From dc521f59c333724b29b7fb2874d510dfb1f09e48 Mon Sep 17 00:00:00 2001
From: bioloni <nico.schcolnicov@gmail.com>
Date: Fri, 2 Feb 2024 17:20:14 +0000
Subject: [PATCH 01/13] Addressed assess_significance error when running
 controlfreec, updated makegraph module to 2

---
 conf/modules/controlfreec.config              |  2 +-
 modules.json                                  |  5 ++
 .../controlfreec/makegraph2/environment.yml   |  7 +++
 .../nf-core/controlfreec/makegraph2/main.nf   | 54 +++++++++++++++++
 .../nf-core/controlfreec/makegraph2/meta.yml  | 58 +++++++++++++++++++
 .../main.nf                                   | 48 +++++++++++++--
 6 files changed, 169 insertions(+), 5 deletions(-)
 create mode 100644 modules/nf-core/controlfreec/makegraph2/environment.yml
 create mode 100644 modules/nf-core/controlfreec/makegraph2/main.nf
 create mode 100644 modules/nf-core/controlfreec/makegraph2/meta.yml

diff --git a/conf/modules/controlfreec.config b/conf/modules/controlfreec.config
index 8ed3920c4..99a50ad4a 100644
--- a/conf/modules/controlfreec.config
+++ b/conf/modules/controlfreec.config
@@ -18,7 +18,7 @@ process {
     withName: 'ASSESS_SIGNIFICANCE' {
         publishDir = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
+            path: { (meta.id.contains("_tumor") || meta.id.contains("_normal")) ? "${params.outdir}/variant_calling/controlfreec/${meta.id}/".replaceAll(/_normal|_control/, "") : "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
             pattern: "*{.p.value.txt}"
         ]
     }
diff --git a/modules.json b/modules.json
index eb2c5fa7d..1bd8fb78d 100644
--- a/modules.json
+++ b/modules.json
@@ -113,6 +113,11 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/controlfreec/makegraph/controlfreec-makegraph.diff"
                     },
+                    "controlfreec/makegraph2": {
+                        "branch": "master",
+                        "git_sha": "a7bae48d8bccfae99e3b862fa07bbd50a8df6b82",
+                        "installed_by": ["modules"]
+                    },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
diff --git a/modules/nf-core/controlfreec/makegraph2/environment.yml b/modules/nf-core/controlfreec/makegraph2/environment.yml
new file mode 100644
index 000000000..720c2e950
--- /dev/null
+++ b/modules/nf-core/controlfreec/makegraph2/environment.yml
@@ -0,0 +1,7 @@
+name: controlfreec_makegraph2
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::control-freec=11.6b
diff --git a/modules/nf-core/controlfreec/makegraph2/main.nf b/modules/nf-core/controlfreec/makegraph2/main.nf
new file mode 100644
index 000000000..a85589d6f
--- /dev/null
+++ b/modules/nf-core/controlfreec/makegraph2/main.nf
@@ -0,0 +1,54 @@
+process CONTROLFREEC_MAKEGRAPH2 {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0':
+        'biocontainers/control-freec:11.6b--hdbdd923_0' }"
+
+    input:
+    tuple val(meta), path(ratio), path(baf)
+
+    output:
+    tuple val(meta), path("*_BAF.png")       , emit: png_baf
+    tuple val(meta), path("*_ratio.log2.png"), emit: png_ratio_log2
+    tuple val(meta), path("*_ratio.png")     , emit: png_ratio
+
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ""
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def baf = baf ?: ""
+    def VERSION = '11.6b' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    cat \$(which makeGraph2.0.R) | R --slave --args ${args} ${ratio} ${baf}
+
+    mv *_BAF.txt.png ${prefix}_BAF.png
+    mv *_ratio.txt.log2.png ${prefix}_ratio.log2.png
+    mv *_ratio.txt.png ${prefix}_ratio.png
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        controlfreec: $VERSION
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '11.6b' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    touch ${prefix}_BAF.png
+    touch ${prefix}_ratio.log2.png
+    touch ${prefix}_ratio.png
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        controlfreec: $VERSION
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/controlfreec/makegraph2/meta.yml b/modules/nf-core/controlfreec/makegraph2/meta.yml
new file mode 100644
index 000000000..1325da4a8
--- /dev/null
+++ b/modules/nf-core/controlfreec/makegraph2/meta.yml
@@ -0,0 +1,58 @@
+name: controlfreec_makegraph2
+description: Plot Freec output
+keywords:
+  - cna
+  - cnv
+  - somatic
+  - single
+  - tumor-only
+tools:
+  - controlfreec:
+      description: Copy number and genotype annotation from whole genome and whole exome sequencing data.
+      homepage: http://boevalab.inf.ethz.ch/FREEC
+      documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html
+      tool_dev_url: https://github.com/BoevaLab/FREEC/
+      doi: "10.1093/bioinformatics/btq635"
+      licence: ["GPL >=2"]
+
+input:
+  # Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - ratio:
+      type: file
+      description: ratio file generated by FREEC
+      pattern: "*.ratio.txt"
+  - baf:
+      type: file
+      description: .BAF file generated by FREEC
+      pattern: "*.BAF"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - png_baf:
+      type: file
+      description: Image of BAF plot
+      pattern: "*_BAF.png"
+  - png_ratio_log2:
+      type: file
+      description: Image of ratio log2 plot
+      pattern: "*_ratio.log2.png"
+  - png_ratio:
+      type: file
+      description: Image of ratio plot
+      pattern: "*_ratio.png"
+
+authors:
+  - "@FriederikeHanssen"
diff --git a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
index a2e7e17cf..f6a9b7832 100644
--- a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
+++ b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
@@ -8,7 +8,7 @@ include { CONTROLFREEC_FREEC              as FREEC_SOMATIC       } from '../../.
 include { CONTROLFREEC_ASSESSSIGNIFICANCE as ASSESS_SIGNIFICANCE } from '../../../modules/nf-core/controlfreec/assesssignificance/main'
 include { CONTROLFREEC_FREEC2BED          as FREEC2BED           } from '../../../modules/nf-core/controlfreec/freec2bed/main'
 include { CONTROLFREEC_FREEC2CIRCOS       as FREEC2CIRCOS        } from '../../../modules/nf-core/controlfreec/freec2circos/main'
-include { CONTROLFREEC_MAKEGRAPH          as MAKEGRAPH           } from '../../../modules/nf-core/controlfreec/makegraph/main'
+include { CONTROLFREEC_MAKEGRAPH2         as MAKEGRAPH2           } from '../../../modules/nf-core/controlfreec/makegraph2/main'
 
