From 37b24a661d1253032d175794130e5748691e0ed3 Mon Sep 17 00:00:00 2001
From: Georgia Kesisoglou <georgiakes@gmail.com>
Date: Wed, 10 Jul 2024 20:28:08 +0300
Subject: [PATCH 1/6] Initial commit

---
 .../collectduplexseqmetrics/environment.yml   |  10 +
 .../fgbio/collectduplexseqmetrics/main.nf     |  78 ++++++
 .../fgbio/collectduplexseqmetrics/meta.yml    |  78 ++++++
 .../tests/main.nf.test                        |  64 +++++
 .../tests/main.nf.test.snap                   | 228 ++++++++++++++++++
 .../collectduplexseqmetrics/tests/tags.yml    |   2 +
 6 files changed, 460 insertions(+)
 create mode 100644 modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml
 create mode 100644 modules/nf-core/fgbio/collectduplexseqmetrics/main.nf
 create mode 100644 modules/nf-core/fgbio/collectduplexseqmetrics/meta.yml
 create mode 100644 modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test
 create mode 100644 modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/fgbio/collectduplexseqmetrics/tests/tags.yml

diff --git a/modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml b/modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml
new file mode 100644
index 00000000000..c766174a1aa
--- /dev/null
+++ b/modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml
@@ -0,0 +1,10 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "fgbio_collectduplexseqmetrics"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::fgbio=2.2.1"
+  - "conda-forge::r-ggplot2=3.4.3"
diff --git a/modules/nf-core/fgbio/collectduplexseqmetrics/main.nf b/modules/nf-core/fgbio/collectduplexseqmetrics/main.nf
new file mode 100644
index 00000000000..55c3cba7bcb
--- /dev/null
+++ b/modules/nf-core/fgbio/collectduplexseqmetrics/main.nf
@@ -0,0 +1,78 @@
+process FGBIO_COLLECTDUPLEXSEQMETRICS {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-51891ad0b60843e4aade9cde2eb5d40c5ae92b80:72c944cdea5caff7f03b96034968ce2a4f1737bc-0':
+        'biocontainers/mulled-v2-51891ad0b60843e4aade9cde2eb5d40c5ae92b80:72c944cdea5caff7f03b96034968ce2a4f1737bc-0' }"
+
+    input:
+    tuple val(meta), path(grouped_bam)
+    path interval_list
+
+    output:
+    tuple val(meta), path("**.family_sizes.txt")        , emit: family_sizes
+    tuple val(meta), path("**.duplex_family_sizes.txt") , emit: duplex_family_sizes
+    tuple val(meta), path("**.duplex_yield_metrics.txt"), emit: duplex_yield_metrics
+    tuple val(meta), path("**.umi_counts.txt")          , emit: umi_counts
+    tuple val(meta), path("**.duplex_qc.pdf")           , emit: duplex_qc
+    tuple val(meta), path("**.duplex_umi_counts.txt")   , emit: duplex_umi_counts, optional: true
+    path "versions.yml"                                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def intervals = interval_list ? "--intervals ${bed}" : ""
+    def mem_gb = 8
+
+    if (!task.memory) {
+        log.info '[fgbio CollectDuplexSeqMetrics] Available memory not known - defaulting to 8GB. Specify process memory requirements to change this.'
+    } else if (mem_gb > task.memory.giga) {
+        if (task.memory.giga < 2) {
+            mem_gb = 1
+        } else {
+            mem_gb = task.memory.giga - 1
+        }
+    }
+
+    """
+    fgbio \\
+        -Xmx${mem_gb}g \\
+        --tmp-dir=. \\
+        --async-io=true \\
+        --compression=1 \\
+        CollectDuplexSeqMetrics \\
+        --input $grouped_bam \\
+        --output ${prefix} \\
+        $intervals \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fgbio: \$( echo \$(fgbio --version 2>&1 | tr -d '[:cntrl:]' ) | sed -e 's/^.*Version: //;s/\\[.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def touch_duplex_umi = args.contains("--duplex-umi-counts") || args.contains("-u") ? "touch ${prefix}.duplex_umi_counts.txt" : ""
+
+    """
+    touch ${prefix}.family_sizes.txt
+    touch ${prefix}.duplex_family_sizes.txt
+    touch ${prefix}.duplex_yield_metrics.txt
+    touch ${prefix}.umi_counts.txt
+    touch ${prefix}.duplex_qc.pdf
+    $touch_duplex_umi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fgbio: \$( echo \$(fgbio --version 2>&1 | tr -d '[:cntrl:]' ) | sed -e 's/^.*Version: //;s/\\[.*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/fgbio/collectduplexseqmetrics/meta.yml b/modules/nf-core/fgbio/collectduplexseqmetrics/meta.yml
new file mode 100644
index 00000000000..f7afa4b4101
--- /dev/null
+++ b/modules/nf-core/fgbio/collectduplexseqmetrics/meta.yml
@@ -0,0 +1,78 @@
+---
+name: "fgbio_collectduplexseqmetrics"
+description: Collects a suite of metrics to QC duplex sequencing data.
+keywords:
+  - UMIs
+  - QC
+  - bam
+  - duplex
+tools:
+  - "fgbio":
+      description: "A set of tools for working with genomic and high throughput sequencing data, including UMIs"
+      homepage: "http://fulcrumgenomics.github.io/fgbio/"
+      documentation: "http://fulcrumgenomics.github.io/fgbio/"
+      tool_dev_url: "https://github.com/fulcrumgenomics/fgbio"
+      licence: ["MIT"]
+  - "r-ggplot2":
+      description: "ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics. "
+      homepage: "https://ggplot2.tidyverse.org/"
+      documentation: "https://ggplot2.tidyverse.org/"
+      tool_dev_url: "https://github.com/tidyverse/ggplot2"
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+
+  - grouped_bam:
+      type: file
+      description: It has to be either 1)The exact BAM output by the GroupReadsByUmi tool (in the sort-order it was produced in) 2)A BAM file that has MI tags present on all reads (usually set by GroupReadsByUmi and has been sorted with SortBam into TemplateCoordinate order.
+      pattern: "*.bam"
+
+  - interval_list:
+      type: file
+      description: Calculation of metrics may be restricted to a set of regions using the --intervals parameter. The file format is descripted here  https://samtools.github.io/htsjdk/javadoc/htsjdk/index.html?htsjdk/samtools/util/Interval.html
+      pattern: "*.{tsv|txt|interval_list}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1' ]`
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - family_sizes:
+      type: file
+      description: Metrics on the frequency of different types of families of different sizes
+      pattern: "*.txt"
+  - duplex_family_sizes:
+      type: file
+      description: Metrics on the frequency of duplex tag families by the number of observations from each strand
+      pattern: "*.txt"
+  - duplex_yield_metrics:
+      type: file
+      description: Summary QC metrics produced using 5%, 10%, 15%...100% of the data
+      pattern: "*.txt"
+  - umi_counts:
+      type: file
+      description: Metrics on the frequency of observations of UMIs within reads and tag families
+      pattern: "*.txt"
+  - duplex_qc:
+      type: file
+      description: A series of plots generated from the preceding metrics files for visualization
+      pattern: "*.pdf"
+  - duplex_umi_counts:
+      type: file
+      description: Metrics on the frequency of observations of duplex UMIs within reads and tag families.
+      pattern: "*.txt"
+
+authors:
+  - "@georgiakes"
+maintainers:
+  - "@georgiakes"
diff --git a/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test b/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test
new file mode 100644
index 00000000000..f6fc0cb40f3
--- /dev/null
+++ b/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test
@@ -0,0 +1,64 @@
+nextflow_process {
+
+    name "Test Process FGBIO_COLLECTDUPLEXSEQMETRICS"
+    script "../main.nf"
+    process "FGBIO_COLLECTDUPLEXSEQMETRICS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "fgbio"
+    tag "fgbio/collectduplexseqmetrics"
+
+
+    test("homo_sapiens - bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_grouped.bam', checkIfExists: true)
+                ]
+                input[1]=[]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_grouped.bam', checkIfExists: true)
+                ]
+                input[1] = []
+
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
\ No newline at end of file
diff --git a/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test.snap b/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test.snap
new file mode 100644
index 00000000000..98fbc88cd28
--- /dev/null
+++ b/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test.snap
@@ -0,0 +1,228 @@
+{
+    "homo_sapiens - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.family_sizes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.duplex_family_sizes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.duplex_yield_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.umi_counts.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.duplex_qc.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    "versions.yml:md5,06a64f50eafe7cae569853b0d493b5e1"
+                ],
+                "duplex_family_sizes": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.duplex_family_sizes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "duplex_plots": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.duplex_qc.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "duplex_umi_counts": [
+                    
+                ],
+                "duplex_yield_metrics": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.duplex_yield_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "family_sizes": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.family_sizes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "umi_counts": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.umi_counts.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,06a64f50eafe7cae569853b0d493b5e1"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-10T19:17:28.687879866"
+    },
+    "homo_sapiens - bam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.family_sizes.txt:md5,a49de49bd587440c316fec830f502620"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.duplex_family_sizes.txt:md5,129e41170b9f5f2f8edce62a686c8548"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.duplex_yield_metrics.txt:md5,237e4e4ee713fdf672b0ee796827fb9d"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.umi_counts.txt:md5,9fe38b2a49ca80492b3a1c6a55679155"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.duplex_qc.pdf:md5,906584434125bf80841073634e383b8b"
+                    ]
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    "versions.yml:md5,06a64f50eafe7cae569853b0d493b5e1"
+                ],
+                "duplex_family_sizes": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.duplex_family_sizes.txt:md5,129e41170b9f5f2f8edce62a686c8548"
+                    ]
+                ],
+                "duplex_plots": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.duplex_qc.pdf:md5,906584434125bf80841073634e383b8b"
+                    ]
+                ],
+                "duplex_umi_counts": [
+                    
+                ],
+                "duplex_yield_metrics": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.duplex_yield_metrics.txt:md5,237e4e4ee713fdf672b0ee796827fb9d"
+                    ]
+                ],
+                "family_sizes": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.family_sizes.txt:md5,a49de49bd587440c316fec830f502620"
+                    ]
+                ],
+                "umi_counts": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.umi_counts.txt:md5,9fe38b2a49ca80492b3a1c6a55679155"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,06a64f50eafe7cae569853b0d493b5e1"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-10T19:17:01.278022829"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/fgbio/collectduplexseqmetrics/tests/tags.yml b/modules/nf-core/fgbio/collectduplexseqmetrics/tests/tags.yml
new file mode 100644
index 00000000000..603caca5db5
--- /dev/null
+++ b/modules/nf-core/fgbio/collectduplexseqmetrics/tests/tags.yml
@@ -0,0 +1,2 @@
+fgbio/collectduplexseqmetrics:
+  - "modules/nf-core/fgbio/collectduplexseqmetrics/**"

