mosdept: cram compatiblility

modules/mosdepth/main.nf

@@ -10,13 +10,13 @@ process MOSDEPTH {
     input:
     tuple val(meta), path(bam), path(bai)
     path  bed
-    val   window_size
+    path  fasta
 
     output:
     tuple val(meta), path('*.global.dist.txt')    , emit: global_txt
     tuple val(meta), path('*.region.dist.txt')    , emit: regions_txt , optional:true
     tuple val(meta), path('*.summary.txt')        , emit: summary_txt
-    tuple val(meta), path('*.per-base.d4')        , emit: d4          , optional:true
+    tuple val(meta), path('*.per-base.d4')        , emit: per_base_d4 , optional:true
     tuple val(meta), path('*.per-base.bed.gz')    , emit: per_base_bed, optional:true
     tuple val(meta), path('*.per-base.bed.gz.csi'), emit: per_base_csi, optional:true
     tuple val(meta), path('*.regions.bed.gz')     , emit: regions_bed , optional:true
@@ -29,36 +29,17 @@ process MOSDEPTH {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    if (window_size) {
+    def reference = fasta ? "--fasta ${fasta}" : ""
-        interval = "--by ${window_size}"
+    def interval = bed ? "--by ${bed}" : ""
-    } else if ( bed ) {
+
-        interval = "--by ${bed}"
-    } else {
-        interval = ""
-    }
     """
     mosdepth \\
+        --threads ${task.cpus} \\
         $interval \\
+        $reference \\
         $args \\
         $prefix \\
         $bam
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//')
-    END_VERSIONS
-    """
-
-    stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    """
-    touch ${prefix}.global.dist.txt
-    touch ${prefix}.region.dist.txt
-    touch ${prefix}.summary.txt
-    touch ${prefix}.per-base.d4
-    touch ${prefix}.per-base.bed.gz
-    touch ${prefix}.per-base.bed.gz.csi
-    touch ${prefix}.regions.bed.gz
-    touch ${prefix}.regions.bed.gz.csi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/mosdepth/meta.yml

@@ -30,10 +30,10 @@ input:
       type: file
       description: BED file with intersected intervals
       pattern: "*.{bed}"
-  - window_size:
+  - fasta:
-      type: integer
+      type: file
-      description: Window size
+      description: Reference genome FASTA file
-      pattern: "[0-9]+"
+      pattern: "*.{fa,fasta}"
 output:
   - meta:
       type: map
@@ -60,6 +60,10 @@ output:
       type: file
       description: Index file for BED file with per-base coverage
       pattern: "*.{per-base.bed.gz.csi}"
+  - per_base_d4:
+      type: file
+      description: D4 file with per-base coverage
+      pattern: "*.{per-base.d4}"
   - regions_bed:
       type: file
       description: BED file with per-region coverage
@@ -76,3 +80,4 @@ authors:
   - "@joseespinosa"
   - "@drpatelh"
   - "@ramprasadn"
+  - "@matthdsm"

tests/modules/mosdepth/main.nf

@@ -5,32 +5,45 @@ nextflow.enable.dsl = 2
 include { MOSDEPTH } from '../../../modules/mosdepth/main.nf'
 
 workflow test_mosdepth {
-    input  = [ [ id:'test', single_end:true ],
+    input  = [
-               [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
+                [ id:'test', single_end:true ],
-               [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
+                [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
-             ]
+                [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
+            ]
 
     MOSDEPTH ( input, [], [] )
 }
 
-
-workflow test_mosdepth_window {
-    input  = [ [ id:'test', single_end:true ],
-               [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
-               [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
-             ]
-    window = 100
-
-    MOSDEPTH ( input, [], window )
-}
-
-
 workflow test_mosdepth_bed {
-    input  = [ [ id:'test', single_end:true ],
+    input  = [
-               [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
+                [ id:'test', single_end:true ],
-               [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
+                [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
-             ]
+                [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
-    bed  = [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
+            ]
+    bed  = [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ]
 
     MOSDEPTH ( input, bed, [] )
 }
+
+workflow test_mosdepth_cram {
+    input  = [
+                [ id:'test', single_end:true ],
+                [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ],
+                [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) ]
+            ]
+    fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    MOSDEPTH ( input, [], fasta )
+}
+
+workflow test_mosdepth_cram_bed {
+    input  = [
+                [ id:'test', single_end:true ],
+                [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ],
+                [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) ]
+            ]
+    bed  = [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ]
+    fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    MOSDEPTH ( input, bed, fasta )
+}

tests/modules/mosdepth/test.yml

@@ -1,53 +1,67 @@
-- name: mosdepth
+- name: mosdepth test_mosdepth
-  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config
+  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth -c ./tests/config/nextflow.config  -c ./tests/modules/mosdepth/nextflow.config
   tags:
     - mosdepth
   files:
-    - path: ./output/mosdepth/test.per-base.bed.gz.csi
+    - path: output/mosdepth/test.mosdepth.global.dist.txt
-      md5sum: b2aad62c41a7146680d31df505fcc8c5
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
-    - path: ./output/mosdepth/test.per-base.bed.gz
+    - path: output/mosdepth/test.mosdepth.summary.txt
-      md5sum: 11b3f649072c2c7453febb085b1a9c33
+      md5sum: 4f0d231060cbde4efdd673863bd2fb59
-    - path: ./output/mosdepth/test.mosdepth.global.dist.txt
+    - path: output/mosdepth/test.per-base.bed.gz
-      md5sum: 2a1de1b0ecc361a21cd296ec4e1efd6a
+      md5sum: bc1df47d46f818fee5275975925d769a
-    - path: ./output/mosdepth/test.mosdepth.summary.txt
+    - path: output/mosdepth/test.per-base.bed.gz.csi
-      md5sum: 7b249dd3b3e58cc122fbd25ea84aa25d
+      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
 
