From 532465849d840c8a2678f90eb84a950722a204d6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Noirot=20C=C3=A9line?= <celine.noirot@inra.fr>
Date: Mon, 10 Feb 2025 15:01:02 +0100
Subject: [PATCH 1/3] Upgrade multiQC
---
conf/base.config | 1 +
conf/test.config | 1 +
modules/multiqc.nf | 2 +-
3 files changed, 3 insertions(+), 1 deletion(-)
diff --git a/conf/base.config b/conf/base.config
index aa3d2cd..768c2dc 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -28,6 +28,7 @@ process {
memory = { 8.GB * task.attempt }
}
withName: MULTIQC {
+ container = 'quay.io/biocontainers/multiqc:1.27.1--pyhdfd78af_0'
memory = { 8.GB * task.attempt }
}
withName: HOST_FILTER {
diff --git a/conf/test.config b/conf/test.config
index 9bac780..cd3005c 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -18,6 +18,7 @@ process {
memory = { 2.GB * task.attempt }
}
withName: MULTIQC {
+ container = 'quay.io/biocontainers/multiqc:1.27.1--pyhdfd78af_0'
executor = "local"
memory = { 2.GB * task.attempt }
}
diff --git a/modules/multiqc.nf b/modules/multiqc.nf
index d4581ad..68b8816 100644
--- a/modules/multiqc.nf
+++ b/modules/multiqc.nf
@@ -26,7 +26,7 @@ process MULTIQC {
script:
"""
- multiqc . --config ${multiqc_config} -m custom_content -m fastqc -m cutadapt -m sickle -m kaiju -m quast -m prokka -m featureCounts -m samtools
+ multiqc . --config ${multiqc_config} -m custom_content -m fastqc -m cutadapt -m sickle -m kaiju -m quast -m prokka -m featurecounts -m samtools
multiqc --version > v_multiqc.txt
"""
}
--
GitLab
From 94e369f4c893acb7b5905c5518cbcb2bcfc4fca9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Noirot=20C=C3=A9line?= <celine.noirot@inra.fr>
Date: Mon, 10 Feb 2025 15:08:41 +0100
Subject: [PATCH 2/3] remove multiQC version from process
---
modules/get_software_versions.nf | 1 -
1 file changed, 1 deletion(-)
diff --git a/modules/get_software_versions.nf b/modules/get_software_versions.nf
index a60f217..97cbef9 100644
--- a/modules/get_software_versions.nf
+++ b/modules/get_software_versions.nf
@@ -17,7 +17,6 @@ process GET_SOFTWARE_VERSIONS {
echo $workflow.manifest.version > v_pipeline.txt
echo $workflow.nextflow.version > v_nextflow.txt
python --version &> v_python.txt
- multiqc --version &> v_multiqc.txt
scrape_software_versions.py > software_versions_mqc.yaml
"""
}
\ No newline at end of file
--
GitLab
From 2fc41a912e1f6c6ceea9787235feea99c1e5ad55 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Noirot=20C=C3=A9line?= <celine.noirot@inra.fr>
Date: Mon, 10 Feb 2025 15:36:54 +0100
Subject: [PATCH 3/3] remove multiQC from yml
---
env/metagWGS.yml | 1 -
1 file changed, 1 deletion(-)
diff --git a/env/metagWGS.yml b/env/metagWGS.yml
index 463510d..dbde1c5 100644
--- a/env/metagWGS.yml
+++ b/env/metagWGS.yml
@@ -19,7 +19,6 @@ dependencies:
- krona=2.8.1
- megahit=1.2.9
- minimap2=2.24
- - multiqc=1.14
- pandas=1.5.2
- plotly
- prodigal=2.6.3
--
GitLab