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.*".

As an example, this publishDir directive...

pipeline-call-sSV/module/sha512.nf

Lines 18 to 21 in 1ee4910

	publishDir "${params.log_output_dir}/process-log",
	pattern: ".command.*",
	mode: "copy",
	saveAs: { "${task.process}/${task.process}-${task.index}/log${file(it).getName()}" }

... should be replaced with this directive:

ext log_dir { "${task.process}/${task.process}-${task.index}" }

(Just a note, most of our other pipelines use "${task.process.replace(':', '/')}" - I don't know if that `:`` replacement is relevant here.)

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