-- name: mosdepth window
+- name: mosdepth test_mosdepth_bed
-  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_window -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config
+  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_bed -c ./tests/config/nextflow.config  -c ./tests/modules/mosdepth/nextflow.config
   tags:
     - mosdepth
   files:
-    - path: ./output/mosdepth/test.per-base.bed.gz.csi
+    - path: output/mosdepth/test.mosdepth.global.dist.txt
-      md5sum: b2aad62c41a7146680d31df505fcc8c5
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
-    - path: ./output/mosdepth/test.per-base.bed.gz
+    - path: output/mosdepth/test.mosdepth.region.dist.txt
-      md5sum: 11b3f649072c2c7453febb085b1a9c33
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
-    - path: ./output/mosdepth/test.mosdepth.global.dist.txt
+    - path: output/mosdepth/test.mosdepth.summary.txt
-      md5sum: 2a1de1b0ecc361a21cd296ec4e1efd6a
+      md5sum: 96c037f769974b904beb53edc4f56d82
-    - path: ./output/mosdepth/test.regions.bed.gz
+    - path: output/mosdepth/test.per-base.bed.gz
-      md5sum: 64e1ced01c4443d7c1796ef553992f0c
+      md5sum: bc1df47d46f818fee5275975925d769a
-    - path: ./output/mosdepth/test.regions.bed.gz.csi
+    - path: output/mosdepth/test.per-base.bed.gz.csi
-      md5sum: 9e312b4b0784bd46dfbd23b3a8afed6a
+      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
-    - path: ./output/mosdepth/test.mosdepth.region.dist.txt
+    - path: output/mosdepth/test.regions.bed.gz
-      md5sum: 65fbc824c4212c6884354d8ac72ad37e
+      md5sum: 5d398caf7171ec4406278e2add3009ae
-    - path: ./output/mosdepth/test.mosdepth.summary.txt
+    - path: output/mosdepth/test.regions.bed.gz.csi
-      md5sum: 11804907dab069ddb99ca97bf2698572
+      md5sum: 47669cfe41f3e222e74d81e1b1be191f
 
-- name: mosdepth bed
+- name: mosdepth test_mosdepth_cram
-  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_bed -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config
+  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_cram -c ./tests/config/nextflow.config  -c ./tests/modules/mosdepth/nextflow.config
   tags:
     - mosdepth
   files:
-    - path: ./output/mosdepth/test.per-base.bed.gz.csi
+    - path: output/mosdepth/test.mosdepth.global.dist.txt
-      md5sum: b2aad62c41a7146680d31df505fcc8c5
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
-    - path: ./output/mosdepth/test.per-base.bed.gz
+    - path: output/mosdepth/test.mosdepth.summary.txt
-      md5sum: 11b3f649072c2c7453febb085b1a9c33
+      md5sum: 4f0d231060cbde4efdd673863bd2fb59
-    - path: ./output/mosdepth/test.mosdepth.global.dist.txt
+    - path: output/mosdepth/test.per-base.bed.gz
-      md5sum: 2a1de1b0ecc361a21cd296ec4e1efd6a
+      md5sum: bc1df47d46f818fee5275975925d769a
-    - path: ./output/mosdepth/test.regions.bed.gz
+    - path: output/mosdepth/test.per-base.bed.gz.csi
-      md5sum: 347f877700d1dc42c95157199eff25d5
+      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
-    - path: ./output/mosdepth/test.regions.bed.gz.csi
+
-      md5sum: ed5fbf46e3bdcbf60094df295bc40356
+- name: mosdepth test_mosdepth_cram_bed
-    - path: ./output/mosdepth/test.mosdepth.region.dist.txt
+  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_cram_bed -c ./tests/config/nextflow.config  -c ./tests/modules/mosdepth/nextflow.config
-      md5sum: 295564628113d2ec0ca34d7f661cfea8
+  tags:
-    - path: ./output/mosdepth/test.mosdepth.summary.txt
+    - mosdepth
-      md5sum: b07817412fd17819c14541e63bc4926c
+  files:
+    - path: output/mosdepth/test.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: output/mosdepth/test.mosdepth.region.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: output/mosdepth/test.mosdepth.summary.txt
+      md5sum: 96c037f769974b904beb53edc4f56d82
+    - path: output/mosdepth/test.per-base.bed.gz
+      md5sum: bc1df47d46f818fee5275975925d769a
+    - path: output/mosdepth/test.per-base.bed.gz.csi
+      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
+    - path: output/mosdepth/test.regions.bed.gz
+      md5sum: 5d398caf7171ec4406278e2add3009ae
+    - path: output/mosdepth/test.regions.bed.gz.csi
+      md5sum: 47669cfe41f3e222e74d81e1b1be191f