From dcc027e674ec14aad4cc2e53afc1f3811cf86966 Mon Sep 17 00:00:00 2001
From: verku <verena.kutschera@scilifelab.se>
Date: Fri, 6 Oct 2023 09:53:46 +0200
Subject: [PATCH] Update fastqc to version 0.12.1 to increase default memory
 allocation

---
 workflow/rules/1.1_fastq_processing.smk         | 10 +++++-----
 workflow/rules/13_GERP.smk                      |  2 +-
 workflow/rules/3.1_bam_rmdup_realign_indels.smk |  2 +-
 workflow/rules/3.2_historical_bam_mapDamage.smk |  2 +-
 4 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/workflow/rules/1.1_fastq_processing.smk b/workflow/rules/1.1_fastq_processing.smk
index d6c5a25..ad405e0 100644
--- a/workflow/rules/1.1_fastq_processing.smk
+++ b/workflow/rules/1.1_fastq_processing.smk
@@ -50,7 +50,7 @@ rule fastqc_historical_raw:
         "data/logs/1.1_fastq_processing/historical/{sample}_{index}_{lane}_R{nr}_fastqc_historical_raw.log",
     threads: 2
     singularity:
-        "docker://biocontainers/fastqc:v0.11.9_cv7"
+        "docker://quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0"
     shell:
         """
         fastqc -o {params.dir} -t {threads} --extract {input.fastq} 2> {log}
@@ -115,7 +115,7 @@ rule fastqc_modern_raw:
         "data/logs/1.1_fastq_processing/modern/{sample}_{index}_{lane}_R{nr}_fastqc_modern_raw.log",
     threads: 2
     singularity:
-        "docker://biocontainers/fastqc:v0.11.9_cv7"
+        "docker://quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0"
     shell:
         """
         fastqc -o {params.dir} -t {threads} --extract {input.fastq} 2> {log}
@@ -219,7 +219,7 @@ rule fastqc_historical_merged:
         "historical_fastq_trimmed_group"
     threads: 2
     singularity:
-        "docker://biocontainers/fastqc:v0.11.9_cv7"
+        "docker://quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0"
     shell:
         """
         fastqc -o {params.dir} -t {threads} --extract {input} 2> {log}
@@ -242,7 +242,7 @@ rule fastqc_historical_unmerged:
         "historical_fastq_trimmed_group"
     threads: 2
     singularity:
-        "docker://biocontainers/fastqc:v0.11.9_cv7"
+        "docker://quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0"
     shell:
         """
         if [ -s {input} ]
@@ -270,7 +270,7 @@ rule fastqc_modern_trimmed:
         "results/logs/1.1_fastq_processing/modern/{sample}_{index}_{lane}_R{nr}_trimmed_fastqc_modern_trimmed.log",
     threads: 2
     singularity:
-        "docker://biocontainers/fastqc:v0.11.9_cv7"
+        "docker://quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0"
     shell:
         """
         fastqc -o {params.dir} -t {threads} --extract {input} 2> {log}
diff --git a/workflow/rules/13_GERP.smk b/workflow/rules/13_GERP.smk
index cdf9c17..e88d846 100644
--- a/workflow/rules/13_GERP.smk
+++ b/workflow/rules/13_GERP.smk
@@ -361,7 +361,7 @@ rule outgroup_fastqc:
         "results/logs/13_GERP/fastq/{gerpref}_outgroup_fastqc.log",
     threads: 2
     singularity:
-        "docker://biocontainers/fastqc:v0.11.9_cv7"
+        "docker://quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0"
     shell:
         """
         fastqc -o {params.dir} -t {threads} --extract {input.fastq} 2> {log}
diff --git a/workflow/rules/3.1_bam_rmdup_realign_indels.smk b/workflow/rules/3.1_bam_rmdup_realign_indels.smk
index 6eba498..a876557 100644
--- a/workflow/rules/3.1_bam_rmdup_realign_indels.smk
+++ b/workflow/rules/3.1_bam_rmdup_realign_indels.smk
@@ -594,7 +594,7 @@ rule realigned_bam_fastqc:
         "results/logs/3.1_bam_rmdup_realign_indels/{dataset}/" + REF_NAME + "/{sample}_realigned_bam_fastqc.log",
     threads: 2
     singularity:
-        "docker://biocontainers/fastqc:v0.11.9_cv7"
+        "docker://quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0"
     shell:
         """
         fastqc -o {params.dir} -t {threads} --extract {input.bam} 2> {log}
diff --git a/workflow/rules/3.2_historical_bam_mapDamage.smk b/workflow/rules/3.2_historical_bam_mapDamage.smk
index 6eccf10..3d4ad83 100644
--- a/workflow/rules/3.2_historical_bam_mapDamage.smk
+++ b/workflow/rules/3.2_historical_bam_mapDamage.smk
@@ -100,7 +100,7 @@ rule rescaled_bam_fastqc:
         "results/logs/3.2_historical_bam_mapDamage/" + REF_NAME + "/{sample}_rescaled_bam_fastqc.log",
     threads: 2
     singularity:
-        "docker://biocontainers/fastqc:v0.11.9_cv7"
+        "docker://quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0"
     shell:
         """
         fastqc -o {params.dir} -t {threads} --extract {input.bam} 2> {log}