refactor: spades for ica CDCgov#149

modules/local/spades.nf

@@ -24,10 +24,6 @@ process SPADES {
     tuple val(meta), path("*_spades_outcome.csv") ,                emit: spades_outcome
 
     script:
-    // Adding if/else for if running on ICA it is a requirement to state where the script is, however, this causes CLI users to not run the pipeline from any directory.
-    if (params.ica==false) { ica = "" } 
-    else if (params.ica==true) { ica = "bash ${workflow.launchDir}/bin/" }
-    else { error "Please set params.ica to either \"true\" if running on ICA or \"false\" for all other methods." }
     // define variables
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
@@ -37,14 +33,17 @@ process SPADES {
     def phred_offset = params.phred
     def extended_qc_arg = extended_qc ? "-c" : ""
     def container = task.container.toString() - "staphb/spades@"
+    def script_stats = params.ica ? "${params.ica_path}/pipeline_stats_writer_trimd.sh" : "pipeline_stats_writer_trimd.sh"
+    def script_before = params.ica ? "${params.ica_path}/beforeSpades.sh" : "beforeSpades.sh"
+    def script_after = params.ica ? "${params.ica_path}/afterSpades.sh" : "afterSpades.sh"
     """
     # preemptively create _summary_line.csv and .synopsis file in case spades fails (no contigs or scaffolds created) we can still collect upstream stats. 
-    ${ica}pipeline_stats_writer_trimd.sh -a ${fastp_raw_qc} -b ${fastp_total_qc} -c ${reads[0]} -d ${reads[1]} -e ${kraken2_trimd_report} -f ${k2_bh_summary} -g ${krona_trimd}
-    ${ica}beforeSpades.sh -k ${k2_bh_summary} -n ${prefix} -d ${full_outdir} ${extended_qc_arg}
+    ${script_stats} -a ${fastp_raw_qc} -b ${fastp_total_qc} -c ${reads[0]} -d ${reads[1]} -e ${kraken2_trimd_report} -f ${k2_bh_summary} -g ${krona_trimd}
+    ${script_before} -k ${k2_bh_summary} -n ${prefix} -d ${full_outdir} ${extended_qc_arg}
     #get version information
-    bspades_version=\$(${ica}beforeSpades.sh -V)
-    pipestats_version=\$(${ica}pipeline_stats_writer_trimd.sh -V)
-    aspades_version=\$(${ica}afterSpades.sh -V)
+    bspades_version=\$(${script_before} -V)
+    pipestats_version=\$(${script_stats} -V)
+    aspades_version=\$(${script_after} -V)
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -93,6 +92,6 @@ process SPADES {
     #Create a summaryline file that will be deleted later if spades is successful if not this line shows up in the final Phoenix_output_summary file
     #create file '*_spades_outcome.csv' to state if spades fails, if contigs or scaffolds are created. See spades_failure.nf subworkflow
     #This file will determine if downstream process GENERATE_PIPELINE_STATS_FAILURE and CREATE_SUMMARY_LINE_FAILURE will run (if spades creates contigs, but not scaffolds).
-    ${ica}afterSpades.sh
+    ${script_after}
     """
 }