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 -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