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Merged
maxulysse merged 4 commits into from
Jul 14, 2022
Merged

Adjust samtools and mosdepth in multiqc_report #635

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72ac6b6
make samtools/mosdepth work in multiqc
SusiJo Jul 14, 2022
62a7514
add changelog + ran prettier
SusiJo Jul 14, 2022
6187aa6
fix default test
SusiJo Jul 14, 2022
f59a114
fix other ymls due to new mosdepth name
SusiJo Jul 14, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -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

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3 changes: 3 additions & 0 deletions assets/multiqc_config.yml
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion conf/modules.config
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Expand Up @@ -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}" },
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3 changes: 2 additions & 1 deletion subworkflows/nf-core/gatk4/markduplicates/main.nf
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3 changes: 2 additions & 1 deletion subworkflows/nf-core/gatk4/markduplicates_spark/main.nf
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16 changes: 8 additions & 8 deletions tests/test_aligner.yml
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Expand Up @@ -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
Expand Down Expand Up @@ -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
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24 changes: 12 additions & 12 deletions tests/test_default.yml
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Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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
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8 changes: 4 additions & 4 deletions tests/test_gatk_spark.yml
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Expand Up @@ -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
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16 changes: 8 additions & 8 deletions tests/test_markduplicates.yml
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Expand Up @@ -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
Expand Down Expand Up @@ -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
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16 changes: 8 additions & 8 deletions tests/test_pair.yml
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Expand Up @@ -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
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8 changes: 4 additions & 4 deletions tests/test_save_bam_mapped.yml
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Expand Up @@ -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
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16 changes: 8 additions & 8 deletions tests/test_save_output_bam.yml
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Expand Up @@ -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
Expand All @@ -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
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24 changes: 12 additions & 12 deletions tests/test_skip_markduplicates.yml
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
8 changes: 4 additions & 4 deletions tests/test_targeted.yml
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Expand Up @@ -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
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8 changes: 4 additions & 4 deletions tests/test_trimming.yml
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Expand Up @@ -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
Expand Down
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