From eaa69b65d81b6ede5f0afca7d8f24a56b025ff08 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Wed, 13 Jul 2022 12:38:30 +0200
Subject: [PATCH 1/3] Update mOTUs profile module and mix log for multiqc

---
 modules.json                                   | 2 +-
 modules/nf-core/modules/motus/profile/main.nf  | 6 ++++--
 modules/nf-core/modules/motus/profile/meta.yml | 4 ++++
 subworkflows/local/profiling.nf                | 1 +
 4 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/modules.json b/modules.json
index 1d40748..faa267d 100644
--- a/modules.json
+++ b/modules.json
@@ -79,7 +79,7 @@
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "motus/profile": {
-                "git_sha": "6b960f0e75bbb4d5bd301cd3875fa078d0eab4d1"
+                "git_sha": "b6ed584443ad68ac41e6975994139454a4f23c18"
             },
             "multiqc": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
diff --git a/modules/nf-core/modules/motus/profile/main.nf b/modules/nf-core/modules/motus/profile/main.nf
index 6a1acd3..bd7a127 100644
--- a/modules/nf-core/modules/motus/profile/main.nf
+++ b/modules/nf-core/modules/motus/profile/main.nf
@@ -15,6 +15,7 @@ process MOTUS_PROFILE {
     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
+    tuple val(meta), path("*.log")                , emit: log
     path "versions.yml"           , emit: versions
 
     when:
@@ -36,7 +37,8 @@ process MOTUS_PROFILE {
         $refdb \\
         -t $task.cpus \\
         -n $prefix \\
-        -o ${prefix}.out
+        -o ${prefix}.out \\
+        2> ${prefix}.log
 
     ## mOTUs version number is not available from command line.
     ## mOTUs save the version number in index database folder.
@@ -48,7 +50,7 @@ process MOTUS_PROFILE {
     fi
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        mOTUs: \$VERSION
+        motus: \$VERSION
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/modules/motus/profile/meta.yml b/modules/nf-core/modules/motus/profile/meta.yml
index 19803bd..3c3b660 100644
--- a/modules/nf-core/modules/motus/profile/meta.yml
+++ b/modules/nf-core/modules/motus/profile/meta.yml
@@ -56,6 +56,10 @@ output:
       type: file
       description: Optional intermediate mgc read count table file saved with `-M`.
       pattern: "*.{mgc}"
+  - log:
+      type: file
+      description: Standard error logging file containing summary statistics
+      pattern: "*.log"
 
 authors:
   - "@jianhong"
diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf
index 60963c9..0de726b 100644
--- a/subworkflows/local/profiling.nf
+++ b/subworkflows/local/profiling.nf
@@ -227,6 +227,7 @@ workflow PROFILING {
         MOTUS_PROFILE ( ch_input_for_motus.reads, ch_input_for_motus.db )
         ch_versions        = ch_versions.mix( MOTUS_PROFILE.out.versions.first() )
         ch_raw_profiles    = ch_raw_profiles.mix( MOTUS_PROFILE.out.out )
+        ch_multiqc_files   = ch_multiqc_files.mix( MOTUS_PROFILE.out.log )
 
     }
 

From 31119f83c23622783cb647577afffbdfb4f8153b Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Wed, 13 Jul 2022 14:29:47 +0200
Subject: [PATCH 2/3] Send to MQC only the log file not the meta

---
 subworkflows/local/profiling.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf
index 0de726b..38bc9a8 100644
--- a/subworkflows/local/profiling.nf
+++ b/subworkflows/local/profiling.nf
@@ -227,7 +227,7 @@ workflow PROFILING {
         MOTUS_PROFILE ( ch_input_for_motus.reads, ch_input_for_motus.db )
         ch_versions        = ch_versions.mix( MOTUS_PROFILE.out.versions.first() )
         ch_raw_profiles    = ch_raw_profiles.mix( MOTUS_PROFILE.out.out )
-        ch_multiqc_files   = ch_multiqc_files.mix( MOTUS_PROFILE.out.log )
+        ch_multiqc_files   = ch_multiqc_files.mix( MOTUS_PROFILE.out.log.map{it[1]} )
 
     }
 

From 449b6a55537e85e1be45461609c8d9c0fda44bd0 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Wed, 13 Jul 2022 15:25:58 +0200
Subject: [PATCH 3/3] Fix file name output clashing wiht multiqc

---
 conf/modules.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conf/modules.config b/conf/modules.config
index b858ec3..df90c38 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -391,6 +391,7 @@ process {
     }
 
     withName: MOTUS_PROFILE {
+        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
             path: { "${params.outdir}/motus/${meta.db_name}" },
             mode: params.publish_dir_mode