Merge branch 'dev' into public_aws_ecr_singularity

nf-core · Jun 14, 2023 · 9c350a8 · 9c350a8
2 parents c940aca + 8306a79
commit 9c350a8
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Showing 9 changed files with 35 additions and 29 deletions.
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -23,6 +23,7 @@ jobs:
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/sarek/work-${{ github.sha }}/somatic_test
           parameters: |
             {
+              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/somatic_test"
             }
           profiles: test_full,public_aws_ecr

diff --git a/.github/workflows/awsfulltest_germline.yml b/.github/workflows/awsfulltest_germline.yml
@@ -23,6 +23,7 @@ jobs:
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/sarek/work-${{ github.sha }}/germline_test
           parameters: |
             {
+              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/germline_test"
             }
           profiles: test_full_germline,public_aws_ecr

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 Vuoinesluobbalah is a lake close to Bierikjávrre.
 
+### Added
+
+- [#1106](https://github.com/nf-core/sarek/pull/1106) - Add Slack integration to Megatests
+
 ### Changed
 
 - [#1087](https://github.com/nf-core/sarek/pull/1087) - Back to dev
@@ -23,6 +27,9 @@ 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
 

diff --git a/modules.json b/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": {

diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf
diff --git a/modules/nf-core/gatk4/markduplicatesspark/main.nf b/modules/nf-core/gatk4/markduplicatesspark/main.nf
diff --git a/nextflow.config b/nextflow.config
@@ -99,7 +99,6 @@ params {
 
     // Boilerplate options
     outdir                     = null
-    tracedir                   = "${params.outdir}/pipeline_info"
     publish_dir_mode           = 'copy'
     email                      = null
     email_on_fail              = null
@@ -302,19 +301,19 @@ singularity.registry = 'quay.io'
 def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true
-    file    = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
 }
 report {
     enabled = true
-    file    = "${params.tracedir}/execution_report_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
 }
 trace {
     enabled = true
-    file    = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
+    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
 }
 dag {
     enabled = true
-    file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
+    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
 }
 
 manifest {

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -959,13 +959,6 @@
                     "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                     "fa_icon": "fas fa-cog"
                 },
-                "tracedir": {
-                    "type": "string",
-                    "description": "Directory to keep pipeline Nextflow logs and reports.",
-                    "default": "${params.outdir}/pipeline_info",
-                    "fa_icon": "fas fa-cogs",
-                    "hidden": true
-                },
                 "validate_params": {
                     "type": "boolean",
                     "description": "Boolean whether to validate parameters against the schema at runtime",

diff --git a/subworkflows/local/bam_markduplicates/main.nf b/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: