Merge branch 'dev' of https://github.com/nf-core/sarek into dev

nf-core · Feb 16, 2024 · 8514c54 · 8514c54
2 parents 587475d + a5e892b
commit 8514c54
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Showing 34 changed files with 83 additions and 67 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -52,6 +52,15 @@ jobs:
         NXF_VER:
           - "23.04.0"
           - "latest-everything"
+        exclude:
+          - tags: "sentieon/bwamem"
+          - tags: "sentieon/dedup"
+          - tags: "sentieon/dnascope"
+          - tags: "sentieon/dnascope_joint_germline"
+          - tags: "sentieon/dnascope_skip_filter"
+          - tags: "sentieon/haplotyper"
+          - tags: "sentieon/haplotyper_joint_germline"
+          - tags: "sentieon/haplotyper_skip_filter"
     env:
       NXF_ANSI_LOG: false
       TEST_DATA_BASE: "${{ github.workspace }}/test-datasets"

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,14 +14,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1335](https://github.com/nf-core/sarek/pull/1335) - Add index computation of `bcftools_annotations`, if not provided
 - [#1340](https://github.com/nf-core/sarek/pull/1340) - Adds Azure test profiles and megatests.
 - [#1372](https://github.com/nf-core/sarek/pull/1372) - Add NCBench test profile for Agilent datasets
+- [#1409](https://github.com/nf-core/sarek/pull/1409) - Add params `modules_testdata_base_path` to test profile
 
 ### Changed
 
-- [#1339](https://github.com/nf-core/sarek/pull/1339) - Update sentieon-modules
+- [#1339](https://githu.com/nf-core/sarek/pull/1339), [#1401](https://github.com/nf-core/sarek/pull/1401) - Update sentieon-modules to Sentieon `202308.01` and adding support for running Sentieon with Conda and Apptainer
 - [#1344](https://github.com/nf-core/sarek/pull/1344) - Enable CRAM QC, when starting from variantcalling
 - [#1359](https://github.com/nf-core/sarek/pull/1359) - Removing params usage from local modules
 - [#1359](https://github.com/nf-core/sarek/pull/1359) - Removing params usage from local subworkflows
 - [#1360](https://github.com/nf-core/sarek/pull/1360) - Sync `TEMPLATE` with `tools` `2.11`
+- [#1411](https://github.com/nf-core/sarek/pull/1411) - Temporally disable sentieon related tests
 
 ### Fixed
 
@@ -32,7 +34,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1351](https://github.com/nf-core/sarek/pull/1351) - Fix params name for test profiles (`bcftools_annotations`)
 - [#1357](https://github.com/nf-core/sarek/pull/1364) - Fixed bug where samples were dropped while reconstituting BAM files
 - [#1373](https://github.com/nf-core/sarek/pull/1373) - Add `chr` prefix to NCBench bed file & enable trimming
-- [#1373](https://github.com/nf-core/sarek/pull/1381) - Swap NGSCheckMate bed file for GATK.GRCh37 to one without the `chr` prefix
+- [#1381](https://github.com/nf-core/sarek/pull/1381) - Swap NGSCheckMate bed file for GATK.GRCh37 to one without the `chr` prefix
+- [#1383](https://github.com/nf-core/sarek/pull/1383) - Fix `--three_prime_clip_r{1,2}` parameter documentation
+- [#1390](https://github.com/nf-core/sarek/pull/1390) - Fix badges in README
+- [#1403](https://github.com/nf-core/sarek/pull/1403) - Fix intervals usage with dot in chromosome names
 
 ### Removed
 

diff --git a/README.md b/README.md
@@ -4,6 +4,7 @@
     <img alt="nf-core/sarek" src="docs/images/nf-core-sarek_logo_light.png">
   </picture>
 </h1>
+
 [![GitHub Actions CI Status](https://github.com/nf-core/sarek/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/sarek/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/nf-core/sarek/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/sarek/actions?query=workflow%3A%22nf-core+linting%22)
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/sarek/results)
@@ -40,7 +41,7 @@ Depending on the options and samples provided, the pipeline can currently perfor
 - Map Reads to Reference (`BWA-mem`, `BWA-mem2`, `dragmap` or `Sentieon BWA-mem`)
 - Process BAM file (`GATK MarkDuplicates`, `GATK BaseRecalibrator` and `GATK ApplyBQSR` or `Sentieon LocusCollector` and `Sentieon Dedup`)
 - Summarise alignment statistics (`samtools stats`, `mosdepth`)
-- Variant calling (enabled by `--tools`, see [compatibility](#which-variant-calling-tool-is-implemented-for-which-data-type)):
+- Variant calling (enabled by `--tools`, see [compatibility](https://nf-co.re/sarek/latest/docs/usage#which-variant-calling-tool-is-implemented-for-which-data-type)):
   - `ASCAT`
   - `CNVkit`
   - `Control-FREEC`