 workflow BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC {
     take:
@@ -25,18 +25,58 @@ workflow BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC {
 
     ch_versions = Channel.empty()
 
+    assess_significance_input = Channel.empty()
+
     FREEC_SOMATIC(controlfreec_input, fasta, fasta_fai, [], dbsnp, dbsnp_tbi, chr_files, mappability, intervals_bed, [])
 
-    ASSESS_SIGNIFICANCE(FREEC_SOMATIC.out.CNV.join(FREEC_SOMATIC.out.ratio, failOnDuplicate: true, failOnMismatch: true))
+    //Filter the files that come out of freec somatic as ASSESS_SIGNIFICANCE only takes one cnv and one ratio file, there should be one normal and one non normal pair?
+    //Creates empty channel if file is missing
+    cnv_files = FREEC_SOMATIC.out.CNV
+    .multiMap{ meta, cnv ->
+        def meta_clone_tumor = meta.clone()
+        def meta_clone_normal = meta.clone()
+        meta_clone_tumor.id = meta.id + "_tumor" //updating meta id so that the p.value file is named differently
+        meta_clone_normal.id = meta.id + "_normal" //updating meta id so that the p.value file is named differently
+
+        def tumor_file = cnv instanceof List ? cnv.find { it.toString().endsWith("gz_CNVs") } : cnv //only find if its a list, else it returns only the filename without the path
+        def normal_file = cnv instanceof List ? cnv.find { it.toString().endsWith("gz_normal_CNVs") } : null //only find if its a list, else it returns only the filename without the path
+
+        normal: normal_file == null ? [] : [meta_clone_normal,normal_file] //only fill channel if file was found, else leave it empty
+        tumor: tumor_file == null ? [] : [meta_clone_tumor,tumor_file] //only fill channel if file was found, else leave it empty
+    }
+
+    ratio_files = FREEC_SOMATIC.out.ratio
+    .multiMap{ meta, ratio ->
+        def meta_clone_tumor = meta.clone()
+        def meta_clone_normal = meta.clone()
+        meta_clone_tumor.id = meta.id + "_tumor" //updating meta id so that the p.value file is named differently
+        meta_clone_normal.id = meta.id + "_normal" //updating meta id so that the p.value file is named differently
+
+        def tumor_file = ratio instanceof List ? ratio.find { it.toString().endsWith("gz_ratio.txt") } : ratio //same here as cnv
+        def normal_file = ratio instanceof List ? ratio.find { it.toString().endsWith("gz_normal_ratio.txt") } : null //same here as cnv
+
+        normal: normal_file == null ? [] : [meta_clone_normal,normal_file] //same here as ratio
+        tumor: tumor_file == null ? [] : [meta_clone_tumor,tumor_file] //same here as ratio
+    }
+
+    //Join the pairs
+    normal_files = cnv_files.normal.join(ratio_files.normal, failOnDuplicate: true, failOnMismatch: true)
+    tumor_files = cnv_files.tumor.join(ratio_files.tumor, failOnDuplicate: true, failOnMismatch: true)
+
+    //Mix all the pairs into input channel
+    assess_significance_input = assess_significance_input.mix(tumor_files)
+    assess_significance_input = assess_significance_input.mix(normal_files)
+
+    ASSESS_SIGNIFICANCE(assess_significance_input)
     FREEC2BED(FREEC_SOMATIC.out.ratio)
     FREEC2CIRCOS(FREEC_SOMATIC.out.ratio)
-    MAKEGRAPH(FREEC_SOMATIC.out.ratio.join(FREEC_SOMATIC.out.BAF, failOnDuplicate: true, failOnMismatch: true))
+    MAKEGRAPH2(FREEC_SOMATIC.out.ratio.join(FREEC_SOMATIC.out.BAF, failOnDuplicate: true, failOnMismatch: true))
 
     ch_versions = ch_versions.mix(FREEC_SOMATIC.out.versions)
     ch_versions = ch_versions.mix(ASSESS_SIGNIFICANCE.out.versions)
     ch_versions = ch_versions.mix(FREEC2BED.out.versions)
     ch_versions = ch_versions.mix(FREEC2CIRCOS.out.versions)
-    ch_versions = ch_versions.mix(MAKEGRAPH.out.versions)
+    ch_versions = ch_versions.mix(MAKEGRAPH2.out.versions)
 
     emit:
     versions = ch_versions

From ebc8f705a18865c0169ad3787e74b4f350587b56 Mon Sep 17 00:00:00 2001
From: bioloni <nico.schcolnicov@gmail.com>
Date: Fri, 2 Feb 2024 17:26:23 +0000
Subject: [PATCH 02/13] Fixed substring match value