From e163c483f881d8096bd02a09920e8105f568e78b Mon Sep 17 00:00:00 2001
From: Georgia Kesisoglou <georgiakes@gmail.com>
Date: Thu, 11 Jul 2024 10:51:05 +0300
Subject: [PATCH 2/6] Rerun nf-test

---
 .../collectduplexseqmetrics/tests/main.nf.test.snap  | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test.snap b/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test.snap
index 98fbc88cd28..86301f80a0e 100644
--- a/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test.snap
+++ b/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test.snap
@@ -62,7 +62,7 @@
                         "test.duplex_family_sizes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "duplex_plots": [
+                "duplex_qc": [
                     [
                         {
                             "id": "test",
@@ -110,7 +110,7 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.3"
         },
-        "timestamp": "2024-07-10T19:17:28.687879866"
+        "timestamp": "2024-07-11T10:47:48.745854401"
     },
     "homo_sapiens - bam": {
         "content": [
@@ -157,7 +157,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.duplex_qc.pdf:md5,906584434125bf80841073634e383b8b"
+                        "test.duplex_qc.pdf:md5,e2234e533e3606541cbe530c7858a711"
                     ]
                 ],
                 "5": [
@@ -175,13 +175,13 @@
                         "test.duplex_family_sizes.txt:md5,129e41170b9f5f2f8edce62a686c8548"
                     ]
                 ],
-                "duplex_plots": [
+                "duplex_qc": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test.duplex_qc.pdf:md5,906584434125bf80841073634e383b8b"
+                        "test.duplex_qc.pdf:md5,e2234e533e3606541cbe530c7858a711"
                     ]
                 ],
                 "duplex_umi_counts": [
@@ -223,6 +223,6 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.3"
         },
-        "timestamp": "2024-07-10T19:17:01.278022829"
+        "timestamp": "2024-07-11T10:47:29.281841324"
     }
 }
\ No newline at end of file

From 082c2e566f094e2a5c4dc97c83dba0da76028092 Mon Sep 17 00:00:00 2001
From: Georgia Kesisoglou <georgiakes@gmail.com>
Date: Fri, 12 Jul 2024 16:32:31 +0300
Subject: [PATCH 3/6] Change assertion for duplex_qc output

