Bump container rnaseq-nf:v1.3.1

Signed-off-by: Paolo Di Tommaso <[email protected]>

Author: pditommaso

docker/Dockerfile

@@ -3,12 +3,14 @@
 # use seqera containers https://seqera.io/containers/
 #
 FROM mambaorg/micromamba:1.5.10-noble
-MAINTAINER Paolo Di Tommaso <[email protected]>
+
+ARG MAMBA_USER=mambauser
+ENV MAMBA_USER=${MAMBA_USER}
+
 
 COPY --chown=$MAMBA_USER:$MAMBA_USER conda.yml /tmp/conda.yml
 RUN micromamba install -y -n base -f /tmp/conda.yml \
     && micromamba install -y -n base conda-forge::procps-ng \
     && micromamba clean -a -y
 
-ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"
-USER root
+ENV PATH="$MAMBA_ROOT_PREFIX/bin:$PATH"

docker/Makefile

@@ -1,4 +1,4 @@
-version ?= v1.3.0
+version ?= v1.3.1
 
 all: build push
 

modules/multiqc/main.nf

@@ -1,7 +1,7 @@
 params.outdir = 'results'
 
 process MULTIQC {
-    conda 'bioconda::multiqc=1.25'
+    conda 'bioconda::multiqc=1.27.1'
     publishDir params.outdir, mode:'copy'
 
     input:

nextflow.config

@@ -31,7 +31,7 @@ params.multiqc = "${projectDir}/multiqc"
 
 profiles {
   standard {
-    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
+    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
   }
 
   'all-reads' {
@@ -58,12 +58,12 @@ profiles {
   }
 
   'docker' {
-    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
+    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
     docker.enabled = true
   }
 
   'singularity' {
-    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
+    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
     singularity.enabled = true
     singularity.autoMounts = true
   }
@@ -80,15 +80,15 @@ profiles {
   }
 
   'slurm' {
-    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
+    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
     process.executor = 'slurm'
     singularity.enabled = true
   }
 
   'batch' {
     params.reads = 's3://rnaseq-nf/data/ggal/lung_{1,2}.fq'
     params.transcriptome = 's3://rnaseq-nf/data/ggal/transcript.fa'
-    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
+    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
     process.executor = 'awsbatch'
     process.queue = 'nextflow-ci'
     workDir = 's3://nextflow-ci/work'
@@ -97,7 +97,7 @@ profiles {
   }
 
   's3-data' {
-    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
+    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
     params.reads = 's3://rnaseq-nf/data/ggal/lung_{1,2}.fq'
     params.transcriptome = 's3://rnaseq-nf/data/ggal/transcript.fa'
   }
@@ -107,19 +107,19 @@ profiles {
       params.reads = 'gs://rnaseq-nf/data/ggal/gut_{1,2}.fq'
       params.multiqc = 'gs://rnaseq-nf/multiqc'
       process.executor = 'google-batch'
-      process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
+      process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
       workDir = 'gs://rnaseq-nf/scratch' // <- replace with your own bucket!
       google.region  = 'europe-west2'
   }
 
   'gs-data' {
-      process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
+      process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
       params.transcriptome = 'gs://rnaseq-nf/data/ggal/transcript.fa'
       params.reads = 'gs://rnaseq-nf/data/ggal/gut_{1,2}.fq'
   }
 
   'azure-batch' {
-    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
+    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'
     workDir = 'az://nf-scratch/work'
     process.executor = 'azurebatch'
     process.queue = 'nextflow-ci' // replace with your own Azure pool name