---
 conf/modules/controlfreec.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/modules/controlfreec.config b/conf/modules/controlfreec.config
index 99a50ad4a..389ba72bb 100644
--- a/conf/modules/controlfreec.config
+++ b/conf/modules/controlfreec.config
@@ -18,7 +18,7 @@ process {
     withName: 'ASSESS_SIGNIFICANCE' {
         publishDir = [
             mode: params.publish_dir_mode,
-            path: { (meta.id.contains("_tumor") || meta.id.contains("_normal")) ? "${params.outdir}/variant_calling/controlfreec/${meta.id}/".replaceAll(/_normal|_control/, "") : "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
+            path: { (meta.id.contains("_tumor") || meta.id.contains("_normal")) ? "${params.outdir}/variant_calling/controlfreec/${meta.id}/".replaceAll(/_tumor|_normal/, "") : "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
             pattern: "*{.p.value.txt}"
         ]
     }

From 3df81a9d08e9fedc9c41f7e83ca275c41dcf6108 Mon Sep 17 00:00:00 2001
From: bioloni <nico.schcolnicov@gmail.com>
Date: Fri, 9 Feb 2024 15:22:44 +0000
Subject: [PATCH 03/13] Removed normal files from assess_significance

---
 CHANGELOG.md                                       |  1 +
 conf/modules/controlfreec.config                   |  2 +-
 .../main.nf                                        | 14 --------------
 3 files changed, 2 insertions(+), 15 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 766c417dc..8b55a11fd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- [#1391](https://github.com/nf-core/sarek/pull/1391) - Fixed input channel for ASSESS_SIGNIFICANCE module, updated makegraph to makegraph2.
 - [#1334](https://github.com/nf-core/sarek/pull/1334) - Remove extra v, when reporting tower runs on slack
 - [#1335](https://github.com/nf-core/sarek/pull/1335) - Add docs and validation for bcftools annotation parameters
 - [#1345](https://github.com/nf-core/sarek/pull/1345) - Preserve STDERR for easier debugging
diff --git a/conf/modules/controlfreec.config b/conf/modules/controlfreec.config
index 389ba72bb..2a1ba8e3c 100644
--- a/conf/modules/controlfreec.config
+++ b/conf/modules/controlfreec.config
@@ -18,7 +18,7 @@ process {
     withName: 'ASSESS_SIGNIFICANCE' {
         publishDir = [
             mode: params.publish_dir_mode,
-            path: { (meta.id.contains("_tumor") || meta.id.contains("_normal")) ? "${params.outdir}/variant_calling/controlfreec/${meta.id}/".replaceAll(/_tumor|_normal/, "") : "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
+            path: { meta.id.contains("_normal") ? "${params.outdir}/variant_calling/controlfreec/${meta.id}/".replaceAll(/_normal/, "") : "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
             pattern: "*{.p.value.txt}"
         ]
     }
diff --git a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
index f6a9b7832..074d44eaa 100644
--- a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
+++ b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
@@ -34,38 +34,24 @@ workflow BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC {
     cnv_files = FREEC_SOMATIC.out.CNV
     .multiMap{ meta, cnv ->
         def meta_clone_tumor = meta.clone()
-        def meta_clone_normal = meta.clone()
-        meta_clone_tumor.id = meta.id + "_tumor" //updating meta id so that the p.value file is named differently
-        meta_clone_normal.id = meta.id + "_normal" //updating meta id so that the p.value file is named differently
-
         def tumor_file = cnv instanceof List ? cnv.find { it.toString().endsWith("gz_CNVs") } : cnv //only find if its a list, else it returns only the filename without the path
-        def normal_file = cnv instanceof List ? cnv.find { it.toString().endsWith("gz_normal_CNVs") } : null //only find if its a list, else it returns only the filename without the path
 
-        normal: normal_file == null ? [] : [meta_clone_normal,normal_file] //only fill channel if file was found, else leave it empty
         tumor: tumor_file == null ? [] : [meta_clone_tumor,tumor_file] //only fill channel if file was found, else leave it empty
     }
 
     ratio_files = FREEC_SOMATIC.out.ratio
     .multiMap{ meta, ratio ->
         def meta_clone_tumor = meta.clone()
-        def meta_clone_normal = meta.clone()
-        meta_clone_tumor.id = meta.id + "_tumor" //updating meta id so that the p.value file is named differently
-        meta_clone_normal.id = meta.id + "_normal" //updating meta id so that the p.value file is named differently
-
         def tumor_file = ratio instanceof List ? ratio.find { it.toString().endsWith("gz_ratio.txt") } : ratio //same here as cnv
-        def normal_file = ratio instanceof List ? ratio.find { it.toString().endsWith("gz_normal_ratio.txt") } : null //same here as cnv
 
-        normal: normal_file == null ? [] : [meta_clone_normal,normal_file] //same here as ratio
         tumor: tumor_file == null ? [] : [meta_clone_tumor,tumor_file] //same here as ratio
     }
 
     //Join the pairs
-    normal_files = cnv_files.normal.join(ratio_files.normal, failOnDuplicate: true, failOnMismatch: true)
     tumor_files = cnv_files.tumor.join(ratio_files.tumor, failOnDuplicate: true, failOnMismatch: true)
 
     //Mix all the pairs into input channel
     assess_significance_input = assess_significance_input.mix(tumor_files)
-    assess_significance_input = assess_significance_input.mix(normal_files)
 
     ASSESS_SIGNIFICANCE(assess_significance_input)
     FREEC2BED(FREEC_SOMATIC.out.ratio)

From bac3885aa2d8478f18e19cdbff4b4770e2125655 Mon Sep 17 00:00:00 2001
From: bioloni <nico.schcolnicov@gmail.com>
Date: Fri, 9 Feb 2024 18:17:07 +0000
Subject: [PATCH 04/13] Reverted change in assess_significance module config

---
 conf/modules/controlfreec.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/modules/controlfreec.config b/conf/modules/controlfreec.config
index 2a1ba8e3c..8ed3920c4 100644
--- a/conf/modules/controlfreec.config
+++ b/conf/modules/controlfreec.config
@@ -18,7 +18,7 @@ process {
     withName: 'ASSESS_SIGNIFICANCE' {
         publishDir = [
             mode: params.publish_dir_mode,
-            path: { meta.id.contains("_normal") ? "${params.outdir}/variant_calling/controlfreec/${meta.id}/".replaceAll(/_normal/, "") : "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
+            path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
             pattern: "*{.p.value.txt}"
         ]
     }

From 29c284f49d15725657ce96b3938e885a091934c5 Mon Sep 17 00:00:00 2001
From: bioloni <nico.schcolnicov@gmail.com>
Date: Fri, 9 Feb 2024 18:18:06 +0000
Subject: [PATCH 05/13] Removed unnecesary comment

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

diff --git a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
index 074d44eaa..2a9c13e30 100644
--- a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
+++ b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
@@ -29,7 +29,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC {
 
     FREEC_SOMATIC(controlfreec_input, fasta, fasta_fai, [], dbsnp, dbsnp_tbi, chr_files, mappability, intervals_bed, [])
 
-    //Filter the files that come out of freec somatic as ASSESS_SIGNIFICANCE only takes one cnv and one ratio file, there should be one normal and one non normal pair?
+    //Filter the files that come out of freec somatic as ASSESS_SIGNIFICANCE only takes one cnv and one ratio file
     //Creates empty channel if file is missing
     cnv_files = FREEC_SOMATIC.out.CNV
     .multiMap{ meta, cnv ->

From a12e03894ba0d4a09c177beda221582baaf64cb7 Mon Sep 17 00:00:00 2001
From: bioloni <nico.schcolnicov@gmail.com>
Date: Thu, 15 Feb 2024 17:28:02 +0000
Subject: [PATCH 06/13] Updated makegraph to makegraph2

---
 CHANGELOG.md                                  |  2 +-
 README.md                                     |  1 +
 conf/modules/controlfreec.config              |  2 +-
 modules.json                                  |  6 --
 .../makegraph/controlfreec-makegraph.diff     | 23 -------
 .../controlfreec/makegraph/environment.yml    |  7 ---
 .../nf-core/controlfreec/makegraph/main.nf    | 52 ----------------
 .../nf-core/controlfreec/makegraph/meta.yml   | 60 -------------------
 .../main.nf                                   |  6 +-
 tests/config/pytesttags.yml                   |  2 +-
 10 files changed, 7 insertions(+), 154 deletions(-)
 delete mode 100644 modules/nf-core/controlfreec/makegraph/controlfreec-makegraph.diff
 delete mode 100644 modules/nf-core/controlfreec/makegraph/environment.yml
 delete mode 100644 modules/nf-core/controlfreec/makegraph/main.nf
 delete mode 100644 modules/nf-core/controlfreec/makegraph/meta.yml

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8b55a11fd..afe7020a2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -25,7 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
-- [#1391](https://github.com/nf-core/sarek/pull/1391) - Fixed input channel for ASSESS_SIGNIFICANCE module, updated makegraph to makegraph2.
+- [#1400](https://github.com/nf-core/sarek/pull/1400) - Fixed input channel for ASSESS_SIGNIFICANCE module, updated makegraph to makegraph2.
 - [#1334](https://github.com/nf-core/sarek/pull/1334) - Remove extra v, when reporting tower runs on slack
 - [#1335](https://github.com/nf-core/sarek/pull/1335) - Add docs and validation for bcftools annotation parameters
 - [#1345](https://github.com/nf-core/sarek/pull/1345) - Preserve STDERR for easier debugging
diff --git a/README.md b/README.md
index 770d39032..6df2cd5b0 100644
--- a/README.md
+++ b/README.md
@@ -151,6 +151,7 @@ We thank the following people for their extensive assistance in the development
 - [Malin Larsson](https://github.com/malinlarsson)
 - [Marcel Martin](https://github.com/marcelm)
 - [Nick Smith](https://github.com/nickhsmith)
+- [Nicolas Schcolnicov](https://github.com/nschcolnicov)
 - [Nilesh Tawari](https://github.com/nilesh-tawari)
 - [Olga Botvinnik](https://github.com/olgabot)
 - [Oskar Wacker](https://github.com/WackerO)
diff --git a/conf/modules/controlfreec.config b/conf/modules/controlfreec.config
index 8ed3920c4..d177b1c45 100644
--- a/conf/modules/controlfreec.config
+++ b/conf/modules/controlfreec.config
@@ -50,7 +50,7 @@ process {
         ]
     }
 
-    withName: 'MAKEGRAPH' {
+    withName: 'MAKEGRAPH2' {
         ext.args   = { "${params.cf_ploidy}" }
         publishDir = [
             mode: params.publish_dir_mode,
diff --git a/modules.json b/modules.json
index 1bd8fb78d..a8f8a7e43 100644
--- a/modules.json
+++ b/modules.json
@@ -107,12 +107,6 @@
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
-                    "controlfreec/makegraph": {
-                        "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/controlfreec/makegraph/controlfreec-makegraph.diff"
-                    },
                     "controlfreec/makegraph2": {
                         "branch": "master",
                         "git_sha": "a7bae48d8bccfae99e3b862fa07bbd50a8df6b82",
diff --git a/modules/nf-core/controlfreec/makegraph/controlfreec-makegraph.diff b/modules/nf-core/controlfreec/makegraph/controlfreec-makegraph.diff
deleted file mode 100644
index 13f4208a0..000000000
--- a/modules/nf-core/controlfreec/makegraph/controlfreec-makegraph.diff
+++ /dev/null
@@ -1,23 +0,0 @@
-Changes in module 'nf-core/controlfreec/makegraph'
---- modules/nf-core/controlfreec/makegraph/main.nf
-+++ modules/nf-core/controlfreec/makegraph/main.nf
-@@ -8,7 +8,7 @@
-         'biocontainers/control-freec:11.6b--hdbdd923_0' }"
- 
-     input:
--    tuple val(meta), path(ratio), path(baf), val(ploidy)
-+    tuple val(meta), path(ratio), path(baf)
- 
-     output:
-     tuple val(meta), path("*_BAF.png")       , emit: png_baf
-@@ -25,7 +25,7 @@
-     def prefix = task.ext.prefix ?: "${meta.id}"
-     def baf = baf ?: ""
-     """
--    cat \$(which makeGraph.R) | R --slave --args ${ploidy} ${args} ${ratio} ${baf}
-+    cat \$(which makeGraph.R) | R --slave --args ${args} ${ratio} ${baf}
- 
-     mv *_BAF.txt.png ${prefix}_BAF.png
-     mv *_ratio.txt.log2.png ${prefix}_ratio.log2.png
-
-************************************************************
diff --git a/modules/nf-core/controlfreec/makegraph/environment.yml b/modules/nf-core/controlfreec/makegraph/environment.yml
deleted file mode 100644
index 897eadf3b..000000000
--- a/modules/nf-core/controlfreec/makegraph/environment.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-name: controlfreec_makegraph
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - bioconda::control-freec=11.6b
diff --git a/modules/nf-core/controlfreec/makegraph/main.nf b/modules/nf-core/controlfreec/makegraph/main.nf
deleted file mode 100644
index 8d489f71f..000000000
--- a/modules/nf-core/controlfreec/makegraph/main.nf
+++ /dev/null
@@ -1,52 +0,0 @@
-process CONTROLFREEC_MAKEGRAPH {
-    tag "$meta.id"
-    label 'process_low'
-
-    conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0' :
-        'biocontainers/control-freec:11.6b--hdbdd923_0' }"
-
-    input:
-    tuple val(meta), path(ratio), path(baf)
-
-    output:
-    tuple val(meta), path("*_BAF.png")       , emit: png_baf
-    tuple val(meta), path("*_ratio.log2.png"), emit: png_ratio_log2
-    tuple val(meta), path("*_ratio.png")     , emit: png_ratio
-
-    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 baf = baf ?: ""
-    """
-    cat \$(which makeGraph.R) | R --slave --args ${args} ${ratio} ${baf}
-
-    mv *_BAF.txt.png ${prefix}_BAF.png
-    mv *_ratio.txt.log2.png ${prefix}_ratio.log2.png
-    mv *_ratio.txt.png ${prefix}_ratio.png
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
-    END_VERSIONS
-    """
-
-    stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    """
-    touch ${prefix}_BAF.png
-    touch ${prefix}_ratio.log2.png
-    touch ${prefix}_ratio.png
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC  //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/controlfreec/makegraph/meta.yml b/modules/nf-core/controlfreec/makegraph/meta.yml
deleted file mode 100644
index 6f91db38a..000000000
--- a/modules/nf-core/controlfreec/makegraph/meta.yml
+++ /dev/null
@@ -1,60 +0,0 @@
-name: controlfreec_makegraph
-description: Plot Freec output
-keywords:
-  - cna
-  - cnv
-  - somatic
-  - single
-  - tumor-only
-tools:
-  - controlfreec:
-      description: Copy number and genotype annotation from whole genome and whole exome sequencing data.
-      homepage: http://boevalab.inf.ethz.ch/FREEC
-      documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html
-      tool_dev_url: https://github.com/BoevaLab/FREEC/
-      doi: "10.1093/bioinformatics/btq635"
-      licence: ["GPL >=2"]
-input:
-  # Only when we have meta
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - ratio:
-      type: file
-      description: ratio file generated by FREEC
-      pattern: "*.ratio.txt"
-  - baf:
-      type: file
-      description: .BAF file generated by FREEC
-      pattern: "*.BAF"
-  - ploidy:
-      type: integer
-      description: Ploidy value for which graph should be created
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-  - png_baf:
-      type: file
-      description: Image of BAF plot
-      pattern: "*_BAF.png"
-  - png_ratio_log2:
-      type: file
-      description: Image of ratio log2 plot
-      pattern: "*_ratio.log2.png"
-  - png_ratio:
-      type: file
-      description: Image of ratio plot
-      pattern: "*_ratio.png"
-authors:
-  - "@FriederikeHanssen"
-maintainers:
-  - "@FriederikeHanssen"
diff --git a/subworkflows/local/bam_variant_calling_tumor_only_controlfreec/main.nf b/subworkflows/local/bam_variant_calling_tumor_only_controlfreec/main.nf
index 993faf127..e7178cbaa 100644
--- a/subworkflows/local/bam_variant_calling_tumor_only_controlfreec/main.nf
+++ b/subworkflows/local/bam_variant_calling_tumor_only_controlfreec/main.nf
@@ -8,7 +8,7 @@ include { CONTROLFREEC_FREEC as FREEC_TUMORONLY                  } from '../../.
 include { CONTROLFREEC_ASSESSSIGNIFICANCE as ASSESS_SIGNIFICANCE } from '../../../modules/nf-core/controlfreec/assesssignificance/main'
 include { CONTROLFREEC_FREEC2BED as FREEC2BED                    } from '../../../modules/nf-core/controlfreec/freec2bed/main'
 include { CONTROLFREEC_FREEC2CIRCOS as FREEC2CIRCOS              } from '../../../modules/nf-core/controlfreec/freec2circos/main'
-include { CONTROLFREEC_MAKEGRAPH as MAKEGRAPH                    } from '../../../modules/nf-core/controlfreec/makegraph/main'
+include { CONTROLFREEC_MAKEGRAPH2 as MAKEGRAPH2                  } from '../../../modules/nf-core/controlfreec/makegraph2/main'
 
