From fb5c5d310abfdd4267eb5bd5f3d90596db597097 Mon Sep 17 00:00:00 2001
From: JIANHONG OU <jianhong@users.noreply.github.com>
Date: Thu, 5 May 2022 13:38:46 -0400
Subject: [PATCH] update motus module.

---
 modules/motus/profile/main.nf        | 13 +++++++++----
 modules/motus/profile/meta.yml       |  9 +++------
 tests/modules/motus/profile/main.nf  |  6 +++---
 tests/modules/motus/profile/test.yml | 27 +++++++++++++++------------
 4 files changed, 30 insertions(+), 25 deletions(-)

diff --git a/modules/motus/profile/main.nf b/modules/motus/profile/main.nf
index 23ee2531..99004ee6 100644
--- a/modules/motus/profile/main.nf
+++ b/modules/motus/profile/main.nf
@@ -10,7 +10,6 @@ process MOTUS_PROFILE {
     input:
     tuple val(meta), path(reads)
     path db
-    path bam
 
     output:
     tuple val(meta), path("*.out"), emit: out
@@ -28,20 +27,26 @@ process MOTUS_PROFILE {
                     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 \\
         -o ${prefix}.out
 
+    ## mOTUs version number is not available from command line.
+    ## mOTUs save the version number in index database folder.
+    ## mOTUs will check the database version is same version as exec version.
+    if [ "$refdb" == "" ]; then
+        VERSION=\$(echo \$(motus -h 2>&1) | sed 's/^.*Version: //; s/References.*\$//')
+    else
+        VERSION=\$(grep motus $refdb/db_mOTU_versions | sed 's/motus\\t//g')
+    fi
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        mOTUs: \$(echo \$(motus -h 2>&1) | sed 's/^.*Version: //; s/References.*\$//')
+        mOTUs: \$VERSION
     END_VERSIONS
     """
 }
diff --git a/modules/motus/profile/meta.yml b/modules/motus/profile/meta.yml
index 98b24c45..2e4a7997 100644
--- a/modules/motus/profile/meta.yml
+++ b/modules/motus/profile/meta.yml
@@ -25,16 +25,13 @@ input:
       description: |
         List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data,
         respectively.
-      pattern: "*.{fastq,fq,fasta,fa,fastq.gz,fq.gz,fasta.gz,fa.gz}"
+        Or the intermediate bam file mapped by bwa to the mOTUs database or
+        the output bam file from motus profile
+      pattern: "*.{fastq,fq,fasta,fa,fastq.gz,fq.gz,fasta.gz,fa.gz,.bam}"
   - db:
       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 e6fdc23b..d06c73ab 100644
--- a/tests/modules/motus/profile/main.nf
+++ b/tests/modules/motus/profile/main.nf
@@ -8,13 +8,13 @@ include { MOTUS_PROFILE    } from '../../../../modules/motus/profile/main.nf'
 workflow test_motus_profile_single_end {
 
     input = [
-        [ id:'test', single_end:false ], // meta map
+        [ id:'test', single_end:true ], // meta map
         file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
     ]
 
     MOTUS_DOWNLOADDB(file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py'))
 
-    MOTUS_PROFILE ( input,  MOTUS_DOWNLOADDB.out.db, [])
+    MOTUS_PROFILE ( input,  MOTUS_DOWNLOADDB.out.db)
 }
 
 workflow test_motus_profile_paired_end {
@@ -27,5 +27,5 @@ workflow test_motus_profile_paired_end {
 
     MOTUS_DOWNLOADDB(file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py'))
 
-    MOTUS_PROFILE ( input,  MOTUS_DOWNLOADDB.out.db, [])
+    MOTUS_PROFILE ( input,  MOTUS_DOWNLOADDB.out.db)
 }
diff --git a/tests/modules/motus/profile/test.yml b/tests/modules/motus/profile/test.yml
index c4c69bb6..f163adb4 100644
--- a/tests/modules/motus/profile/test.yml
+++ b/tests/modules/motus/profile/test.yml
@@ -1,14 +1,17 @@
-## TODO nf-core: Please run the following command to build this file:
-#                nf-core modules create-test-yml motus/profile
-- name: "motus profile"
-  command: nextflow run ./tests/modules/motus/profile -entry test_motus_profile -c ./tests/config/nextflow.config -c ./tests/modules/motus/profile/nextflow.config
+- name: motus profile test_motus_profile_single_end
+  command: nextflow run tests/modules/motus/profile -entry test_motus_profile_single_end -c tests/config/nextflow.config
   tags:
-    - "motus"
-    #
-    - "motus/profile"
-    #
+    - motus
+    - motus/profile
   files:
-    - path: "output/motus/test.bam"
-      md5sum: e667c7caad0bc4b7ac383fd023c654fc
-    - path: output/motus/versions.yml
-      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b
+    - path: output/motus/test.out
+      contains: ["#consensus_taxonomy\ttest"]
+
+- name: motus profile test_motus_profile_paired_end
+  command: nextflow run tests/modules/motus/profile -entry test_motus_profile_paired_end -c tests/config/nextflow.config
+  tags:
+    - motus
+    - motus/profile
+  files:
+    - path: output/motus/test.out
+      contains: ["#consensus_taxonomy\ttest"]