From 0a5627df873aeb52ae580384e6021edda40bd18b Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Tue, 22 Oct 2024 17:10:49 +0200
Subject: [PATCH] Bump container rnaseq-nf:v1.3.0

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
---
 conda.yml         | 12 +++++-------
 docker/Dockerfile | 21 ++++++++++-----------
 docker/Makefile   |  6 +++---
 nextflow.config   | 18 +++++++++---------
 4 files changed, 27 insertions(+), 30 deletions(-)

diff --git a/conda.yml b/conda.yml
index 8ed4151..0cfdcc7 100644
--- a/conda.yml
+++ b/conda.yml
@@ -1,10 +1,8 @@
 name: rnaseq-nf
 channels:
-  - seqera
-  - bioconda
-  - conda-forge
-  - defaults
+- conda-forge
+- bioconda
 dependencies:
-  - salmon=1.10.2
-  - fastqc=0.12.1
-  - multiqc=1.15
+- bioconda::fastqc=0.12.1
+- bioconda::multiqc=1.25
+- bioconda::salmon=1.10.3
\ No newline at end of file
diff --git a/docker/Dockerfile b/docker/Dockerfile
index f6147f8..4f7addf 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -1,16 +1,15 @@
-FROM mambaorg/micromamba
+#
+# don't waste time with this
+# use seqera containers 
+# https://seqera.io/containers/
+#
+FROM mambaorg/micromamba:1.5.10-noble
 MAINTAINER Paolo Di Tommaso <paolo.ditommaso@gmail.com>
 
-RUN \
-   micromamba install -y -n base -c defaults -c bioconda -c conda-forge \
-      salmon=1.10.2 \
-      fastqc=0.12.1 \
-      multiqc=1.17 \
-      python=3.11 \
-      typing_extensions \
-      importlib_metadata \
-      procps-ng \
-   && micromamba clean -a -y
+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
diff --git a/docker/Makefile b/docker/Makefile
index 8cc51da..82599a8 100644
--- a/docker/Makefile
+++ b/docker/Makefile
@@ -1,10 +1,10 @@
-version ?= v1.2.1
+version ?= v1.3.0
 
 all: build push
 
 build:
 	cp ../conda.yml .
-	docker build --output=type=docker --progress=plain --tag quay.io/nextflow/rnaseq-nf:${version} .
+	docker build --output=type=docker --progress=plain --tag docker.io/nextflow/rnaseq-nf:${version} .
 	
 push:
-	docker push quay.io/nextflow/rnaseq-nf:${version}
+	docker push docker.io/nextflow/rnaseq-nf:${version}
diff --git a/nextflow.config b/nextflow.config
index 4e8f2b8..19617f7 100755
--- a/nextflow.config
+++ b/nextflow.config
@@ -31,7 +31,7 @@ params.multiqc = "${projectDir}/multiqc"
 
 profiles {
   standard {
-    process.container = 'docker.io/nextflow/rnaseq-nf:v1.2.1'
+    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
   }
 
   'all-reads' {
@@ -54,12 +54,12 @@ profiles {
   }
 
   'docker' {
-    process.container = 'docker.io/nextflow/rnaseq-nf:v1.2.1'
+    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
     docker.enabled = true
   }
 
   'singularity' {
-    process.container = 'docker.io/nextflow/rnaseq-nf:v1.2.1'
+    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
     singularity.enabled = true
     singularity.autoMounts = true
   }
@@ -70,7 +70,7 @@ profiles {
   }
   
   'slurm' {
-    process.container = 'docker.io/nextflow/rnaseq-nf:v1.2.1'
+    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
     process.executor = 'slurm'
     singularity.enabled = true
   }
@@ -78,7 +78,7 @@ profiles {
   '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:v1.2.1'
+    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
     process.executor = 'awsbatch'
     process.queue = 'nextflow-ci'
     workDir = 's3://nextflow-ci/work'
@@ -87,7 +87,7 @@ profiles {
   }
 
   's3-data' {
-    process.container = 'docker.io/nextflow/rnaseq-nf:v1.2.1'
+    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
     params.reads = 's3://rnaseq-nf/data/ggal/lung_{1,2}.fq'
     params.transcriptome = 's3://rnaseq-nf/data/ggal/transcript.fa'
   } 
@@ -97,19 +97,19 @@ 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:v1.2.1'
+      process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
       workDir = 'gs://rnaseq-nf/scratch' // <- replace with your own bucket!
       google.region  = 'europe-west2'
   }
 
   'gs-data' {
-      process.container = 'docker.io/nextflow/rnaseq-nf:v1.2.1'
+      process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
       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:v1.2.1'
+    process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
     workDir = 'az://nf-scratch/work'
     process.executor = 'azurebatch'
     process.queue = 'nextflow-ci' // replace with your own Azure pool name