From 283613159e079152f1336cef0db1c836086206e0 Mon Sep 17 00:00:00 2001
From: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Date: Mon, 14 Oct 2024 11:47:35 +0200
Subject: [PATCH] Update MaxBin2: allow multiple abund files (#6776)

* allow multiple abund files

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/nf-core/maxbin2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

---------

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
---
 modules/nf-core/maxbin2/main.nf  | 12 +++++++++++-
 modules/nf-core/maxbin2/meta.yml | 15 +++++++++++++--
 2 files changed, 24 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/maxbin2/main.nf b/modules/nf-core/maxbin2/main.nf
index 9b7a0fd41c2..845c8e4ed91 100644
--- a/modules/nf-core/maxbin2/main.nf
+++ b/modules/nf-core/maxbin2/main.nf
@@ -13,6 +13,7 @@ process MAXBIN2 {
     output:
     tuple val(meta), path("*.fasta.gz")   , emit: binned_fastas
     tuple val(meta), path("*.summary")    , emit: summary
+    tuple val(meta), path("*.abundance")  , emit: abundance   , optional: true
     tuple val(meta), path("*.log.gz")     , emit: log
     tuple val(meta), path("*.marker.gz")  , emit: marker_counts
     tuple val(meta), path("*.noclass.gz") , emit: unbinned_fasta
@@ -27,7 +28,16 @@ process MAXBIN2 {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def associate_files = reads ? "-reads $reads" : "-abund $abund"
+    if (reads && abund) { error("ERROR: MaxBin2 can only accept one of `reads` or `abund`, no both. Check input.") }
+    def associate_files = ""
+    if ( reads ) {
+        associate_files = "-reads $reads"
+    } else if ( abund instanceof List ) {
+        associate_files = "-abund ${abund[0]}"
+        for (i in 2..abund.size()) { associate_files += " -abund$i ${abund[i-1]}" }
+    } else {
+        associate_files = "-abund $abund"
+    }
     """
     mkdir input/ && mv $contigs input/
     run_MaxBin.pl \\
diff --git a/modules/nf-core/maxbin2/meta.yml b/modules/nf-core/maxbin2/meta.yml
index 538ba07f3fd..9546afb1aaa 100644
--- a/modules/nf-core/maxbin2/meta.yml
+++ b/modules/nf-core/maxbin2/meta.yml
@@ -35,8 +35,8 @@ input:
           supply at the same time as abundance files.
         pattern: "*.fasta"
     - abund:
-        type: file
-        description: Contig abundance files, i.e. reads against each contig. See MaxBin2
+        type: list
+        description: One or more contig abundance files, i.e. average depth of reads against each contig. See MaxBin2
           README for details. Do not supply at the same time as read files.
 output:
   - binned_fastas:
@@ -60,6 +60,17 @@ output:
           description: Summary file describing which contigs are being classified into
             which bin
           pattern: "*.summary"
+  - abundance:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.abundance":
+          type: file
+          description: Abundance of each bin if multiple abundance files were supplied
+            which bin
+          pattern: "*.abundance"
   - log:
       - meta:
           type: map