Merge branch 'master' into rhocall

modules/cnvkit/reference/main.nf

@@ -1,5 +1,5 @@
 process CNVKIT_REFERENCE {
-    tag "$reference"
+    tag "$fasta"
     label 'process_low'
 
     conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null)
@@ -8,19 +8,20 @@ process CNVKIT_REFERENCE {
         'quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
 
     input:
-    path    fasta
-    path    targets
-    path    antitargets
+    path fasta
+    path targets
+    path antitargets
 
     output:
-    path("*.cnn")                 , emit: cnn
-    path "versions.yml"           , emit: versions
+    path "*.cnn"       , emit: cnn
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: targets.BaseName
 
     """
     cnvkit.py \\
@@ -28,7 +29,7 @@ process CNVKIT_REFERENCE {
         --fasta $fasta \\
         --targets $targets \\
         --antitargets $antitargets \\
-        --output reference.cnn \\
+        --output ${prefix}.reference.cnn \\
         $args
 
     cat <<-END_VERSIONS > versions.yml

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
@@ -29,19 +29,21 @@ process MOSDEPTH {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    if (window_size) {
-        interval = "--by ${window_size}"
-    } else if ( bed ) {
-        interval = "--by ${bed}"
-    } else {
-        interval = ""
+    def reference = fasta ? "--fasta ${fasta}" : ""
+    def interval = bed ? "--by ${bed}" : ""
+    if (bed && args.contains("--by")) {
+        exit 1, "'--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition"
     }
+
     """
     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/ .*\$//')

modules/mosdepth/meta.yml

@@ -30,10 +30,10 @@ input:
       type: file
       description: BED file with intersected intervals
       pattern: "*.{bed}"
-  - window_size:
-      type: integer
-      description: Window size
-      pattern: "[0-9]+"
+  - fasta:
+      type: file
+      description: Reference genome FASTA file
+      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"

modules/umitools/dedup/main.nf

@@ -9,12 +9,13 @@ process UMITOOLS_DEDUP {
 
     input:
     tuple val(meta), path(bam), path(bai)
+    val get_output_stats
 
     output:
     tuple val(meta), path("*.bam")             , emit: bam
-    tuple val(meta), path("*edit_distance.tsv"), emit: tsv_edit_distance
-    tuple val(meta), path("*per_umi.tsv")      , emit: tsv_per_umi
-    tuple val(meta), path("*per_position.tsv") , emit: tsv_umi_per_position
+    tuple val(meta), path("*edit_distance.tsv"), optional:true, emit: tsv_edit_distance
+    tuple val(meta), path("*per_umi.tsv")      , optional:true, emit: tsv_per_umi
+    tuple val(meta), path("*per_position.tsv") , optional:true, emit: tsv_umi_per_position
     path  "versions.yml"                       , emit: versions
 
     when:
@@ -24,12 +25,13 @@ process UMITOOLS_DEDUP {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def paired = meta.single_end ? "" : "--paired"
+    def stats = get_output_stats ? "--output-stats $prefix" : ""
     """
     umi_tools \\
         dedup \\
         -I $bam \\
         -S ${prefix}.bam \\
-        --output-stats $prefix \\
+        $stats \\
         $paired \\
         $args
 

modules/umitools/dedup/meta.yml

@@ -26,6 +26,10 @@ input:
     description: |
       BAM index files corresponding to the input BAM file.
     pattern: "*.{bai}"
+  - get_output_stats:
+    type: boolean
+    description: |
+      Whether or not to generate output stats.
 output:
   - meta:
     type: map

tests/modules/cnvkit/reference/test.yml

@@ -4,5 +4,5 @@
     - cnvkit/reference
     - cnvkit
   files:
-    - path: output/cnvkit/reference.cnn
+    - path: output/cnvkit/multi_intervals.reference.cnn
       md5sum: 7c4a7902f5ab101b1f9d6038d331b3d9

