Enhancing documentation for viral-pipelines

pipes/WDL/tasks/tasks_16S_amplicon.wdl

@@ -61,7 +61,7 @@ task qiime_import_from_bam {
     }
     runtime {
         docker: docker
-        memory: "~{memory_mb} MiB"
+        memory: "~{memory_mb} GB"
         cpu: cpu
         disk: disk_size_gb + " GB"
         disks: "local-disk " + disk_size_gb + " HDD"
@@ -142,7 +142,7 @@ task trim_reads {
 
     runtime {
         docker: docker
-        memory: "${memory_mb} MiB"
+        memory: "${memory_mb} GB"
         cpu: cpu
         disk: disk_size_gb + " GB"
         disks: "local-disk " + disk_size_gb + " HDD"
@@ -192,7 +192,7 @@ task join_paired_ends {
     }
     runtime {
         docker: docker
-        memory: "${memory_mb} MiB"
+        memory: "${memory_mb} GB"
         cpu: cpu
         disk: disk_size_gb + " GB"
         disks: "local-disk " + disk_size_gb + " HDD"
@@ -267,7 +267,7 @@ task deblur {
     }
     runtime {
         docker: docker
-        memory: "${memory_mb} MiB"
+        memory: "${memory_mb} GB"
         cpu: cpu
         disk: disk_size_gb + " GB"
         disks: "local-disk " + disk_size_gb + " HDD"
@@ -355,7 +355,7 @@ task train_classifier {
     }
     runtime {
         docker: docker
-        memory: "${memory_mb} MiB"
+        memory: "${memory_mb} GB"
         cpu: cpu
         disk: disk_size_gb + " GB"
         disks: "local-disk " + disk_size_gb + " HDD"

pipes/WDL/tasks/tasks_assembly.wdl

@@ -185,7 +185,6 @@ task scaffold {
         patterns: ["*.fasta"],
         category: "other"
       }
-  #didnt include other outputs, not sure if i should
     }
 
     Int disk_size = 375

pipes/WDL/workflows/demux_deplete.wdl

@@ -39,7 +39,7 @@ workflow demux_deplete {
     parameter_meta {
         flowcell_tgz: {
             description: "Illumina BCL directory compressed as tarball. Must contain RunInfo.xml, SampleSheet.csv, RTAComplete.txt, and Data/Intensities/BaseCalls/*",
-            patterns: ["*.tar.gz", ".tar.zst", ".tar.bz2", ".tar.lz4", ".tgz"],
+            patterns: ["*.tar.gz", ".tar.zst", ".tar.bz2", ".tar.lz4", ".tgz", ".tar"],
             category: "required"
 
         }
@@ -59,39 +59,39 @@ workflow demux_deplete {
             category: "advanced"
         }
         spikein_db: {
-            description: "Archeal DNA that is used to track potential contamination within sequencing plate processing.",
+            description: "Synthetic sequences (e.g. ERCC, SDSI) that are used to track potential contamination within sequencing plate processing.",
             category: "advanced"
         }
         read_structure: { 
             description: "Details how the bases should be organized into logical reads.",
             category: "advanced"
         }
         sort_reads: {
-            description: "Barcode/index information organized into barcode files to sort data to separate files for each sample.",
+            description: "Output bam files will be sorted by read name.",
             category: "advanced"
         }
         bmtaggerDbs: {
             description: "Tool that can discriminate between human and bacterial reads and other reads by using short fragments. Databases must be provided to onset depletion.Sequences in fasta format will be indexed on the fly, pre-bmtagger-indexed databases may be provided as tarballs.",
             category: "advanced"
         }
         cleaned_bams_tiny: {
-            description: "BAM files that did not meet the sufficient amount of minimum reads mapped.",
+            description: "cleaned BAM files that contain less than min_reads_per_bam will be included here and omitted from cleaned_reads_unaligned_bams and cleaned_bam_uris",
             category: "other"
         }
         cleaned_bam_uris: {
-            description: "BAM files' URIs tags to clearly define which assembly has been used ",
+            description: "A text file containing a string-serialized version of each File in cleaned_reads_unaligned_bams on a separate line.",
             category: "other"
         }
         cleaned_reads_unaligned_bams: {
-            description: "Unaligned reads without PCR duplicates in BAM format.",
+            description: "Unaligned reads without human reads or PCR duplicates in BAM format. This will not include any bams that contain less than min_reads_per_bam reads.",
             category: "other"
         }
         demux_commonBarcodes: {
             description: "a TSV report of all barcode counts, in descending order.",
             category: "other"
         }
         demux_metrics: { 
-            description: "Output ExtractIlluminaBarcodes metrics file. Default is to dump to a temp file.",
+            description: "Output ExtractIlluminaBarcodes metrics file.",
             category: "other"
         }
         multiqc_report_cleaned: {
@@ -107,7 +107,7 @@ workflow demux_deplete {
             category: "other"
         }
         read_counts_raw: {
-            description: "The number of reads that aligned to gene.",
+            description: "A list of the read counts of each file in raw_reads_unaligned_bams",
             category: "other"
         }
     }