.2.1) - Pierikjaure

modules.json

@@ -258,12 +258,12 @@
                     },
                     "gatk4/markduplicates": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "0a261469640941da2488e1a5aa023b64db837c70",
                         "installed_by": ["modules"]
                     },
                     "gatk4/markduplicatesspark": {
                         "branch": "master",
-                        "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0",
+                        "git_sha": "0a261469640941da2488e1a5aa023b64db837c70",
                         "installed_by": ["modules"]
                     },
                     "gatk4/mergemutectstats": {

subworkflows/local/bam_markduplicates/main.nf

@@ -6,7 +6,6 @@
 
 include { CRAM_QC_MOSDEPTH_SAMTOOLS              } from '../cram_qc_mosdepth_samtools/main'
 include { GATK4_MARKDUPLICATES                   } from '../../../modules/nf-core/gatk4/markduplicates/main'
-include { SAMTOOLS_INDEX as INDEX_MARKDUPLICATES } from '../../../modules/nf-core/samtools/index/main'
 
 workflow BAM_MARKDUPLICATES {
     take:
@@ -22,11 +21,8 @@ workflow BAM_MARKDUPLICATES {
     // RUN MARKUPDUPLICATES
     GATK4_MARKDUPLICATES(bam, fasta, fasta_fai)
 
-    // Index cram
-    INDEX_MARKDUPLICATES(GATK4_MARKDUPLICATES.out.cram)
-
     // Join with the crai file
-    cram = GATK4_MARKDUPLICATES.out.cram.join(INDEX_MARKDUPLICATES.out.crai, failOnDuplicate: true, failOnMismatch: true)
+    cram = GATK4_MARKDUPLICATES.out.cram.join(GATK4_MARKDUPLICATES.out.crai, failOnDuplicate: true, failOnMismatch: true)
 
     // QC on CRAM
     CRAM_QC_MOSDEPTH_SAMTOOLS(cram, fasta, intervals_bed_combined)
@@ -37,7 +33,6 @@ workflow BAM_MARKDUPLICATES {
 
     // Gather versions of all tools used
     versions = versions.mix(GATK4_MARKDUPLICATES.out.versions)
-    versions = versions.mix(INDEX_MARKDUPLICATES.out.versions)
     versions = versions.mix(CRAM_QC_MOSDEPTH_SAMTOOLS.out.versions)
 
     emit: