Update fastqc to version 0.12.1 to increase default memory allocation

NBISweden · Oct 6, 2023 · dcc027e · dcc027e
1 parent 5f1aae8
commit dcc027e
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Showing 4 changed files with 8 additions and 8 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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}