Add stub for multiqc path cleaning

Author: torres-alexis

RNAseq/Workflow_Documentation/NF_RCP/workflow_code/conf/by_docker_image.config

@@ -60,7 +60,7 @@ process {
         container = "quay.io/biocontainers/rsem:1.3.3--pl526ha52163a_0"
     }
 
-    withName: 'GET_ACCESSIONS|FETCH_ISA|ISA_TO_RUNSHEET|RUNSHEET_FROM_ISA|GENERATE_MD5SUMS|SOFTWARE_VERSIONS|UPDATE_ISA_TABLES|PARSE_QC_METRICS|REMOVE_RRNA_FEATURECOUNTS|MD5SUM' {
+    withName: 'GET_ACCESSIONS|FETCH_ISA|ISA_TO_RUNSHEET|RUNSHEET_FROM_ISA|GENERATE_MD5SUMS|SOFTWARE_VERSIONS|UPDATE_ISA_TABLES|PARSE_QC_METRICS|REMOVE_RRNA_FEATURECOUNTS|MD5SUM|CLEAN_MULTIQC_PATHS' {
         container = "quay.io/nasa_genelab/dp_tools:1.3.5"
     }
 

RNAseq/Workflow_Documentation/NF_RCP/workflow_code/conf/local.config

@@ -17,7 +17,7 @@ process {
     maxErrors     = '-1'
 
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
-    withName:'GET_ACCESSIONS|FETCH_ISA|ISA_TO_RUNSHEET|PARSE_ANNOTATIONS_TABLE|COPY_READS|GET_MAX_READ_LENGTH|ADD_GENE_ANNOTATIONS|EXTEND_DGE_TABLE|VV_RAW_READS|GET_GTF_FEATURES|REMOVE_RRNA_FEATURECOUNTS|MD5SUM' {
+    withName:'GET_ACCESSIONS|FETCH_ISA|ISA_TO_RUNSHEET|PARSE_ANNOTATIONS_TABLE|COPY_READS|GET_MAX_READ_LENGTH|ADD_GENE_ANNOTATIONS|EXTEND_DGE_TABLE|VV_RAW_READS|GET_GTF_FEATURES|REMOVE_RRNA_FEATURECOUNTS|MD5SUM|CLEAN_MULTIQC_PATHS' {
         cpus   = { 1                    }
         memory = { 2.GB                 }
     }

RNAseq/Workflow_Documentation/NF_RCP/workflow_code/conf/slurm.config

@@ -18,7 +18,7 @@ process {
     cache = 'lenient'
 
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
-    withName:'GET_ACCESSIONS|FETCH_ISA|ISA_TO_RUNSHEET|PARSE_ANNOTATIONS_TABLE|COPY_READS|GET_MAX_READ_LENGTH|ADD_GENE_ANNOTATIONS|EXTEND_DGE_TABLE|VV_RAW_READS|GET_GTF_FEATURES|REMOVE_RRNA_FEATURECOUNTS|MD5SUM' {
+    withName:'GET_ACCESSIONS|FETCH_ISA|ISA_TO_RUNSHEET|PARSE_ANNOTATIONS_TABLE|COPY_READS|GET_MAX_READ_LENGTH|ADD_GENE_ANNOTATIONS|EXTEND_DGE_TABLE|VV_RAW_READS|GET_GTF_FEATURES|REMOVE_RRNA_FEATURECOUNTS|MD5SUM|CLEAN_MULTIQC_PATHS' {
         cpus   = { 1                    }
         memory = { 2.GB                 }
     }

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

@@ -0,0 +1,20 @@
+process CLEAN_MULTIQC_PATHS {
+    tag "${mqc_label}"
+
+    input:
+        path(multiqc_report_zip)
+        val(mqc_label)
+
+    output:
+        path("output/${mqc_label}_multiqc${params.assay_suffix}_report.zip"), emit: zipped_report
+
+    script:
+        """
+        # Setup
+        mkdir -p output
+        unzip -q ${multiqc_report_zip} -d ./output
+        
+        cd ./output
+        zip -r ${multiqc_report_zip} . -i "*_data" "*.html"
+        """
+}