diff --git a/conf/modules/deepvariant.config b/conf/modules/deepvariant.config
@@ -17,7 +17,7 @@ process {
 
     withName: 'DEEPVARIANT' {
         ext.args   = { params.wes ?  "--model_type WES" : "--model_type WGS" }
-        ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.deepvariant" : "${meta.id}.deepvariant.${intervals.simpleName}" }
+        ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.deepvariant" : "${meta.id}.deepvariant.${intervals.baseName}" }
         ext.when   = { params.tools && params.tools.split(',').contains('deepvariant') }
         publishDir = [
             mode: params.publish_dir_mode,

diff --git a/conf/modules/freebayes.config b/conf/modules/freebayes.config
@@ -27,7 +27,7 @@ process {
     withName: 'FREEBAYES' {
         ext.args   = { '--min-alternate-fraction 0.1 --min-mapping-quality 1' }
         //To make sure no naming conflicts ensure with module BCFTOOLS_SORT & the naming being correct in the output folder
-        ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}" : "${meta.id}.${target_bed.simpleName}" }
+        ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}" : "${meta.id}.${target_bed.baseName}" }
         ext.when   = { params.tools && params.tools.split(',').contains('freebayes') }
         publishDir = [
             enabled: false

diff --git a/conf/modules/haplotypecaller.config b/conf/modules/haplotypecaller.config
@@ -17,7 +17,7 @@ process {
 
     withName: 'GATK4_HAPLOTYPECALLER' {
         ext.args   = { params.joint_germline ? "-ERC GVCF" : "" }
-        ext.prefix = { meta.num_intervals <= 1 ? ( params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" ) : ( params.joint_germline ? "${meta.id}.haplotypecaller.${intervals.simpleName}.g" :"${meta.id}.haplotypecaller.${intervals.simpleName}" ) }
+        ext.prefix = { meta.num_intervals <= 1 ? ( params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" ) : ( params.joint_germline ? "${meta.id}.haplotypecaller.${intervals.baseName}.g" :"${meta.id}.haplotypecaller.${intervals.baseName}" ) }
         ext.when   = { params.tools && params.tools.split(',').contains('haplotypecaller') }
         publishDir = [
             mode: params.publish_dir_mode,

diff --git a/conf/modules/mpileup.config b/conf/modules/mpileup.config
@@ -24,7 +24,7 @@ process {
     withName: 'BCFTOOLS_MPILEUP' {
         ext.args2  = { '--multiallelic-caller' }
         ext.args3  = { "-i 'count(GT==\"RR\")==0'" } // only report non homozygous reference variants
-        ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.bcftools" : "${meta.id}_${intervals.simpleName}.bcftools" }
+        ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.bcftools" : "${meta.id}_${intervals.baseName}.bcftools" }
         ext.when   = { params.tools && params.tools.split(',').contains('mpileup') }
         publishDir = [
             mode: params.publish_dir_mode,

diff --git a/conf/modules/mutect2.config b/conf/modules/mutect2.config
@@ -18,7 +18,7 @@ process {
 
         withName: 'GATK4_MUTECT2' {
             ext.args   = { params.ignore_soft_clipped_bases ? "--dont-use-soft-clipped-bases true --f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz" : "--f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz" }
-            ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" }
+            ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.baseName}" }
             ext.when   = { params.tools && params.tools.split(',').contains('mutect2') }
             publishDir = [
                 mode: params.publish_dir_mode,
@@ -91,7 +91,7 @@ process {
         }
 
         withName: 'GETPILEUPSUMMARIES.*' {
-            ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" }
+            ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.baseName}" }
             publishDir = [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/variant_calling/" },

diff --git a/conf/modules/recalibrate.config b/conf/modules/recalibrate.config
@@ -16,7 +16,7 @@
 process {
 
     withName: 'GATK4_APPLYBQSR|GATK4SPARK_APPLYBQSR' {
-        ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.recal" : "${meta.id}_${intervals.simpleName}.recal" }
+        ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.recal" : "${meta.id}_${intervals.baseName}.recal" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/preprocessing/" },