tests/modules/mosdepth/main.nf

@@ -2,35 +2,72 @@
 
 nextflow.enable.dsl = 2
 
-include { MOSDEPTH } from '../../../modules/mosdepth/main.nf'
+include { MOSDEPTH                    } from '../../../modules/mosdepth/main.nf'
+include { MOSDEPTH as MOSDEPTH_FAIL   } from '../../../modules/mosdepth/main.nf'
+include { MOSDEPTH as MOSDEPTH_WINDOW } from '../../../modules/mosdepth/main.nf'
 
 workflow test_mosdepth {
-    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) ]
-             ]
+    input  = [
+                [ id:'test', single_end: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 ],
-               [ 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) ]
-             ]
-    bed  = [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
+    input  = [
+                [ id:'test', single_end: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['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 )
+}
+
+workflow test_mosdepth_window {
+    input  = [
+                [ id:'test', single_end: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['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ]
+
+    MOSDEPTH_WINDOW ( input, [], [] )
+}
+
+workflow test_mosdepth_fail {
+    input  = [
+                [ id:'test', single_end: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['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ]
+
+    MOSDEPTH_FAIL ( input, bed, [] )
+}

tests/modules/mosdepth/nextflow.config

@@ -1,5 +1,10 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
+    withName: MOSDEPTH_FAIL {
+        ext.args = "--by 100"
+    }
+    withName: MOSDEPTH_WINDOW {
+        ext.args = "--by 100"
+    }
 }

tests/modules/mosdepth/test.yml

@@ -1,53 +1,93 @@
-- name: mosdepth
-  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config
+- name: mosdepth test_mosdepth
+  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
-      md5sum: b2aad62c41a7146680d31df505fcc8c5
-    - path: ./output/mosdepth/test.per-base.bed.gz
-      md5sum: 11b3f649072c2c7453febb085b1a9c33
-    - path: ./output/mosdepth/test.mosdepth.global.dist.txt
-      md5sum: 2a1de1b0ecc361a21cd296ec4e1efd6a
-    - path: ./output/mosdepth/test.mosdepth.summary.txt
-      md5sum: 7b249dd3b3e58cc122fbd25ea84aa25d
+    - path: output/mosdepth/test.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: output/mosdepth/test.mosdepth.summary.txt
+      md5sum: 4f0d231060cbde4efdd673863bd2fb59
+    - path: output/mosdepth/test.per-base.bed.gz
+      md5sum: bc1df47d46f818fee5275975925d769a
+    - path: output/mosdepth/test.per-base.bed.gz.csi
+      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
 
-- name: mosdepth window
-  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_window -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config
+- name: mosdepth test_mosdepth_bed
+  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
-      md5sum: b2aad62c41a7146680d31df505fcc8c5
-    - path: ./output/mosdepth/test.per-base.bed.gz
-      md5sum: 11b3f649072c2c7453febb085b1a9c33
-    - path: ./output/mosdepth/test.mosdepth.global.dist.txt
-      md5sum: 2a1de1b0ecc361a21cd296ec4e1efd6a
-    - path: ./output/mosdepth/test.regions.bed.gz
-      md5sum: 64e1ced01c4443d7c1796ef553992f0c
-    - path: ./output/mosdepth/test.regions.bed.gz.csi
-      md5sum: 9e312b4b0784bd46dfbd23b3a8afed6a
-    - path: ./output/mosdepth/test.mosdepth.region.dist.txt
-      md5sum: 65fbc824c4212c6884354d8ac72ad37e
-    - path: ./output/mosdepth/test.mosdepth.summary.txt
-      md5sum: 11804907dab069ddb99ca97bf2698572
+    - 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
 
-- name: mosdepth bed
-  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_bed -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config
+- name: mosdepth test_mosdepth_cram
+  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
-      md5sum: b2aad62c41a7146680d31df505fcc8c5
-    - path: ./output/mosdepth/test.per-base.bed.gz
-      md5sum: 11b3f649072c2c7453febb085b1a9c33
-    - path: ./output/mosdepth/test.mosdepth.global.dist.txt
-      md5sum: 2a1de1b0ecc361a21cd296ec4e1efd6a
-    - path: ./output/mosdepth/test.regions.bed.gz
-      md5sum: 347f877700d1dc42c95157199eff25d5
-    - path: ./output/mosdepth/test.regions.bed.gz.csi
-      md5sum: ed5fbf46e3bdcbf60094df295bc40356
-    - path: ./output/mosdepth/test.mosdepth.region.dist.txt
-      md5sum: 295564628113d2ec0ca34d7f661cfea8
-    - path: ./output/mosdepth/test.mosdepth.summary.txt
-      md5sum: b07817412fd17819c14541e63bc4926c
+    - path: output/mosdepth/test.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: output/mosdepth/test.mosdepth.summary.txt
+      md5sum: 4f0d231060cbde4efdd673863bd2fb59
+    - path: output/mosdepth/test.per-base.bed.gz
+      md5sum: bc1df47d46f818fee5275975925d769a
+    - path: output/mosdepth/test.per-base.bed.gz.csi
+      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
+
+- name: mosdepth test_mosdepth_cram_bed
+  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_cram_bed -c ./tests/config/nextflow.config  -c ./tests/modules/mosdepth/nextflow.config
+  tags:
+    - mosdepth
+  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
+
+- name: mosdepth test_mosdepth_window
+  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_window -c ./tests/config/nextflow.config  -c ./tests/modules/mosdepth/nextflow.config
+  tags:
+    - mosdepth
+  files:
+    - path: output/mosdepth/test.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: output/mosdepth/test.mosdepth.region.dist.txt
+      md5sum: 39e0e707ec32feb5176fd20a95f1f468
+    - 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: f02e2cb49cc050e13d76942d6960827a
+    - path: output/mosdepth/test.regions.bed.gz.csi
+      md5sum: 257d67678136963d9dd904330079609d
+
+- name: mosdepth test_mosdepth_fail
+  command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_fail -c ./tests/config/nextflow.config  -c ./tests/modules/mosdepth/nextflow.config
+  tags:
+    - mosdepth
+  exit_code: 1

tests/modules/umitools/dedup/main.nf

@@ -3,54 +3,81 @@
 nextflow.enable.dsl = 2
 
 include { UMITOOLS_EXTRACT } from '../../../../modules/umitools/extract/main.nf'
-include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf'
-include { BWA_MEM   } from '../../../../modules/bwa/mem/main.nf'
+include { BWA_INDEX        } from '../../../../modules/bwa/index/main.nf'
+include { BWA_MEM          } from '../../../../modules/bwa/mem/main.nf'
 include { SAMTOOLS_INDEX   } from '../../../../modules/samtools/index/main.nf'
-include { UMITOOLS_DEDUP } from '../../../../modules/umitools/dedup/main.nf'
+include { UMITOOLS_DEDUP   } from '../../../../modules/umitools/dedup/main.nf'
 
 //
 // Test with no UMI
 //
 workflow test_umitools_dedup_no_umi {
-    input = [ [ id:'test'], // meta map
-              [ 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) ]
-            ]
+    input = [ 
+        [ id:'test'], // meta map
+        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)
+    ]
+    get_output_stats = false
 
-    UMITOOLS_DEDUP ( input )
+    UMITOOLS_DEDUP ( input, get_output_stats )
 }
 
 //
-// Test with single-end data
+// Test with single-end data without --output-stats
 //
-workflow test_umitools_dedup_single_end {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-
+workflow test_umitools_dedup_single_end_no_stats {
+    input = [ 
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    get_output_stats = false
 
     UMITOOLS_EXTRACT ( input )
     BWA_INDEX ( fasta )
     BWA_MEM ( UMITOOLS_EXTRACT.out.reads, BWA_INDEX.out.index, true )
-    SAMTOOLS_INDEX (BWA_MEM.out.bam)
-    UMITOOLS_DEDUP(BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]))
+    SAMTOOLS_INDEX ( BWA_MEM.out.bam )
+    UMITOOLS_DEDUP ( BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]), get_output_stats )
 }
 
 //
-// Test with paired-end data
+// Test with paired-end data without --output-stats
 //
-workflow test_umitools_dedup_paired_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-
+workflow test_umitools_dedup_paired_end_no_stats {
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        [ 
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) 
+        ]
+    ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    get_output_stats = false
 
