Merge pull request #635 from SusiJo/samtools_mosdepth

Adjust samtools and mosdepth in multiqc_report
nf-core · Jul 14, 2022 · 677b69f · 677b69f
2 parents 5949d5f + f59a114
commit 677b69f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -131,6 +131,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#618](https://github.com/nf-core/sarek/pull/618) - Fix `bcftools/vcftools` sample labelling in multiqc report
 - [#618](https://github.com/nf-core/sarek/pull/618) - Fix issue with tiddit [#621](https://github.com/nf-core/sarek/issues/621)
 - [#618](https://github.com/nf-core/sarek/pull/618) - Fix channel issue with `targets.bed` in prepare_intervals
+- [#634](https://github.com/nf-core/sarek/pull/634) - Fix issue with samtools/mosdepth plots in multiqc_report
 
 ### Deprecated
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -55,6 +55,9 @@ module_order:
 
 extra_fn_clean_exts:
   - "_val"
+  - type: regex_keep
+    pattern: "^.*.(md|recal).mosdepth.(global|region).dist"
+    module: mosdepth
 
 sp:
   snpeff:

diff --git a/conf/modules.config b/conf/modules.config
@@ -476,7 +476,7 @@ process {
 
     withName: 'MOSDEPTH' {
         ext.args = { !params.wes ? "-n --fast-mode --by 500" : ""}
-        ext.prefix       = { "${meta.id}.mapped" }
+        ext.prefix       = { "${meta.id}.md" }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reports/mosdepth/${meta.id}" },

diff --git a/subworkflows/nf-core/gatk4/markduplicates/main.nf b/subworkflows/nf-core/gatk4/markduplicates/main.nf
diff --git a/subworkflows/nf-core/gatk4/markduplicates_spark/main.nf b/subworkflows/nf-core/gatk4/markduplicates_spark/main.nf
diff --git a/tests/test_aligner.yml b/tests/test_aligner.yml
@@ -20,10 +20,10 @@
     - path: results/reference/bwamem2/genome.fasta.bwt.2bit.64
     - path: results/reference/bwamem2/genome.fasta.pac
     - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
@@ -55,10 +55,10 @@
     - path: results/reference/dragmap/repeat_mask.bin
     - path: results/reference/dragmap/str_table.bin
     - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt

diff --git a/tests/test_default.yml b/tests/test_default.yml
@@ -15,10 +15,10 @@
     - path: results/csv/recalibrated.csv
     - path: results/reports/fastqc/test-test_L1
     - path: results/reports/markduplicates/test/test.md.metrics
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
@@ -44,10 +44,10 @@
     - path: results/csv/recalibrated.csv
     - path: results/reports/fastqc/test-test_L1
     - path: results/reports/markduplicates/test/test.md.metrics
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
@@ -72,10 +72,10 @@
     - path: results/csv/recalibrated.csv
     - path: results/reports/fastqc/test-test_L1
     - path: results/reports/markduplicates/test/test.md.metrics
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt

diff --git a/tests/test_gatk_spark.yml b/tests/test_gatk_spark.yml
@@ -16,10 +16,10 @@
     - path: results/csv/recalibrated.csv
     - path: results/reports/fastqc/test-test_L1
     - path: results/reports/markduplicates/test/test.md.metrics
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt

diff --git a/tests/test_markduplicates.yml b/tests/test_markduplicates.yml
@@ -14,10 +14,10 @@
     - path: results/csv/markduplicates.csv
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
@@ -45,10 +45,10 @@
     - path: results/csv/markduplicates.csv
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt

diff --git a/tests/test_pair.yml b/tests/test_pair.yml
@@ -22,18 +22,18 @@
     - path: results/reports/fastqc/test2-test_L1
     - path: results/reports/markduplicates/test/test.md.metrics
     - path: results/reports/markduplicates/test2/test2.md.metrics
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
-    - path: results/reports/mosdepth/test2/test2.mapped.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test2/test2.mapped.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test2/test2.mapped.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test2/test2.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz
     - path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt
     - path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt

diff --git a/tests/test_save_bam_mapped.yml b/tests/test_save_bam_mapped.yml
@@ -17,10 +17,10 @@
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
     - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt

diff --git a/tests/test_save_output_bam.yml b/tests/test_save_output_bam.yml
@@ -14,10 +14,10 @@
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
     - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
@@ -41,10 +41,10 @@
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
     - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt

diff --git a/tests/test_skip_markduplicates.yml b/tests/test_skip_markduplicates.yml
@@ -16,10 +16,10 @@
     - path: results/csv/markduplicates_no_table.csv # TODO These are no actually duplicate marked crams, but just mapped converted crams TODO renaming
     - path: results/csv/recalibrated.csv
     - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
@@ -47,10 +47,10 @@
     - path: results/csv/recalibrated.csv
     - path: results/csv/markduplicates.csv
     - path: results/csv/markduplicates_no_table.csv # TODO These are no actually duplicate marked crams, but just mapped converted crams TODO renaming
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
@@ -82,10 +82,10 @@
       should_exist: false
     - path: results/csv/markduplicates_no_table.csv
       should_exist: false
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt

diff --git a/tests/test_targeted.yml b/tests/test_targeted.yml
@@ -15,10 +15,10 @@
     - path: results/csv/recalibrated.csv
     - path: results/reports/fastqc/test-test_L1
     - path: results/reports/markduplicates/test/test.md.metrics
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt

diff --git a/tests/test_trimming.yml b/tests/test_trimming.yml
@@ -17,10 +17,10 @@
     - path: results/csv/recalibrated.csv
     - path: results/reports/fastqc/test-test_L1
     - path: results/reports/markduplicates/test/test.md.metrics
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
-    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt