From 44cffd6feae13394af093ec478c7d81ebac977d2 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Wed, 6 Sep 2023 10:21:22 +0200
Subject: [PATCH] update cnvkit

---
 modules.json                          |  2 +-
 modules/nf-core/cnvkit/batch/main.nf  | 14 ++++++-------
 modules/nf-core/cnvkit/batch/meta.yml | 30 ++++++++++++++++++++++++---
 3 files changed, 35 insertions(+), 11 deletions(-)

diff --git a/modules.json b/modules.json
index 29e931c..4b01925 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "cnvkit/batch": {
                         "branch": "master",
-                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "git_sha": "016397249f05f5af7b97e3ea8d64458a07df2928",
                         "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
diff --git a/modules/nf-core/cnvkit/batch/main.nf b/modules/nf-core/cnvkit/batch/main.nf
index 1e4d81e..795053a 100644
--- a/modules/nf-core/cnvkit/batch/main.nf
+++ b/modules/nf-core/cnvkit/batch/main.nf
@@ -2,17 +2,17 @@ process CNVKIT_BATCH {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::cnvkit=0.9.9 bioconda::samtools=1.16.1"
+    conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:3bdd798e4b9aed6d3e1aaa1596c913a3eeb865cb-0' :
-        'biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:3bdd798e4b9aed6d3e1aaa1596c913a3eeb865cb-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:c94363856059151a2974dc501fb07a0360cc60a3-0' :
+        'biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:c94363856059151a2974dc501fb07a0360cc60a3-0' }"
 
     input:
     tuple val(meta), path(tumor), path(normal)
-    path  fasta
-    path  fasta_fai
-    path  targets
-    path  reference
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fasta_fai)
+    tuple val(meta4), path(targets)
+    tuple val(meta5), path(reference)
     val   panel_of_normals
 
     output:
diff --git a/modules/nf-core/cnvkit/batch/meta.yml b/modules/nf-core/cnvkit/batch/meta.yml
index 3fc00f1..1543304 100644
--- a/modules/nf-core/cnvkit/batch/meta.yml
+++ b/modules/nf-core/cnvkit/batch/meta.yml
@@ -26,22 +26,43 @@ input:
       type: file
       description: |
         Input normal sample bam file (or cram)
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test' ]
   - fasta:
       type: file
       description: |
         Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided)
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test' ]
   - fasta_fai:
       type: file
       description: |
         Input reference genome fasta index (optional, but recommended for cram_input)
+  - meta4:
+      type: map
+      description: |
+        Groovy Map containing information about target file
+        e.g. [ id:'test' ]
   - targetfile:
       type: file
       description: |
         Input target bed file
+  - meta5:
+      type: map
+      description: |
+        Groovy Map containing information about reference file
+        e.g. [ id:'test' ]
   - reference:
       type: file
       description: |
         Input reference cnn-file (only for germline and tumor-only running)
+
 output:
   - meta:
       type: map
@@ -76,11 +97,14 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
+
 authors:
-  - "@kaurravneet4123"
-  - "@KevinMenden"
-  - "@MaxUlysse"
+  - "@adamrtalbot"
   - "@drpatelh"
   - "@fbdtemme"
+  - "@kaurravneet4123"
+  - "@KevinMenden"
   - "@lassefolkersen"
+  - "@MaxUlysse"
+  - "@priesgo"
   - "@SusiJo"