     UMITOOLS_EXTRACT ( input )
     BWA_INDEX ( fasta )
     BWA_MEM ( UMITOOLS_EXTRACT.out.reads, BWA_INDEX.out.index, true )
-    SAMTOOLS_INDEX (BWA_MEM.out.bam)
-    UMITOOLS_DEDUP(BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]))
+    SAMTOOLS_INDEX ( BWA_MEM.out.bam )
+    UMITOOLS_DEDUP ( BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]), get_output_stats )
+}
+
+//
+// Test with paired-end data with --output-stats
+//
+workflow test_umitools_dedup_paired_end_stats {
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        [ 
+            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) 
+        ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    get_output_stats = true
+
+    UMITOOLS_EXTRACT ( input )
+    BWA_INDEX ( fasta )
+    BWA_MEM ( UMITOOLS_EXTRACT.out.reads, BWA_INDEX.out.index, true )
+    SAMTOOLS_INDEX ( BWA_MEM.out.bam )
+    UMITOOLS_DEDUP ( BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]), get_output_stats )
 }

tests/modules/umitools/dedup/nextflow.config

@@ -7,11 +7,7 @@ process {
     }
 
     withName: UMITOOLS_DEDUP {
-        ext.args = ''
-        ext.prefix = 'dedup'
+        ext.prefix = { "${meta.id}.dedup" }
     }
 
-    withName: BWA_MEM {
-        ext.args2 = ''
-    }
 }

tests/modules/umitools/dedup/test.yml

@@ -1,54 +1,87 @@
 - name: umitools dedup test_umitools_dedup_no_umi
-  command: nextflow run tests/modules/umitools/dedup -entry test_umitools_dedup_no_umi -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/umitools/dedup -entry test_umitools_dedup_no_umi -c ./tests/config/nextflow.config  -c ./tests/modules/umitools/dedup/nextflow.config
   tags:
     - umitools/dedup
     - umitools
   files:
-    - path: output/umitools/dedup.bam
-      md5sum: 53b4edc399db81b87d2343e78af73cf0
-    - path: output/umitools/dedup_edit_distance.tsv
-      md5sum: 65186b0964e2f8d970cc04d736d8b119
-    - path: output/umitools/dedup_per_umi.tsv
-      md5sum: 8e6783a4a79437b095f095f2aefe7c01
-    - path: output/umitools/dedup_per_umi_per_position.tsv
-      md5sum: 9386db4a104b8e4e32f3ca4a84efa4ac
-    - path: output/umitools/versions.yml
-      md5sum: 4aaaa33565bcd9a984255139933d6446
+    - path: output/umitools/test.dedup.bam
 
-- name: umitools dedup test_umitools_dedup_single_end
-  command: nextflow run tests/modules/umitools/dedup -entry test_umitools_dedup_single_end -c tests/config/nextflow.config
+- name: umitools dedup test_umitools_dedup_single_end_no_stats
+  command: nextflow run ./tests/modules/umitools/dedup -entry test_umitools_dedup_single_end_no_stats -c ./tests/config/nextflow.config  -c ./tests/modules/umitools/dedup/nextflow.config
   tags:
-    - umitools
     - umitools/dedup
+    - umitools
   files:
+    - path: output/bwa/bwa/genome.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/bwa/bwa/genome.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/bwa/bwa/genome.bwt
+      md5sum: 0469c30a1e239dd08f68afe66fde99da
+    - path: output/bwa/bwa/genome.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/bwa/bwa/genome.sa
+      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
     - path: output/bwa/test.bam
-      md5sum: ea41a3cdca1856b22845e1067fd31f37
-    - path: output/bwa/versions.yml
-      md5sum: ce4d987f2c53f4c01b31d210c357b24a
+      md5sum: 3ecbe569cadb9b6c881917ce60779f75
     - path: output/samtools/test.bam.bai
       md5sum: 095af0ad3921212597ffd7c342ecd5a0
-    - path: output/samtools/versions.yml
-      md5sum: 69b7cde627c9b4e8403dfc125db71cc7
-    - path: output/umitools/dedup.bam
-      md5sum: d95df177063432748ff33f473910cb1e
-    - path: output/umitools/versions.yml
-      md5sum: 730e768dd199d2f5bfb6fd0850446344
+    - path: output/umitools/test.dedup.bam
+    - path: output/umitools/test.umi_extract.fastq.gz
+    - path: output/umitools/test.umi_extract.log
 