 workflow BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC {
     take:
@@ -30,13 +30,13 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_CONTROLFREEC {
     ASSESS_SIGNIFICANCE(FREEC_TUMORONLY.out.CNV.join(FREEC_TUMORONLY.out.ratio, failOnDuplicate: true, failOnMismatch: true))
     FREEC2BED(FREEC_TUMORONLY.out.ratio)
     FREEC2CIRCOS(FREEC_TUMORONLY.out.ratio)
-    MAKEGRAPH(FREEC_TUMORONLY.out.ratio.join(FREEC_TUMORONLY.out.BAF, failOnDuplicate: true, failOnMismatch: true))
+    MAKEGRAPH2(FREEC_TUMORONLY.out.ratio.join(FREEC_TUMORONLY.out.BAF, failOnDuplicate: true, failOnMismatch: true))
 
     ch_versions = ch_versions.mix(FREEC_TUMORONLY.out.versions)
     ch_versions = ch_versions.mix(ASSESS_SIGNIFICANCE.out.versions)
     ch_versions = ch_versions.mix(FREEC2BED.out.versions)
     ch_versions = ch_versions.mix(FREEC2CIRCOS.out.versions)
-    ch_versions = ch_versions.mix(MAKEGRAPH.out.versions)
+    ch_versions = ch_versions.mix(MAKEGRAPH2.out.versions)
 
     emit:
     versions = ch_versions
diff --git a/tests/config/pytesttags.yml b/tests/config/pytesttags.yml
index f33e55023..1612a9bb1 100644
--- a/tests/config/pytesttags.yml
+++ b/tests/config/pytesttags.yml
@@ -248,7 +248,7 @@ controlfreec:
   - modules/nf-core/controlfreec/freec/**
   - modules/nf-core/controlfreec/freec2bed/**
   - modules/nf-core/controlfreec/freec2circos/**
-  - modules/nf-core/controlfreec/makegraph/**
+  - modules/nf-core/controlfreec/makegraph2/**
   - modules/nf-core/samtools/mpileup/**
   - subworkflows/local/bam_variant_calling_mpileup/**
   - subworkflows/local/bam_variant_calling_somatic_all/**

From 2c6ab3a8b9de87cb276cb1609fd1cc225c16a44f Mon Sep 17 00:00:00 2001
From: bioloni <nico.schcolnicov@gmail.com>
Date: Thu, 22 Feb 2024 12:27:53 +0000
Subject: [PATCH 07/13] Testing changes to dev branch

---
 .../main.nf                                   | 19 ++++++++-----------
 1 file changed, 8 insertions(+), 11 deletions(-)

diff --git a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
index 2a9c13e30..6dcd8e389 100644
--- a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
+++ b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
@@ -25,35 +25,32 @@ workflow BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC {
 
     ch_versions = Channel.empty()
 
-    assess_significance_input = Channel.empty()
-
     FREEC_SOMATIC(controlfreec_input, fasta, fasta_fai, [], dbsnp, dbsnp_tbi, chr_files, mappability, intervals_bed, [])
 
     //Filter the files that come out of freec somatic as ASSESS_SIGNIFICANCE only takes one cnv and one ratio file
     //Creates empty channel if file is missing
     cnv_files = FREEC_SOMATIC.out.CNV
-    .multiMap{ meta, cnv ->
+    .map{ meta, cnv ->
         def meta_clone_tumor = meta.clone()
         def tumor_file = cnv instanceof List ? cnv.find { it.toString().endsWith("gz_CNVs") } : cnv //only find if its a list, else it returns only the filename without the path
+        def tumor = tumor_file == null ? [] : [meta_clone_tumor,tumor_file] //only fill channel if file was found, else leave it empty
 
