From b5825fe6b336352024aebccd274da1d131188bfc Mon Sep 17 00:00:00 2001
From: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Date: Fri, 25 Mar 2022 07:46:51 +0100
Subject: [PATCH] Mpileup also likes intervals (#1445)

* Mpileup also likes intervals

* Also update meta yml with inclusive input and intervals

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
---
 modules/samtools/mpileup/main.nf        |  5 +++--
 modules/samtools/mpileup/meta.yml       |  6 +++++-
 tests/modules/samtools/mpileup/main.nf  | 13 ++++++++++++-
 tests/modules/samtools/mpileup/test.yml | 19 ++++++++++++++++---
 4 files changed, 36 insertions(+), 7 deletions(-)

diff --git a/modules/samtools/mpileup/main.nf b/modules/samtools/mpileup/main.nf
index cea40321..474a2492 100644
--- a/modules/samtools/mpileup/main.nf
+++ b/modules/samtools/mpileup/main.nf
@@ -8,7 +8,7 @@ process SAMTOOLS_MPILEUP {
         'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(input), path(intervals)
     path  fasta
 
     output:
@@ -21,12 +21,13 @@ process SAMTOOLS_MPILEUP {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def intervals = intervals ? "-l ${intervals}" : ""
     """
     samtools mpileup \\
         --fasta-ref $fasta \\
         --output ${prefix}.mpileup \\
         $args \\
-        $bam
+        $input
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
diff --git a/modules/samtools/mpileup/meta.yml b/modules/samtools/mpileup/meta.yml
index c384f5c6..ae499e92 100644
--- a/modules/samtools/mpileup/meta.yml
+++ b/modules/samtools/mpileup/meta.yml
@@ -21,7 +21,7 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - bam:
+  - input:
       type: file
       description: BAM/CRAM/SAM file
       pattern: "*.{bam,cram,sam}"
@@ -29,6 +29,10 @@ input:
       type: file
       description: FASTA reference file
       pattern: "*.{fasta,fa}"
+  - intervals:
+      type: file
+      description: Interval FILE
+      pattern: "*.bed"
 output:
   - meta:
       type: map
diff --git a/tests/modules/samtools/mpileup/main.nf b/tests/modules/samtools/mpileup/main.nf
index dc58cc2c..f7fd4b43 100644
--- a/tests/modules/samtools/mpileup/main.nf
+++ b/tests/modules/samtools/mpileup/main.nf
@@ -6,7 +6,18 @@ include { SAMTOOLS_MPILEUP } from '../../../../modules/samtools/mpileup/main.nf'
 
 workflow test_samtools_mpileup {
     input = [ [ id:'test', single_end:false ], // 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'], checkIfExists: true),
+                []
+            ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    SAMTOOLS_MPILEUP ( input, fasta )
+}
+
+workflow test_samtools_mpileup_intervals {
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
             ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
diff --git a/tests/modules/samtools/mpileup/test.yml b/tests/modules/samtools/mpileup/test.yml
index 53a9c142..405263d1 100644
--- a/tests/modules/samtools/mpileup/test.yml
+++ b/tests/modules/samtools/mpileup/test.yml
@@ -1,8 +1,21 @@
-- name: samtools mpileup
-  command: nextflow run ./tests/modules/samtools/mpileup -entry test_samtools_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/samtools/mpileup/nextflow.config
+- name: samtools mpileup test_samtools_mpileup
+  command: nextflow run tests/modules/samtools/mpileup -entry test_samtools_mpileup -c tests/config/nextflow.config
   tags:
     - samtools
     - samtools/mpileup
   files:
-    - path: ./output/samtools/test.mpileup
+    - path: output/samtools/test.mpileup
       md5sum: 958e6bead4103d72026f80153b6b5150
+    - path: output/samtools/versions.yml
+      md5sum: 26350e1e145451f0b807911db029861e
+
+- name: samtools mpileup test_samtools_mpileup_intervals
+  command: nextflow run tests/modules/samtools/mpileup -entry test_samtools_mpileup_intervals -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools/mpileup
+  files:
+    - path: output/samtools/test.mpileup
+      md5sum: 958e6bead4103d72026f80153b6b5150
+    - path: output/samtools/versions.yml
+      md5sum: 11d8118a558efb9db6798453862d719c