From 9b50036e9b09451285673fcc906038cb1a40b9da Mon Sep 17 00:00:00 2001
From: JIANHONG OU <jianhong@users.noreply.github.com>
Date: Fri, 6 May 2022 08:56:42 -0400
Subject: [PATCH] add test_bam and -m parameter for motus_profile

---
 modules/motus/profile/main.nf        |  6 ++++--
 modules/motus/profile/meta.yml       | 12 ++++++++++--
 tests/modules/motus/profile/main.nf  | 12 ++++++++++++
 tests/modules/motus/profile/test.yml |  9 +++++++++
 4 files changed, 35 insertions(+), 4 deletions(-)

diff --git a/modules/motus/profile/main.nf b/modules/motus/profile/main.nf
index 8b893d5a..9fd65384 100644
--- a/modules/motus/profile/main.nf
+++ b/modules/motus/profile/main.nf
@@ -14,6 +14,7 @@ process MOTUS_PROFILE {
     output:
     tuple val(meta), path("*.out"), emit: out
     tuple val(meta), path("*.bam"), optional: true, emit: bam
+    tuple val(meta), path("*.mgc"), optional: true, emit: mgc
     path "versions.yml"           , emit: versions
 
     when:
@@ -24,8 +25,9 @@ process MOTUS_PROFILE {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def inputs = "$reads[0]".getExtension == ('.bam') ?
                     "-i ${reads}" :
-                    meta.single_end ?
-                        "-s $reads" : "-f ${reads[0]} -r ${reads[1]}"
+                    meta.mgc ? "-m $reads" :
+                        meta.single_end ?
+                            "-s $reads" : "-f ${reads[0]} -r ${reads[1]}"
     def refdb = db ? "-db ${db}" : ""
     """
     motus profile \\
diff --git a/modules/motus/profile/meta.yml b/modules/motus/profile/meta.yml
index e52d4bd5..ff8f990d 100644
--- a/modules/motus/profile/meta.yml
+++ b/modules/motus/profile/meta.yml
@@ -20,14 +20,18 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
+        If input file is the mgc read counts table, the mgc should be set to `true`
+        e.g. [ id:'test', single_end:false, mgc:true ]
   - reads:
       type: file
       description: |
         List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data,
         respectively.
         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}"
+        the output bam file from motus profile.
+        Or the intermediate mgc read counts table. Please note if mgc table is input,
+        the `mgc` in metadata must be `true`.
+      pattern: "*.{fastq,fq,fasta,fa,fastq.gz,fq.gz,fasta.gz,fa.gz,.bam,.tsv,.txt,.mgc}"
   - db:
       type: directory
       description: |
@@ -51,6 +55,10 @@ output:
       type: file
       description: Optional intermediate sorted BAM file from BWA
       pattern: "*.{bam}"
+  - mgc:
+      type: file
+      description: Optional intermediate mgc read count table file saved with `-M`.
+      pattern: "*.{mgc}"
 
 authors:
   - "@jianhong"
diff --git a/tests/modules/motus/profile/main.nf b/tests/modules/motus/profile/main.nf
index 525b3f6d..d9806fd3 100644
--- a/tests/modules/motus/profile/main.nf
+++ b/tests/modules/motus/profile/main.nf
@@ -29,3 +29,15 @@ workflow test_motus_profile_paired_end {
 
     MOTUS_PROFILE ( input,  MOTUS_DOWNLOADDB.out.db)
 }
+
+workflow test_motus_profile_bam {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+    ]
+
+    MOTUS_DOWNLOADDB(file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py'))
+
+    MOTUS_PROFILE ( input,  MOTUS_DOWNLOADDB.out.db)
+}
diff --git a/tests/modules/motus/profile/test.yml b/tests/modules/motus/profile/test.yml
index f163adb4..9b80312d 100644
--- a/tests/modules/motus/profile/test.yml
+++ b/tests/modules/motus/profile/test.yml
@@ -15,3 +15,12 @@
   files:
     - path: output/motus/test.out
       contains: ["#consensus_taxonomy\ttest"]
+
+- name: motus profile test_motus_profile_bam
+  command: nextflow run tests/modules/motus/profile -entry test_motus_profile_bam -c tests/config/nextflow.config
+  tags:
+    - motus
+    - motus/profile
+  files:
+    - path: output/motus/test.out
+      contains: ["#consensus_taxonomy\ttest"]