-        tumor: tumor_file == null ? [] : [meta_clone_tumor,tumor_file] //only fill channel if file was found, else leave it empty
+        tumor
     }
 
     ratio_files = FREEC_SOMATIC.out.ratio
-    .multiMap{ meta, ratio ->
+    .map{ meta, ratio ->
         def meta_clone_tumor = meta.clone()
         def tumor_file = ratio instanceof List ? ratio.find { it.toString().endsWith("gz_ratio.txt") } : ratio //same here as cnv
+        def tumor = tumor_file == null ? [] : [meta_clone_tumor,tumor_file] //same here as ratio
 
-        tumor: tumor_file == null ? [] : [meta_clone_tumor,tumor_file] //same here as ratio
+        tumor
     }
 
     //Join the pairs
-    tumor_files = cnv_files.tumor.join(ratio_files.tumor, failOnDuplicate: true, failOnMismatch: true)
-
-    //Mix all the pairs into input channel
-    assess_significance_input = assess_significance_input.mix(tumor_files)
+    tumor_files = cnv_files.join(ratio_files, failOnDuplicate: true, failOnMismatch: true)
 
-    ASSESS_SIGNIFICANCE(assess_significance_input)
+    ASSESS_SIGNIFICANCE(tumor_files)
     FREEC2BED(FREEC_SOMATIC.out.ratio)
     FREEC2CIRCOS(FREEC_SOMATIC.out.ratio)
     MAKEGRAPH2(FREEC_SOMATIC.out.ratio.join(FREEC_SOMATIC.out.BAF, failOnDuplicate: true, failOnMismatch: true))

From 847799e1489528d060d98dfe6f063b1efd3ba0fe Mon Sep 17 00:00:00 2001
From: bioloni <nico.schcolnicov@gmail.com>
Date: Fri, 23 Feb 2024 15:39:00 +0000
Subject: [PATCH 08/13] Addressed PR comments

---
 CHANGELOG.md                                              | 2 +-
 conf/modules/controlfreec.config                          | 1 -
 .../bam_variant_calling_somatic_controlfreec/main.nf      | 8 +++-----
 3 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fd648ec62..5d582e20a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -27,7 +27,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
-- [#1400](https://github.com/nf-core/sarek/pull/1400) - Fixed input channel for ASSESS_SIGNIFICANCE module, updated makegraph to makegraph2.
 - [#1334](https://github.com/nf-core/sarek/pull/1334) - Remove extra v, when reporting tower runs on slack
 - [#1335](https://github.com/nf-core/sarek/pull/1335) - Add docs and validation for bcftools annotation parameters
 - [#1345](https://github.com/nf-core/sarek/pull/1345) - Preserve STDERR for easier debugging
@@ -37,6 +36,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1381](https://github.com/nf-core/sarek/pull/1381) - Swap NGSCheckMate bed file for GATK.GRCh37 to one without the `chr` prefix
 - [#1383](https://github.com/nf-core/sarek/pull/1383) - Fix `--three_prime_clip_r{1,2}` parameter documentation
 - [#1390](https://github.com/nf-core/sarek/pull/1390) - Fix badges in README
+- [#1400](https://github.com/nf-core/sarek/pull/1400) - Fixed input channel for ASSESS_SIGNIFICANCE module, updated makegraph to makegraph2.
 - [#1403](https://github.com/nf-core/sarek/pull/1403) - Fix intervals usage with dot in chromosome names
 
 ### Removed
diff --git a/conf/modules/controlfreec.config b/conf/modules/controlfreec.config
index d177b1c45..b6fa043d0 100644
--- a/conf/modules/controlfreec.config
+++ b/conf/modules/controlfreec.config
@@ -51,7 +51,6 @@ process {
     }
 
     withName: 'MAKEGRAPH2' {
-        ext.args   = { "${params.cf_ploidy}" }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
diff --git a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
index 6dcd8e389..3944e7759 100644
--- a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
+++ b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
@@ -31,24 +31,22 @@ workflow BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC {
     //Creates empty channel if file is missing
     cnv_files = FREEC_SOMATIC.out.CNV
     .map{ meta, cnv ->
-        def meta_clone_tumor = meta.clone()
         def tumor_file = cnv instanceof List ? cnv.find { it.toString().endsWith("gz_CNVs") } : cnv //only find if its a list, else it returns only the filename without the path
-        def tumor = tumor_file == null ? [] : [meta_clone_tumor,tumor_file] //only fill channel if file was found, else leave it empty
+        def tumor = tumor_file == null ? [] : [meta,tumor_file] //only fill channel if file was found, else leave it empty
 
         tumor
     }
 
     ratio_files = FREEC_SOMATIC.out.ratio
     .map{ meta, ratio ->
-        def meta_clone_tumor = meta.clone()
         def tumor_file = ratio instanceof List ? ratio.find { it.toString().endsWith("gz_ratio.txt") } : ratio //same here as cnv
-        def tumor = tumor_file == null ? [] : [meta_clone_tumor,tumor_file] //same here as ratio
+        def tumor = tumor_file == null ? [] : [meta,tumor_file] //same here as ratio
 
         tumor
     }
 
     //Join the pairs
-    tumor_files = cnv_files.join(ratio_files, failOnDuplicate: true, failOnMismatch: true)
+    assess_significance_input = cnv_files.join(ratio_files, failOnDuplicate: true, failOnMismatch: true)
 
