pass assay suffix into modules with params

Author: torres-alexis

RNAseq/Workflow_Documentation/NF_RCP/workflow_code/modules/extend_dge_table.nf

@@ -13,7 +13,6 @@ process EXTEND_DGE_TABLE {
         path("versions.txt"),    emit: versions_txt
 
     script:
-        def output_filename_suffix = params.assay_suffix ?: ""
         def extend_rmd_file = "${projectDir}/bin/extend_dge_table.Rmd"
 
         """
@@ -23,7 +22,7 @@ process EXTEND_DGE_TABLE {
             params = list(
                 work_dir = '\${PWD}',
                 output_directory = '\${PWD}',
-                output_filename_suffix = '${output_filename_suffix}',
+                output_filename_suffix = '${params.assay_suffix}',
                 input_table_path = '${dge_table}'
             ))"
         """

RNAseq/Workflow_Documentation/NF_RCP/workflow_code/modules/generate_pca_table.nf

@@ -13,7 +13,6 @@ process GENERATE_PCA_TABLE {
         path("versions.txt"),    emit: versions_txt
 
     script:
-        def output_filename_suffix = params.assay_suffix ?: ""
         def pca_rmd_file = "${projectDir}/bin/generate_pca_table.Rmd"
 
         """
@@ -23,7 +22,7 @@ process GENERATE_PCA_TABLE {
             params = list(
                 work_dir = '\${PWD}',
                 output_directory = '\${PWD}',
-                output_filename_suffix = '${output_filename_suffix}',
+                output_filename_suffix = '${params.assay_suffix}',
                 input_table_path = '${normalized_counts}'
             ))"
         """

RNAseq/Workflow_Documentation/NF_RCP/workflow_code/modules/multiqc.nf

@@ -10,10 +10,10 @@ process MULTIQC {
 
     output:
     // path("${ mqc_label }_multiqc_GLbulkRNAseq_report.zip"), emit: zipped_report, to do: reimplement zip output w/ cleaned paths
-    path("${ mqc_label }_multiqc_${ params.assay_suffix }_report"), emit: unzipped_report
-    path("${ mqc_label }_multiqc_${ params.assay_suffix }_report.zip"), emit: zipped_report
-    path("${ mqc_label }_multiqc_${ params.assay_suffix }_report/${ mqc_label }_multiqc_${ params.assay_suffix }.html"), emit: html
-    path("${ mqc_label }_multiqc_${ params.assay_suffix }_report/${ mqc_label }_multiqc_${ params.assay_suffix }_data"), emit: data
+    path("${ mqc_label }_multiqc${ params.assay_suffix }_report"), emit: unzipped_report
+    path("${ mqc_label }_multiqc${ params.assay_suffix }_report.zip"), emit: zipped_report
+    path("${ mqc_label }_multiqc${ params.assay_suffix }_report/${ mqc_label }_multiqc${ params.assay_suffix }.html"), emit: html
+    path("${ mqc_label }_multiqc${ params.assay_suffix }_report/${ mqc_label }_multiqc${ params.assay_suffix }_data"), emit: data
     path("versions.yml"), emit: versions
 
     script:
@@ -22,11 +22,11 @@ process MULTIQC {
     multiqc \\
         --force \\
         --interactive \\
-        -o ${ mqc_label }_multiqc_${ params.assay_suffix }_report \\
-        -n ${ mqc_label }_multiqc_${ params.assay_suffix } \\
+        -o ${ mqc_label }_multiqc${ params.assay_suffix  }_report \\
+        -n ${ mqc_label }_multiqc${ params.assay_suffix  } \\
         ${ config_arg } \\
         .
-    zip -r '${ mqc_label }_multiqc_${ params.assay_suffix }_report.zip' '${ mqc_label }_multiqc_${ params.assay_suffix }_report'
+    zip -r '${ mqc_label }_multiqc${ params.assay_suffix  }_report.zip' '${ mqc_label }_multiqc${ params.assay_suffix  }_report'
 
     echo '"${task.process}":' > versions.yml
     echo "    multiqc: \$(multiqc --version | sed "s/multiqc, version //")" >> versions.yml

RNAseq/Workflow_Documentation/NF_RCP/workflow_code/modules/parse_qc_metrics.nf

@@ -11,7 +11,7 @@ process PARSE_QC_METRICS {
         path(rsem_counts)
 
     output:
-        path("qc_metrics_GLbulkRNAseq.csv"), emit: file
+        path("qc_metrics${params.assay_suffix}.csv"), emit: file
 
     script:
         """

RNAseq/Workflow_Documentation/NF_RCP/workflow_code/modules/quantify_rsem_genes.nf

@@ -7,7 +7,7 @@ process QUANTIFY_RSEM_GENES {
     path("03-RSEM_Counts/*")
 
   output:
-    tuple path("RSEM_Unnormalized_Counts_GLbulkRNAseq.csv"), path("RSEM_NumNonZeroGenes_GLbulkRNAseq.csv"), emit: publishables
+    tuple path("RSEM_Unnormalized_Counts${params.assay_suffix}.csv"), path("RSEM_NumNonZeroGenes${params.assay_suffix}.csv"), emit: publishables
 
   script:
     """

RNAseq/Workflow_Documentation/NF_RCP/workflow_code/modules/quantify_star_genes.nf

@@ -7,7 +7,7 @@ process QUANTIFY_STAR_GENES {
     val(strandedness)
 
   output:
-    tuple path("STAR_Unnormalized_Counts_GLbulkRNAseq.csv"), path("STAR_NumNonZeroGenes_GLbulkRNAseq.csv"), emit: publishables
+    tuple path("STAR_Unnormalized_Counts${params.assay_suffix}.csv"), path("STAR_NumNonZeroGenes${params.assay_suffix}.csv"), emit: publishables
 
   script:
     """

RNAseq/Workflow_Documentation/NF_RCP/workflow_code/modules/remove_rrna_featurecounts.nf

@@ -18,15 +18,15 @@ process REMOVE_RRNA_FEATURECOUNTS {
         path rrna_ids_file
 
     output:
-        path("rRNA_removed_FeatureCounts_GLbulkRNAseq.tsv"), emit: counts_rrnarm
+        path("rRNA_removed_FeatureCounts${params.assay_suffix}.tsv"), emit: counts_rrnarm
         path("rRNA_counts.txt"), emit: rrnarm_summary
 
     script:
         """
         python $projectDir/bin/remove_rrna_featurecounts.py \
             ${counts_file} \
             ${rrna_ids_file} \
-            rRNA_removed_FeatureCounts_GLbulkRNAseq.tsv \
+            rRNA_removed_FeatureCounts${params.assay_suffix}.tsv \
             rRNA_counts.txt
         """
 }