labels,docs and naming

cwl/workflows/workflow_illumina_quality.cwl

@@ -7,29 +7,33 @@ requirements:
   MultipleInputFeatureRequirement: {}
   ScatterFeatureRequirement: {}
 
-label: Read quality control, trimming and contamination filter. 
+label: Illumina read quality control, trimming and contamination filter. 
 doc: | 
-  Workflow for (paired) read quality control, trimming and contamination filtering. 
-  Will output a merged set of read pairs, when multiple datasets are used.
+  Workflow for Illumina paired read quality control, trimming and filtering. 
+  Multiple read pairs will be merged into single paired dataset. 
   Steps:  
-      - FastQC (read quality control)
+      - FastQC (on raw data files)
       - fastp (read quality trimming)
       - Kraken2 taxonomic classification of reads
       - bbduk used for phix and/or rrna filtering
       - bbmap for (contamination) filtering
+      - FastQC (on filtered (merged) data)
 
 outputs:
-  reports_to_folder:
+  reports_folder:
     type: Directory
     label: Filtering reports folder
+    doc: Folder containing all reports of filtering and quality control  
     outputSource: reports_files_to_folder/results
   QC_forward_reads:
     type: File
     label: Filtered forward read
+    doc: Filtered forward read
     outputSource: phix_filter/out_forward_reads
   QC_reverse_reads:
     type: File
     label: Filtered reverse read
+    doc: Filtered reverse read
     outputSource: phix_filter/out_reverse_reads
 
 inputs:
@@ -74,7 +78,7 @@ inputs:
     default: false
   run_kraken2:
     type: boolean?
-    doc: Optionally run Kraken2 contamination inspection
+    doc: Optionally run Kraken2
     label: Kraken2
     default: true
   kraken_database:
@@ -112,9 +116,10 @@ steps:
 
 #############################################
 #### merging of FASTQ files to only one
-  fastq_merge_fwd: 
-    run: ../bash/concatenate.cwl
+  fastq_merge_fwd:
     label: Merge forward reads
+    doc: Merge multiple forward fastq reads to a single file
+    run: ../bash/concatenate.cwl
     in:
       identifier: identifier
       # infiles:
@@ -131,6 +136,7 @@ steps:
 
   fastq_merge_rev:
     label: Merge reverse reads
+    doc: Merge multiple reverse fastq reads to a single file
     run: ../bash/concatenate.cwl
     in:
       identifier: identifier
@@ -189,6 +195,7 @@ steps:
 #### Merging of reference files
   combine_references: 
     label: Combine references
+    doc: Combine references to a single fasta file
     run: ../bash/concatenate.cwl
     in:
       # infiles:

cwl/workflows/workflow_metagenomics_assembly.cwl

@@ -27,7 +27,7 @@ outputs:
     label: Filtered statistics
     doc: Statistics on quality and preprocessing of the reads
     type: Directory
-    outputSource: workflow_quality/reports_to_folder
+    outputSource: workflow_quality/reports_folder
   kraken2_output:
     label: Kraken2 reports
     doc: Kraken2 taxonomic classification reports
@@ -137,7 +137,7 @@ steps:
       identifier: identifier
       step:
         default: 1
-    out: [QC_reverse_reads, QC_forward_reads, reports_to_folder]
+    out: [QC_reverse_reads, QC_forward_reads, reports_folder]
 
 #############################################
 #### Kraken2
@@ -148,7 +148,7 @@ steps:
     in:
       tmp_id: identifier
       identifier: 
-        valueFrom: $(inputs.tmp_id)_filtered_illumina
+        valueFrom: $(inputs.tmp_id)_illumina_filtered
       threads: threads
       database: kraken_database
       forward_reads: workflow_quality/QC_forward_reads

cwl/workflows/workflow_metagenomics_binning.cwl

@@ -300,7 +300,7 @@ steps:
 ### Move to folder if not part of a workflow
   busco_files_to_folder:
     doc: Preparation of BUSCO output files to a specific output folder
-    label: BUSCO output
+    label: BUSCO output folder
     run: ../expressions/files_to_folder.cwl
     in:
       files:

cwl/workflows/workflow_nanopore_assembly.cwl

@@ -31,12 +31,12 @@ outputs:
     label: Read quality and filtering reports
     doc: Quality reports
     type: Directory
-    outputSource: workflow_quality_nanopore/reports_to_folder
+    outputSource: workflow_quality_nanopore/reports_folder
   illumina_quality_stats:
     label: Filtered statistics
     doc: Statistics on quality and preprocessing of the reads
     type: Directory
-    outputSource: workflow_quality_illumina/reports_to_folder
+    outputSource: workflow_quality_illumina/reports_folder
   kraken2_output:
     label: Kraken2 reports
     doc: Kraken2 taxonomic classification reports
@@ -149,7 +149,7 @@ steps:
       identifier: identifier
       step: 
         default: 1
-    out: [filtered_reads, reports_to_folder]
+    out: [filtered_reads, reports_folder]
 #############################################
 #### Quality Illumina
   workflow_quality_illumina:
@@ -169,7 +169,7 @@ steps:
       identifier: identifier
       step: 
         default: 2
-    out: [QC_reverse_reads, QC_forward_reads, reports_to_folder]
+    out: [QC_reverse_reads, QC_forward_reads, reports_folder]
 #############################################
 #### Taxonomic classification of with Kraken2
   nanopore_kraken2:

cwl/workflows/workflow_nanopore_quality.cwl

@@ -17,15 +17,15 @@ doc: |
       - FastQC after filtering (read quality control)
 
 outputs:
-  reports_to_folder:
+  reports_folder:
     type: Directory
-    label: Filtered reads folder
-    doc: Output folder with filtered reads, stats and reports.
+    label: Filtering reports folder
+    doc: Folder containing all reports of filtering and quality control  
     outputSource: reports_files_to_folder/results
   filtered_reads:
     type: File
-    label: Filtered reads
-    doc: Contamination filtered reads
+    label: Filtered nanopore reads
+    doc: Filtered nanopore reads
     outputSource: reference_filter_nanopore/fastq
 
 inputs:
@@ -89,7 +89,7 @@ steps:
       #   source: [nanopore_fastq_reads]
       #   linkMerge: merge_flattened
       #   pickValue: all_non_null
-      file_paths: 
+      file_paths:
         source: reads
         linkMerge: merge_flattened
         pickValue: all_non_null