diff --git a/config/containers/images.json b/config/containers/images.json index 5785c71..5565c3c 100644 --- a/config/containers/images.json +++ b/config/containers/images.json @@ -2,6 +2,7 @@ "images": { "arriba": "docker://nciccbr/ccbr_arriba_2.0.0:v0.0.1", "bam2strandedbw": "docker://nciccbr/ccbr_bam2strandedbw:v0.0.1", + "base": "docker://nciccbr/ccbr_ubuntu_22.04:v4", "bbtools": "docker://nciccbr/ccbr_bbtools_38.87:v0.0.1", "build_rnaseq": "docker://nciccbr/ccbr_build_rnaseq:v0.0.1", "cutadapt": "docker://nciccbr/ccbr_cutadapt_1.18:v032219", @@ -12,7 +13,6 @@ "multiqc": "docker://nciccbr/ccbr_multiqc_1.15:v2", "picard": "docker://nciccbr/ccbr_picard:v0.0.1", "preseq": "docker://nciccbr/ccbr_preseq:v0.0.1", - "python": "docker://nciccbr/ccbr_python:v0.0.1", "qualimap": "docker://nciccbr/ccbr_qualimap:v0.0.1", "rna": "docker://nciccbr/ccbr_rna:v0.0.1", "rsem": "docker://nciccbr/ccbr_rsem_1.3.3:v1.0", diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index 39ec581..13d70e2 100644 --- a/workflow/rules/common.smk +++ b/workflow/rules/common.smk @@ -27,7 +27,7 @@ rule fc_lane: rname='pl:fc_lane', get_flowcell_lanes=join("workflow", "scripts", "get_flowcell_lanes.py"), envmodules: config['bin'][pfamily]['tool_versions']['PYTHONVER'] - container: config['images']['python'] + container: config['images']['base'] shell: """ python {params.get_flowcell_lanes} {input.R1} {wildcards.name} > {output.fqinfo} """ @@ -201,7 +201,7 @@ rule rsem_merge: pythonscript=join("workflow", "scripts", "merge_rsem_results.py"), inputdir=join(workpath, degall_dir) envmodules: config['bin'][pfamily]['tool_versions']['PYTHONVER'], - container: config['images']['python'] + container: config['images']['base'] shell: """ python {params.pythonscript} {params.annotate} {params.inputdir} {params.inputdir} sed 's/\\t/|/1' {output.gene_counts_matrix} | \ @@ -301,7 +301,7 @@ rule tin_merge: rname="pl:tin_merge", create_matrix=join("workflow", "scripts", "create_tin_matrix.py") envmodules: config['bin'][pfamily]['tool_versions']['PYTHONVER'], - container: config['images']['python'] + container: config['images']['base'] shell: """ python {params.create_matrix} {input.tins} > {output.matrix} """