From b2542ee0795bcec2db49566ea08b5e0e9dc68a78 Mon Sep 17 00:00:00 2001
From: JIANHONG OU <jianhong@users.noreply.github.com>
Date: Sun, 8 May 2022 06:21:26 -0400
Subject: [PATCH] remove the mgc in metadata for motus_profile.

---
 modules/motus/profile/main.nf  | 2 +-
 modules/motus/profile/meta.yml | 7 ++-----
 2 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/modules/motus/profile/main.nf b/modules/motus/profile/main.nf
index 9fd65384..8dfe3b9b 100644
--- a/modules/motus/profile/main.nf
+++ b/modules/motus/profile/main.nf
@@ -25,7 +25,7 @@ process MOTUS_PROFILE {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def inputs = "$reads[0]".getExtension == ('.bam') ?
                     "-i ${reads}" :
-                    meta.mgc ? "-m $reads" :
+                    "$reads[0]".getExtension == ('.mgc') ? "-m $reads" :
                         meta.single_end ?
                             "-s $reads" : "-f ${reads[0]} -r ${reads[1]}"
     def refdb = db ? "-db ${db}" : ""
diff --git a/modules/motus/profile/meta.yml b/modules/motus/profile/meta.yml
index ff8f990d..19803bdc 100644
--- a/modules/motus/profile/meta.yml
+++ b/modules/motus/profile/meta.yml
@@ -20,8 +20,6 @@ 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: |
@@ -29,9 +27,8 @@ input:
         respectively.
         Or the intermediate bam file mapped by bwa to the mOTUs database or
         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}"
+        Or the intermediate mgc read counts table.
+      pattern: "*.{fastq,fq,fasta,fa,fastq.gz,fq.gz,fasta.gz,fa.gz,.bam,.mgc}"
   - db:
       type: directory
       description: |