Fix cgpbigwig_bamcoverage step and update workflow example of rnaseq.cwl

definitions/tools/bam_to_bigwig.cwl

@@ -3,7 +3,7 @@
 cwlVersion: v1.0
 class: CommandLineTool
 label: 'cgpBigWig Converting BAM to BigWig'
-baseCommand: ["bam2bw", "-a -F", "1024"]
+baseCommand: ["bam2bw", "-a", "-F", "1024"]
 arguments: ["-o", { valueFrom: $(inputs.bam.nameroot).bw}]
 requirements:
     - class: DockerRequirement
@@ -16,7 +16,7 @@ inputs:
         inputBinding:
             position: 1
             prefix: '-i'
-        secondaryFiles: [^.bai, .bai]
+        secondaryFiles: [.bai]
     reference:
         type:
             - string

example_data/rnaseq/workflow.yaml

@@ -1,39 +1,49 @@
-instrument_data_bams:
-    - class: File
-      path: gerald_H3MYFBBXX_4_GCCAAT_1k.bam
-    - class: File
-      path: gerald_H3MYFBBXX_5_GCCAAT_1k.bam
-reference_index:
-    class: File
-    path: /gscmnt/gc2560/core/GRC-human-build38_human_90_38/rna_seq_annotation/hisat2.1.0_index/GRCh38DH
-reference_annotation:
-    class: File
-    path: /gscmnt/gc2560/core/GRC-human-build38_human_90_38/rna_seq_annotation/Homo_sapiens.GRCh38DH.90.gtf
-kallisto_index:
-  class: File
-  path: /gscmnt/gc2560/core/GRC-human-build38_human_90_38/rna_seq_annotation/Homo_sapiens.GRCh38.cdna.all.fa.kallisto.idx
-gene_transcript_lookup_table:
-  class: File
-  path: /gscmnt/gc2560/core/GRC-human-build38_human_90_38/rna_seq_annotation/ensembl90.transcriptToGene.tsv
-read_group_id:
-    - '2895626107'
-    - '2895626112'
-read_group_fields:
-    - ['PU:H3MYFBBXX5.4.GCCAAT', 'SM:H_NJ-HCC1395-HCC1395_RNA', 'LB:Pooled_RNA_2891007020-cD1-lib1', 'PL:Illumina', 'CN:WUGSC']
-    - ['PU:H3MYFBBXX5.5.GCCAAT', 'SM:H_NJ-HCC1395-HCC1395_RNA', 'LB:Pooled_RNA_2891007020-cD1-lib1', 'PL:Illumina', 'CN:WUGSC']
-trimming_adapters:
-    class: File
-    path: illumina_multiplex.fa
-trimming_adapter_trim_end: 'RIGHT'
-trimming_adapter_min_overlap: 7
-trimming_max_uncalled: 300
-trimming_min_readlength: 25
-sample_name: H_NJ-HCC1395-HCC1395_RNA
-firststrand: TRUE
-refFlat:
-    class: File
-    path: /gscmnt/gc2560/core/GRC-human-build38_human_90_38_U2AF1_fix/rna_seq_annotation/Homo_sapiens.GRCh38.90.refFlat.txt
-ribosomal_intervals:
-    class: File
-    path: /gscmnt/gc2560/core/GRC-human-build38_human_90_38_U2AF1_fix/rna_seq_annotation/Homo_sapiens.GRCh38.90.rRNA.interval_list
-strand: "second"
+instrument_data_bams:
+    - class: File
+      path: gerald_H3MYFBBXX_4_GCCAAT_1k.bam
+    - class: File
+      path: gerald_H3MYFBBXX_5_GCCAAT_1k.bam
+reference: /gscmnt/gc2560/core/model_data/2887491634/build21f22873ebe0486c8e6f69c15435aa96/all_sequences.fa
+reference_index:
+  class: File
+  path: /gscmnt/gc2560/core/GRC-human-build38_human_95_38_U2AF1_fix/rna_seq_annotation/hisat2.1.0_index/GRCh38DH
+reference_annotation:
+  class: File
+  path: /gscmnt/gc2560/core/GRC-human-build38_human_95_38_U2AF1_fix/rna_seq_annotation/Homo_sapiens.GRCh38.95.gtf
+kallisto_index:
+  class: File
+  path: /gscmnt/gc2560/core/GRC-human-build38_human_95_38_U2AF1_fix/rna_seq_annotation/Homo_sapiens.GRCh38.cdna.all.fa.kallisto.idx
+gene_transcript_lookup_table:
+  class: File
+  path: /gscmnt/gc2560/core/GRC-human-build38_human_95_38_U2AF1_fix/rna_seq_annotation/ensembl95.transcriptToGene.tsv
+read_group_id:
+    - '2895626107'
+    - '2895626112'
+read_group_fields:
+- - PU:H3MYFBBXX.4
+  - SM:H_NJ-HCC1395-HCC1395_RNA
+  - LB:Pooled_RNA_2891007020-cD1-lib1
+  - PL:Illumina
+  - CN:WUGSC
+- - PU:H3MYFBBXX.5
+  - SM:H_NJ-HCC1395-HCC1395_RNA
+  - LB:Pooled_RNA_2891007020-cD1-lib1
+  - PL:Illumina
+  - CN:WUGSC
+trimming_adapters:
+    class: File
+    path: illumina_multiplex.fa
+trimming_adapter_trim_end: 'RIGHT'
+trimming_adapter_min_overlap: 7
+trimming_max_uncalled: 300
+trimming_min_readlength: 25
+sample_name: H_NJ-HCC1395-HCC1395_RNA
+strand: first
+refFlat:
+  class: File
+  path: /gscmnt/gc2560/core/GRC-human-build38_human_95_38_U2AF1_fix/rna_seq_annotation/Homo_sapiens.GRCh38.95.refFlat.txt
+ribosomal_intervals:
+  class: File
+  path: /gscmnt/gc2560/core/GRC-human-build38_human_95_38_U2AF1_fix/rna_seq_annotation/Homo_sapiens.GRCh38.95.ribo_intervals
+species: homo_sapiens
+assembly: GRCh38