From 0f24e4dcffb33826debae2ce8b47a039632d304c Mon Sep 17 00:00:00 2001
From: JIANHONG OU <jianhong@users.noreply.github.com>
Date: Mon, 2 May 2022 08:37:12 -0400
Subject: [PATCH] add input database and intermediate bam file.

---
 modules/motus/profile/main.nf       |  8 +++++++-
 modules/motus/profile/meta.yml      |  6 +++++-
 tests/modules/motus/profile/main.nf | 11 ++++++++---
 3 files changed, 20 insertions(+), 5 deletions(-)

diff --git a/modules/motus/profile/main.nf b/modules/motus/profile/main.nf
index 3cf5961c..23ee2531 100644
--- a/modules/motus/profile/main.nf
+++ b/modules/motus/profile/main.nf
@@ -9,6 +9,8 @@ process MOTUS_PROFILE {
 
     input:
     tuple val(meta), path(reads)
+    path db
+    path bam
 
     output:
     tuple val(meta), path("*.out"), emit: out
@@ -25,12 +27,16 @@ process MOTUS_PROFILE {
                     "-i ${reads}" :
                     meta.single_end ?
                         "-s $reads" : "-f ${reads[0]} -r ${reads[1]}"
+    def refdb = db ? "-db ${db}" : ""
+    def intermediateBam = bam ? "-I $bam" : ""
     """
     motus profile \\
         $args \\
         $inputs \\
+        $refdb \\
+        $intermediateBam \\
         -t $task.cpus \\
-        -n ${prefix} \\
+        -n $prefix \\
         -o ${prefix}.out
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/motus/profile/meta.yml b/modules/motus/profile/meta.yml
index 94f6a9fc..98b24c45 100644
--- a/modules/motus/profile/meta.yml
+++ b/modules/motus/profile/meta.yml
@@ -14,7 +14,6 @@ tools:
       doi: "10.1038/s41467-019-08844-4"
       licence: "['GPL v3']"
 
-## TODO nf-core: Add a description of all of the variables used as input
 input:
   - meta:
       type: map
@@ -31,6 +30,11 @@ input:
       type: derectory
       description: |
         mOTUs database downloaded by `motus downloadDB`
+  - bam:
+      type: file
+      description: |
+        The intermediate bam file mapped by bwa to the mOTUs database or
+        the output bam file from motus profile
 
 output:
   - meta:
diff --git a/tests/modules/motus/profile/main.nf b/tests/modules/motus/profile/main.nf
index 54f51bd8..e6fdc23b 100644
--- a/tests/modules/motus/profile/main.nf
+++ b/tests/modules/motus/profile/main.nf
@@ -2,7 +2,8 @@
 
 nextflow.enable.dsl = 2
 
-include { MOTUS_PROFILE } from '../../../../modules/motus/profile/main.nf'
+include { MOTUS_DOWNLOADDB } from '../../../../modules/motus/downloaddb/main.nf'
+include { MOTUS_PROFILE    } from '../../../../modules/motus/profile/main.nf'
 
 workflow test_motus_profile_single_end {
 
@@ -11,7 +12,9 @@ workflow test_motus_profile_single_end {
         file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
     ]
 
-    MOTUS_PROFILE ( input )
+    MOTUS_DOWNLOADDB(file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py'))
+
+    MOTUS_PROFILE ( input,  MOTUS_DOWNLOADDB.out.db, [])
 }
 
 workflow test_motus_profile_paired_end {
@@ -21,6 +24,8 @@ workflow test_motus_profile_paired_end {
         [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
           file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
     ]
-    MOTUS_PROFILE ( input )
 
+    MOTUS_DOWNLOADDB(file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py'))
+
+    MOTUS_PROFILE ( input,  MOTUS_DOWNLOADDB.out.db, [])
 }