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Remove redundant index computation for MD & version for MD Spark #1101

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Merged
maxulysse merged 7 commits into from
Jun 14, 2023
Merged

Remove redundant index computation for MD & version for MD Spark #1101

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c9eaba9
remove redundant index computation [skip ci]
FriederikeHanssen Jun 12, 2023
9c3cc8b
update changelog [skip ci]
FriederikeHanssen Jun 12, 2023
ac63797
update md modules
FriederikeHanssen Jun 14, 2023
72d6026
Merge branch 'dev' into issue_1065
FriederikeHanssen Jun 14, 2023
401cf54
Revert wrong checksum change
FriederikeHanssen Jun 14, 2023
07a4d5f
[automated] Fix linting with Prettier
nf-core-bot Jun 14, 2023
8be49d9
remove unnecessary import
FriederikeHanssen Jun 14, 2023
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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4 changes: 2 additions & 2 deletions modules.json
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Expand Up @@ -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": {
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26 changes: 18 additions & 8 deletions modules/nf-core/gatk4/markduplicates/main.nf
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2 changes: 1 addition & 1 deletion modules/nf-core/gatk4/markduplicatesspark/main.nf
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7 changes: 1 addition & 6 deletions subworkflows/local/bam_markduplicates/main.nf
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Expand Up @@ -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:
Expand All @@ -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)
Expand All @@ -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:
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