labels and naming

cwl/workflows/workflow_illumina_quality.cwl

@@ -21,18 +21,15 @@ doc: |
 outputs:
   reports_to_folder:
     type: Directory
-    label: Filtered reads folder
-    doc: Output folder with filtered reads, stats and reports.
+    label: Filtering reports folder
     outputSource: reports_files_to_folder/results
   QC_forward_reads:
     type: File
     label: Filtered forward read
-    doc: Filtered forward read with fastp and (optionally) rrna filtered. (this output is mainly used for other workflows)
     outputSource: phix_filter/out_forward_reads
   QC_reverse_reads:
     type: File
     label: Filtered reverse read
-    doc: Filtered reverse read with fastp and (optionally) rrna filtered. (this output is mainly used for other workflows)
     outputSource: phix_filter/out_reverse_reads
 
 inputs:
@@ -102,7 +99,7 @@ steps:
 #############################################
 #### FASTQC
   fastqc_illumina_before:
-    label: FastQC
+    label: FastQC before
     doc: Quality assessment and report of reads
     run: ../fastqc/fastqc.cwl
     in:
@@ -117,36 +114,36 @@ steps:
 #### merging of FASTQ files to only one
   fastq_merge_fwd: 
     run: ../bash/concatenate.cwl
-    doc: Merge forward reads
+    label: Merge forward reads
     in:
       identifier: identifier
       # infiles:
       #   source: [nanopore_fastq_reads]
       #   linkMerge: merge_flattened
       #   pickValue: all_non_null
-      file_paths: 
+      file_paths:
         source: forward_reads
         linkMerge: merge_flattened
         pickValue: all_non_null
       outname: 
-        valueFrom: $(inputs.identifier)_merged_1.fq.gz
+        valueFrom: $(inputs.identifier)_illumina_merged_1.fq.gz
     out: [output]
 
-  fastq_merge_rev: 
+  fastq_merge_rev:
+    label: Merge reverse reads
     run: ../bash/concatenate.cwl
-    doc: Merge Reverse reads
     in:
       identifier: identifier
       # infiles:
       #   source: [nanopore_fastq_reads]
       #   linkMerge: merge_flattened
       #   pickValue: all_non_null
-      file_paths: 
+      file_paths:
         source: reverse_reads
         linkMerge: merge_flattened
         pickValue: all_non_null
-      outname: 
-        valueFrom: $(inputs.identifier)_merged_2.fq.gz
+      outname:
+        valueFrom: $(inputs.identifier)_illumina_merged_2.fq.gz
     out: [output]
 
 #############################################
@@ -165,12 +162,12 @@ steps:
 #############################################
 #### Kraken2
   illumina_quality_kraken2:
-    label: Taxonomic classification with Kraken2
-    doc: Taxonomic classification of unfiltered FASTQ reads
+    label: Kraken2
+    doc: Taxonomic classification of FASTQ reads
     run: ../kraken2/kraken2.cwl
     in:
       tmp_id: identifier
-      identifier: 
+      identifier:
         valueFrom: $(inputs.tmp_id)_unfiltered_illumina
       threads: threads
       database: kraken_database
@@ -181,8 +178,8 @@ steps:
     out: [sample_report]
   
   illumina_quality_kraken2_krona:
-    label: taxonomic classification visualization
-    doc: visualization of taxonomic classification with Krona
+    label: Krona
+    doc: Visualization of Kraken2 classification with Krona
     run: ../krona/krona.cwl
     in:
       kraken: illumina_quality_kraken2/sample_report
@@ -190,19 +187,20 @@ steps:
 
 #############################################
 #### Merging of reference files
-  merge_references: 
+  combine_references: 
+    label: Combine references
     run: ../bash/concatenate.cwl
     in:
       # infiles:
       #   source: references
       #   linkMerge: merge_flattened
       #   pickValue: all_non_null
-      file_paths: 
+      file_paths:
         source: filter_references
         linkMerge: merge_flattened
         pickValue: all_non_null
       outname:
-        valueFrom: "merged_references.bbmap.fasta.gz"
+        valueFrom: "combined_references.fasta.gz"
     out: [output]
 #########################################
 #### Read mapping 
@@ -214,7 +212,7 @@ steps:
       identifier: identifier
       forward_reads: fastp/out_forward_reads
       reverse_reads: fastp/out_reverse_reads
-      reference: merge_references/output
+      reference: combine_references/output
       output_mapped: keep_reference_mapped_reads
       threads: threads
       memory: memory
@@ -247,9 +245,9 @@ steps:
     doc: Filters illumina spike-in PhiX sequences from reads using bbduk
     run: ../bbmap/bbduk_filter.cwl
     in:
-      identifier: 
+      identifier:
         source: identifier
-        valueFrom: $(self+"_filtered-phix")
+        valueFrom: $(self+"_illumina_filtered")
       forward_reads:
         source:
         - rrna_filter/out_forward_reads
@@ -269,7 +267,7 @@ steps:
 #############################################
 #### FASTQC
   fastqc_illumina_after:
-    label: FastQC
+    label: FastQC after
     doc: Quality assessment and report of reads
     run: ../fastqc/fastqc.cwl
     in:
@@ -280,22 +278,17 @@ steps:
 #############################################
 #### Move to folder if not part of a workflow
   reports_files_to_folder:
-    label: fastp output
+    label: Reports to folder
     doc: Preparation of fastp output files to a specific output folder
     run: ../expressions/files_to_folder.cwl
     in:
-      files: 
+      files:
         source: [fastqc_illumina_before/html_files, fastqc_illumina_before/zip_files, fastqc_illumina_after/html_files, fastqc_illumina_after/zip_files, fastp/html_report, fastp/json_report, reference_filter_illumina/stats, reference_filter_illumina/covstats, reference_filter_illumina/log, illumina_quality_kraken2/sample_report, illumina_quality_kraken2_krona/krona_html, phix_filter/summary, rrna_filter/summary]
         linkMerge: merge_flattened
         pickValue: all_non_null
       step: step
-      destination: 
+      destination:
         valueFrom: $(inputs.step)_Illumina_Read_Quality
-        # valueFrom: |
-        #   ${
-        #     var step = inputs.step;
-        #     return step+"_Illumina_Read_Quality";
-        #   }
     out:
       [results]