From 45acc79667b58b5888cdea7327e76c728e94d6df Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Wed, 9 Feb 2022 13:45:55 +0100
Subject: [PATCH] Update mosdepth (#1256)

* nf-core create

* svdb merge module and test

* remove to-do from test.yml

* version

* update meta.yml

* mosdepth update

* update md5sums

* add stub

* add stub

* remove svdb

* remove merge

* Add tests

* code linting fix

* undo previous commit

* revert code linting fix
---
 modules/mosdepth/main.nf        | 43 ++++++++++++++++++++++++++-------
 modules/mosdepth/meta.yml       |  1 +
 tests/modules/mosdepth/main.nf  | 26 +++++++++++++++++---
 tests/modules/mosdepth/test.yml | 42 +++++++++++++++++++++++++++++---
 4 files changed, 96 insertions(+), 16 deletions(-)

diff --git a/modules/mosdepth/main.nf b/modules/mosdepth/main.nf
index cc7bc86b..ff91e06f 100644
--- a/modules/mosdepth/main.nf
+++ b/modules/mosdepth/main.nf
@@ -2,10 +2,10 @@ process MOSDEPTH {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::mosdepth=0.3.2' : null)
+    conda (params.enable_conda ? 'bioconda::mosdepth=0.3.3' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mosdepth:0.3.2--h01d7912_0' :
-        'quay.io/biocontainers/mosdepth:0.3.2--h01d7912_0' }"
+        'https://depot.galaxyproject.org/singularity/mosdepth:0.3.3--hdfd78af_1' :
+        'quay.io/biocontainers/mosdepth:0.3.3--hdfd78af_1'}"
 
     input:
     tuple val(meta), path(bam), path(bai)
@@ -14,12 +14,13 @@ process MOSDEPTH {
 
     output:
     tuple val(meta), path('*.global.dist.txt')    , emit: global_txt
-    tuple val(meta), path('*.region.dist.txt')    , emit: regions_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.bed.gz')    , emit: per_base_bed
-    tuple val(meta), path('*.per-base.bed.gz.csi'), emit: per_base_csi
-    tuple val(meta), path('*.regions.bed.gz')     , emit: regions_bed
-    tuple val(meta), path('*.regions.bed.gz.csi') , emit: regions_csi
+    tuple val(meta), path('*.per-base.d4')        , emit: 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
+    tuple val(meta), path('*.regions.bed.gz.csi') , emit: regions_csi , optional:true
     path  "versions.yml"                          , emit: versions
 
     when:
@@ -28,7 +29,13 @@ process MOSDEPTH {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def interval = window_size ? "--by ${window_size}" : "--by ${bed}"
+    if (window_size) {
+        interval = "--by ${window_size}"
+    } else if ( bed ) {
+        interval = "--by ${bed}"
+    } else {
+        interval = ""
+    }
     """
     mosdepth \\
         $interval \\
@@ -40,4 +47,22 @@ process MOSDEPTH {
         mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${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}":
+        mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/mosdepth/meta.yml b/modules/mosdepth/meta.yml
index be568aa6..0ca7bce9 100644
--- a/modules/mosdepth/meta.yml
+++ b/modules/mosdepth/meta.yml
@@ -75,3 +75,4 @@ output:
 authors:
     - "@joseespinosa"
     - "@drpatelh"
+    - "@ramprasadn"
diff --git a/tests/modules/mosdepth/main.nf b/tests/modules/mosdepth/main.nf
index 8862204d..ddd68129 100644
--- a/tests/modules/mosdepth/main.nf
+++ b/tests/modules/mosdepth/main.nf
@@ -7,10 +7,30 @@ include { MOSDEPTH } 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) ] 
+               [ file(params.test_data['sarscov2']['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) ]
              ]
-    dummy  = file("dummy_file.txt")
     window = 100
 
-    MOSDEPTH ( input, dummy, window )
+    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) ]
+
+    MOSDEPTH ( input, bed, [] )
 }
diff --git a/tests/modules/mosdepth/test.yml b/tests/modules/mosdepth/test.yml
index e264ef3b..c66e0b89 100644
--- a/tests/modules/mosdepth/test.yml
+++ b/tests/modules/mosdepth/test.yml
@@ -4,16 +4,50 @@
     - mosdepth
   files:
     - path: ./output/mosdepth/test.per-base.bed.gz.csi
-      md5sum: aa68536f55883aa60f4e68ac9b108358
+      md5sum: b2aad62c41a7146680d31df505fcc8c5
     - path: ./output/mosdepth/test.per-base.bed.gz
-      md5sum: b5f9c8ca49be6128a486f6b56514a6d0
+      md5sum: 11b3f649072c2c7453febb085b1a9c33
+    - path: ./output/mosdepth/test.mosdepth.global.dist.txt
+      md5sum: 2a1de1b0ecc361a21cd296ec4e1efd6a
+    - path: ./output/mosdepth/test.mosdepth.summary.txt
+      md5sum: 7b249dd3b3e58cc122fbd25ea84aa25d
+
+- name: 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.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: 8e020ec602c02d240e0458642cf5ac5a
+      md5sum: 64e1ced01c4443d7c1796ef553992f0c
     - path: ./output/mosdepth/test.regions.bed.gz.csi
-      md5sum: 44aec43fc34785fcbe6d830c907c617a
+      md5sum: 9e312b4b0784bd46dfbd23b3a8afed6a
     - path: ./output/mosdepth/test.mosdepth.region.dist.txt
       md5sum: 65fbc824c4212c6884354d8ac72ad37e
     - path: ./output/mosdepth/test.mosdepth.summary.txt
       md5sum: 11804907dab069ddb99ca97bf2698572
+
+- name: 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: 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