     ASSESS_SIGNIFICANCE(tumor_files)
     FREEC2BED(FREEC_SOMATIC.out.ratio)

From 7c5d3deb4a515bc81f1d5182120e967ce7c2675b Mon Sep 17 00:00:00 2001
From: bioloni <nico.schcolnicov@gmail.com>
Date: Fri, 23 Feb 2024 15:42:28 +0000
Subject: [PATCH 09/13] Fixed input channel name

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

diff --git a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
index 3944e7759..b18cd5136 100644
--- a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
+++ b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
@@ -48,7 +48,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC {
     //Join the pairs
     assess_significance_input = cnv_files.join(ratio_files, failOnDuplicate: true, failOnMismatch: true)
 
-    ASSESS_SIGNIFICANCE(tumor_files)
+    ASSESS_SIGNIFICANCE(assess_significance_input)
     FREEC2BED(FREEC_SOMATIC.out.ratio)
     FREEC2CIRCOS(FREEC_SOMATIC.out.ratio)
     MAKEGRAPH2(FREEC_SOMATIC.out.ratio.join(FREEC_SOMATIC.out.BAF, failOnDuplicate: true, failOnMismatch: true))

From dc5da4435991b5a712c95ccaf1971d3792b569e1 Mon Sep 17 00:00:00 2001
From: bioloni <nico.schcolnicov@gmail.com>
Date: Fri, 23 Feb 2024 16:01:12 +0000
Subject: [PATCH 10/13] Updated subworkflow code

---
 .../main.nf                                        | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
index b18cd5136..5ad8f24f9 100644
--- a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
+++ b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
@@ -32,17 +32,19 @@ workflow BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC {
     cnv_files = FREEC_SOMATIC.out.CNV
     .map{ meta, cnv ->
         def tumor_file = cnv instanceof List ? cnv.find { it.toString().endsWith("gz_CNVs") } : cnv //only find if its a list, else it returns only the filename without the path
-        def tumor = tumor_file == null ? [] : [meta,tumor_file] //only fill channel if file was found, else leave it empty
-
-        tumor
+        if (!tumor_file){
+            log.error "CNVs tumor file not found for sample $meta.id"
+        }
+        [meta,tumor_file]
     }
 
     ratio_files = FREEC_SOMATIC.out.ratio
     .map{ meta, ratio ->
         def tumor_file = ratio instanceof List ? ratio.find { it.toString().endsWith("gz_ratio.txt") } : ratio //same here as cnv
-        def tumor = tumor_file == null ? [] : [meta,tumor_file] //same here as ratio
-
-        tumor
+        if (!tumor_file){
+            log.error "Ratio tumor file not found for sample $meta.id"
+        }
+        [meta,tumor_file]
     }
 
     //Join the pairs

From 165cefd5a6e357281aa2031ec0624fafd5663363 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicol=C3=A1s=20Schcolnicov?=
 <90359308+nschcolnicov@users.noreply.github.com>
Date: Fri, 23 Feb 2024 18:04:35 -0300
Subject: [PATCH 11/13] Update
 subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf

Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
---
 .../local/bam_variant_calling_somatic_controlfreec/main.nf      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
index 5ad8f24f9..563371ca3 100644
--- a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
+++ b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
@@ -33,7 +33,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC {
     .map{ meta, cnv ->
         def tumor_file = cnv instanceof List ? cnv.find { it.toString().endsWith("gz_CNVs") } : cnv //only find if its a list, else it returns only the filename without the path
         if (!tumor_file){
-            log.error "CNVs tumor file not found for sample $meta.id"
+            error("CNVs tumor file not found for sample $meta.id")
         }
         [meta,tumor_file]
     }

From 4e66d7d4954fa3b8009dd81762baf604972632c3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicol=C3=A1s=20Schcolnicov?=
 <90359308+nschcolnicov@users.noreply.github.com>
Date: Fri, 23 Feb 2024 18:04:45 -0300
Subject: [PATCH 12/13] Update
 subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf

Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
---
 .../local/bam_variant_calling_somatic_controlfreec/main.nf      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
index 563371ca3..203fefd31 100644
--- a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
+++ b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
@@ -42,7 +42,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC {
     .map{ meta, ratio ->
         def tumor_file = ratio instanceof List ? ratio.find { it.toString().endsWith("gz_ratio.txt") } : ratio //same here as cnv
         if (!tumor_file){
-            log.error "Ratio tumor file not found for sample $meta.id"
+            error ("Ratio tumor file not found for sample $meta.id")
         }
         [meta,tumor_file]
     }

From 16055ad4f987c4b9b1f6deb257c6110b29d82ee4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicol=C3=A1s=20Schcolnicov?=
 <90359308+nschcolnicov@users.noreply.github.com>
Date: Fri, 23 Feb 2024 18:05:42 -0300
Subject: [PATCH 13/13] Removed extra space

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

diff --git a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
index 203fefd31..3be4da8e4 100644
--- a/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
+++ b/subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf
@@ -42,7 +42,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_CONTROLFREEC {
     .map{ meta, ratio ->
         def tumor_file = ratio instanceof List ? ratio.find { it.toString().endsWith("gz_ratio.txt") } : ratio //same here as cnv
         if (!tumor_file){
-            error ("Ratio tumor file not found for sample $meta.id")
+            error("Ratio tumor file not found for sample $meta.id")
         }
         [meta,tumor_file]
     }