fix: upgrade to containers with pythonpath unset

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",

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}
     """