Use `methods.setup_process_afterscript()` for process logs

[nwiltsie]

We should incorporate the new methods.setup_process_afterscript() from uclahs-cds/pipeline-Nextflow-config#64 into this pipeline.

Under the new method, log files are automatically saved to ${params.log_output_dir}/process-log/${task.ext.log_dir}${task.ext.log_dir_suffix}/ (no need to specify a publishDir directive).

${task.ext.log_dir} defaults to ${task.process.replace(':', '/')}.
${task.ext.log_dir_suffix} defaults to a blank string.

The key steps are:

1. Add methods.setup_process_afterscript() to methods.setup().
2. For each Nextflow process:
   1. Remove the file ".command.*" output directive.
   2. Add ext log_dir { ... } and ext log_sur_suffix { ... } directives, if appropriate.
   3. Remove the publishDir directive with pattern: ".command.*".

This pipeline does some atypical configuration with params.workflow_log_output_dir, but that can still be handled with ext log_dir:

Current

pipeline-call-sSNV/main.nf

Lines 74 to 76 in 772592a

	include { somaticsniper } from './module/somaticsniper' addParams(
	workflow_output_dir: "${params.output_dir_base}/SomaticSniper-${params.somaticsniper_version}",
	workflow_log_output_dir: "${params.log_output_dir}/process-log/SomaticSniper-${params.somaticsniper_version}",

pipeline-call-sSNV/module/somaticsniper-processes.nf

Lines 18 to 21 in 772592a

	publishDir path: "${params.workflow_log_output_dir}",
	mode: "copy",
	pattern: ".command.*",
	saveAs: { "${task.process.split(':')[-1]}/log${file(it).getName()}" }

Updated

-    publishDir path: "${params.workflow_log_output_dir}",
-               mode: "copy",
-               pattern: ".command.*",
-               saveAs: { "${task.process.split(':')[-1]}/log${file(it).getName()}" }
+    ext log_dir { "SomaticSniper-${params.somaticsniper_version}/${task.process.split(':')[-1]}" }

See https://github.com/uclahs-cds/pipeline-recalibrate-BAM/pull/76/files for a full example.