---
 .../tests/main.nf.test                        |  19 +-
 .../tests/main.nf.test.snap                   | 294 +++++-------------
 2 files changed, 103 insertions(+), 210 deletions(-)

diff --git a/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test b/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test
index f6fc0cb40f3..0021229b1ba 100644
--- a/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test
+++ b/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test
@@ -28,7 +28,15 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(process.out.family_sizes,
+                process.out.duplex_family_sizes,
+                process.out.duplex_yield_metrics,
+                process.out.umi_counts,
+                process.out.duplex_umi_counts,
+                process.out.versions,
+                file(process.out.duplex_qc[0][1]).name)
+                .match() }
+                
             )
         }
 
@@ -55,7 +63,14 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(process.out.family_sizes,
+                process.out.duplex_family_sizes,
+                process.out.duplex_yield_metrics,
+                process.out.umi_counts,
+                process.out.duplex_umi_counts,
+                process.out.versions,
+                file(process.out.duplex_qc[0][1]).name)
+                .match() }
             )
         }
 
diff --git a/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test.snap b/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test.snap
index 86301f80a0e..f554f3d236c 100644
--- a/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test.snap
+++ b/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test.snap
@@ -1,228 +1,106 @@
 {
     "homo_sapiens - stub": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.family_sizes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.duplex_family_sizes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.duplex_yield_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "3": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.umi_counts.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "4": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.duplex_qc.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "5": [
-                    
-                ],
-                "6": [
-                    "versions.yml:md5,06a64f50eafe7cae569853b0d493b5e1"
-                ],
-                "duplex_family_sizes": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.duplex_family_sizes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "duplex_qc": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.duplex_qc.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "duplex_umi_counts": [
-                    
-                ],
-                "duplex_yield_metrics": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.duplex_yield_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "family_sizes": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.family_sizes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "umi_counts": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.umi_counts.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,06a64f50eafe7cae569853b0d493b5e1"
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.family_sizes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ]
-            }
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.duplex_family_sizes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.duplex_yield_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.umi_counts.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,06a64f50eafe7cae569853b0d493b5e1"
+            ],
+            "test.duplex_qc.pdf"
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "24.04.3"
         },
-        "timestamp": "2024-07-11T10:47:48.745854401"
+        "timestamp": "2024-07-12T16:22:15.318780796"
     },
     "homo_sapiens - bam": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.family_sizes.txt:md5,a49de49bd587440c316fec830f502620"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.duplex_family_sizes.txt:md5,129e41170b9f5f2f8edce62a686c8548"
-                    ]
-                ],
-                "2": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.duplex_yield_metrics.txt:md5,237e4e4ee713fdf672b0ee796827fb9d"
-                    ]
-                ],
-                "3": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.umi_counts.txt:md5,9fe38b2a49ca80492b3a1c6a55679155"
-                    ]
-                ],
-                "4": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.duplex_qc.pdf:md5,e2234e533e3606541cbe530c7858a711"
-                    ]
-                ],
-                "5": [
-                    
-                ],
-                "6": [
-                    "versions.yml:md5,06a64f50eafe7cae569853b0d493b5e1"
-                ],
-                "duplex_family_sizes": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.duplex_family_sizes.txt:md5,129e41170b9f5f2f8edce62a686c8548"
-                    ]
-                ],
-                "duplex_qc": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.duplex_qc.pdf:md5,e2234e533e3606541cbe530c7858a711"
-                    ]
-                ],
-                "duplex_umi_counts": [
-                    
-                ],
-                "duplex_yield_metrics": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.duplex_yield_metrics.txt:md5,237e4e4ee713fdf672b0ee796827fb9d"
-                    ]
-                ],
-                "family_sizes": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.family_sizes.txt:md5,a49de49bd587440c316fec830f502620"
-                    ]
-                ],
-                "umi_counts": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.umi_counts.txt:md5,9fe38b2a49ca80492b3a1c6a55679155"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,06a64f50eafe7cae569853b0d493b5e1"
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.family_sizes.txt:md5,a49de49bd587440c316fec830f502620"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.duplex_family_sizes.txt:md5,129e41170b9f5f2f8edce62a686c8548"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.duplex_yield_metrics.txt:md5,237e4e4ee713fdf672b0ee796827fb9d"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.umi_counts.txt:md5,9fe38b2a49ca80492b3a1c6a55679155"
                 ]
-            }
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,06a64f50eafe7cae569853b0d493b5e1"
+            ],
+            "test.duplex_qc.pdf"
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "24.04.3"
         },
-        "timestamp": "2024-07-11T10:47:29.281841324"
+        "timestamp": "2024-07-12T16:21:56.304728963"
     }
 }
\ No newline at end of file