-- name: umitools dedup test_umitools_dedup_paired_end
-  command: nextflow run tests/modules/umitools/dedup -entry test_umitools_dedup_paired_end -c tests/config/nextflow.config
+- name: umitools dedup test_umitools_dedup_paired_end_no_stats
+  command: nextflow run ./tests/modules/umitools/dedup -entry test_umitools_dedup_paired_end_no_stats -c ./tests/config/nextflow.config  -c ./tests/modules/umitools/dedup/nextflow.config
   tags:
-    - umitools
     - umitools/dedup
+    - umitools
   files:
+    - path: output/bwa/bwa/genome.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/bwa/bwa/genome.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/bwa/bwa/genome.bwt
+      md5sum: 0469c30a1e239dd08f68afe66fde99da
+    - path: output/bwa/bwa/genome.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/bwa/bwa/genome.sa
+      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
     - path: output/bwa/test.bam
-      md5sum: 1ad786cae0ff2254c655e3a206929617
-    - path: output/bwa/versions.yml
-      md5sum: b524c5ddf61c20f4a0a93ae8fc78b851
+      md5sum: e7dcbac1825bf210409b762dbb4fec8f
     - path: output/samtools/test.bam.bai
-      md5sum: 7496f4056a8e86327ca93e350f282fc2
-    - path: output/samtools/versions.yml
-      md5sum: 72fc2ab934fd4bca0f7f14a705530d34
-    - path: output/umitools/dedup.bam
-      md5sum: e8d1eae2aacef76254948c5568e94555
-    - path: output/umitools/versions.yml
-      md5sum: fd39e05042d354b3d8de49b617d3183d
+      md5sum: f75780d1de7860329b7fb4afeadc4bed
+    - path: output/umitools/test.dedup.bam
+    - path: output/umitools/test.umi_extract.log
+    - path: output/umitools/test.umi_extract_1.fastq.gz
+    - path: output/umitools/test.umi_extract_2.fastq.gz
+
+- name: umitools dedup test_umitools_dedup_paired_end_stats
+  command: nextflow run ./tests/modules/umitools/dedup -entry test_umitools_dedup_paired_end_stats -c ./tests/config/nextflow.config  -c ./tests/modules/umitools/dedup/nextflow.config
+  tags:
+    - umitools/dedup
+    - umitools
+  files:
+    - path: output/bwa/bwa/genome.amb
+      md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
+    - path: output/bwa/bwa/genome.ann
+      md5sum: c32e11f6c859f166c7525a9c1d583567
+    - path: output/bwa/bwa/genome.bwt
+      md5sum: 0469c30a1e239dd08f68afe66fde99da
+    - path: output/bwa/bwa/genome.pac
+      md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
+    - path: output/bwa/bwa/genome.sa
+      md5sum: ab3952cabf026b48cd3eb5bccbb636d1
+    - path: output/bwa/test.bam
+      md5sum: e7dcbac1825bf210409b762dbb4fec8f
+    - path: output/samtools/test.bam.bai
+      md5sum: f75780d1de7860329b7fb4afeadc4bed
+    - path: output/umitools/test.dedup.bam
+    - path: output/umitools/test.dedup_edit_distance.tsv
+      md5sum: c247a49b58768e6e2e86a6c08483e612
+    - path: output/umitools/test.dedup_per_umi.tsv
+      md5sum: 10e35ca37f2bfb521ac6dd7314951a68
+    - path: output/umitools/test.dedup_per_umi_per_position.tsv
+      md5sum: 2e1a12e6f720510880068deddeefe063
+    - path: output/umitools/test.umi_extract.log
+    - path: output/umitools/test.umi_extract_1.fastq.gz
+    - path: output/umitools/test.umi_extract_2.fastq.gz