diff --git a/conf/modules/sentieon_dnascope.config b/conf/modules/sentieon_dnascope.config
@@ -16,7 +16,7 @@
 process {
 
     withName: 'SENTIEON_DNASCOPE' {
-        ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.dnascope" : "${meta.id}.dnascope.${intervals.simpleName}" }
+        ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.dnascope" : "${meta.id}.dnascope.${intervals.baseName}" }
         ext.when         = { params.tools && params.tools.split(',').contains('sentieon_dnascope') }
         publishDir       = [
             mode: params.publish_dir_mode,

diff --git a/conf/modules/sentieon_haplotyper.config b/conf/modules/sentieon_haplotyper.config
@@ -16,7 +16,7 @@
 process {
 
     withName: 'SENTIEON_HAPLOTYPER' {
-        ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.haplotyper" : "${meta.id}.haplotyper.${intervals.simpleName}" }
+        ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.haplotyper" : "${meta.id}.haplotyper.${intervals.baseName}" }
         ext.when         = { params.tools && params.tools.split(',').contains('sentieon_haplotyper') }
         publishDir       = [
             mode: params.publish_dir_mode,

diff --git a/conf/modules/strelka.config b/conf/modules/strelka.config
@@ -17,7 +17,7 @@ process {
 
     withName: 'STRELKA_.*' {
         ext.args   = { params.wes ? '--exome' : '' }
-        ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.strelka" : "${meta.id}.strelka.${target_bed.simpleName}" }
+        ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.strelka" : "${meta.id}.strelka.${target_bed.baseName}" }
         ext.when   = { params.tools && params.tools.split(',').contains('strelka') }
         publishDir = [
             mode: params.publish_dir_mode,

diff --git a/conf/test.config b/conf/test.config
@@ -52,6 +52,9 @@ params {
 
     // Ignore params that will throw warning through params validation
     validationSchemaIgnoreParams = 'genomes'
+
+    // Base directory for nf-core/modules test data
+    modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/'
 }
 
 process {

diff --git a/modules.json b/modules.json
@@ -391,42 +391,42 @@
                     },
                     "sentieon/applyvarcal": {
                         "branch": "master",
-                        "git_sha": "89b6873f15dd31ed17f4d10ede2fa623e2a128ff",
+                        "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
                         "installed_by": ["modules"]
                     },
                     "sentieon/bwamem": {
                         "branch": "master",
-                        "git_sha": "89b6873f15dd31ed17f4d10ede2fa623e2a128ff",
+                        "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
                         "installed_by": ["modules"]
                     },
                     "sentieon/dedup": {
                         "branch": "master",
-                        "git_sha": "89b6873f15dd31ed17f4d10ede2fa623e2a128ff",
+                        "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
                         "installed_by": ["modules"]
                     },
                     "sentieon/dnamodelapply": {
                         "branch": "master",
-                        "git_sha": "89b6873f15dd31ed17f4d10ede2fa623e2a128ff",
+                        "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
                         "installed_by": ["modules"]
                     },
                     "sentieon/dnascope": {
                         "branch": "master",
-                        "git_sha": "89b6873f15dd31ed17f4d10ede2fa623e2a128ff",
+                        "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
                         "installed_by": ["modules"]
                     },
                     "sentieon/gvcftyper": {
                         "branch": "master",
-                        "git_sha": "89b6873f15dd31ed17f4d10ede2fa623e2a128ff",
+                        "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
                         "installed_by": ["modules"]
                     },
                     "sentieon/haplotyper": {
                         "branch": "master",
-                        "git_sha": "89b6873f15dd31ed17f4d10ede2fa623e2a128ff",
+                        "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
                         "installed_by": ["modules"]
                     },
                     "sentieon/varcal": {
                         "branch": "master",
-                        "git_sha": "89b6873f15dd31ed17f4d10ede2fa623e2a128ff",
+                        "git_sha": "220da1aa7d6ab6555817035041dd2fc05cb518d3",
                         "installed_by": ["modules"]
                     },
                     "snpeff/download": {

diff --git a/modules/nf-core/sentieon/applyvarcal/main.nf b/modules/nf-core/sentieon/applyvarcal/main.nf
diff --git a/modules/nf-core/sentieon/bwamem/main.nf b/modules/nf-core/sentieon/bwamem/main.nf
diff --git a/modules/nf-core/sentieon/dedup/main.nf b/modules/nf-core/sentieon/dedup/main.nf