From 6c690a1e9943ff7305391247ea96e3bcf187de8e Mon Sep 17 00:00:00 2001
From: Georgia Kesisoglou <georgiakes@gmail.com>
Date: Wed, 17 Jul 2024 19:06:00 +0300
Subject: [PATCH 4/6] Add ggplot2 to version.yml

---
 modules/nf-core/fgbio/collectduplexseqmetrics/main.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/modules/nf-core/fgbio/collectduplexseqmetrics/main.nf b/modules/nf-core/fgbio/collectduplexseqmetrics/main.nf
index 55c3cba7bcb..d1d6bfc6a14 100644
--- a/modules/nf-core/fgbio/collectduplexseqmetrics/main.nf
+++ b/modules/nf-core/fgbio/collectduplexseqmetrics/main.nf
@@ -54,6 +54,7 @@ process FGBIO_COLLECTDUPLEXSEQMETRICS {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         fgbio: \$( echo \$(fgbio --version 2>&1 | tr -d '[:cntrl:]' ) | sed -e 's/^.*Version: //;s/\\[.*\$//')
+        ggplot2: \$(Rscript -e "library(ggplot2); cat(as.character(packageVersion('ggplot2')))")
     END_VERSIONS
     """
 
@@ -73,6 +74,7 @@ process FGBIO_COLLECTDUPLEXSEQMETRICS {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         fgbio: \$( echo \$(fgbio --version 2>&1 | tr -d '[:cntrl:]' ) | sed -e 's/^.*Version: //;s/\\[.*\$//')
+        ggplot2: \$(Rscript -e "library(ggplot2); cat(as.character(packageVersion('ggplot2')))")
     END_VERSIONS
     """
 }

From 79330bb0fcd49d9d6214b8df81511df36183904f Mon Sep 17 00:00:00 2001
From: Georgia Kesisoglou <georgiakes@gmail.com>
Date: Wed, 17 Jul 2024 19:28:20 +0300
Subject: [PATCH 5/6] Update snapshot

---
 .../fgbio/collectduplexseqmetrics/tests/main.nf.test.snap | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test.snap b/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test.snap
index f554f3d236c..7dfa35f5801 100644
--- a/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test.snap
+++ b/modules/nf-core/fgbio/collectduplexseqmetrics/tests/main.nf.test.snap
@@ -41,7 +41,7 @@
                 
             ],
             [
-                "versions.yml:md5,06a64f50eafe7cae569853b0d493b5e1"
+                "versions.yml:md5,637a7384cd910f0e0541a631c52b95e1"
             ],
             "test.duplex_qc.pdf"
         ],
@@ -49,7 +49,7 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.3"
         },
-        "timestamp": "2024-07-12T16:22:15.318780796"
+        "timestamp": "2024-07-17T19:26:23.325859809"
     },
     "homo_sapiens - bam": {
         "content": [
@@ -93,7 +93,7 @@
                 
             ],
             [
-                "versions.yml:md5,06a64f50eafe7cae569853b0d493b5e1"
+                "versions.yml:md5,637a7384cd910f0e0541a631c52b95e1"
             ],
             "test.duplex_qc.pdf"
         ],
@@ -101,6 +101,6 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.3"
         },
-        "timestamp": "2024-07-12T16:21:56.304728963"
+        "timestamp": "2024-07-17T19:26:03.1373243"
     }
 }
\ No newline at end of file

From 6e99fc886b1921c8a5b9ceef62f9aa972a5ddae3 Mon Sep 17 00:00:00 2001
From: Georgia Kesisoglou <georgiakes@gmail.com>
Date: Wed, 17 Jul 2024 20:04:35 +0300
Subject: [PATCH 6/6] Correct conda packages version

---
 modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml b/modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml
index c766174a1aa..a21a0a390e6 100644
--- a/modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml
+++ b/modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml
@@ -6,5 +6,5 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - "bioconda::fgbio=2.2.1"
-  - "conda-forge::r-ggplot2=3.4.3"
+  - "bioconda::fgbio=2.0.2"
+  - "conda-forge::r-ggplot2=3.4.4"