Fix unit tests: Update outputs

Author: kinow

wdl2cwl/tests/cwl_files/ATAC.cwl

@@ -1106,14 +1106,14 @@ steps:
           - script.bash
 outputs:
   - id: ATAC.bam_chrM_reads_compliant_output
-    outputSource: MakeCompliantChrMBAM/compliant_bam_output
+    outputSource: MakeCompliantChrMBAM.compliant_bam_output
     type: File
   - id: ATAC.bam_filtered_and_sorted_compliant_output
-    outputSource: MakeCompliantFilteredAndSortedBAM/compliant_bam_output
+    outputSource: MakeCompliantFilteredAndSortedBAM.compliant_bam_output
     type: File
   - id: ATAC.snap_qc_output
-    outputSource: SnapPre/snap_qc_output
+    outputSource: SnapPre.snap_qc_output
     type: File
   - id: ATAC.snap_output
-    outputSource: SnapCellByBin/snap_output
+    outputSource: SnapCellByBin.snap_output
     type: File

wdl2cwl/tests/cwl_files/BuildCembaReferences.cwl

@@ -347,24 +347,24 @@ steps:
           - script.bash
 outputs:
   - id: BuildCembaReferences.reference_fasta_dict
-    outputSource: CreateReferenceDictionary/ref_dict_output
+    outputSource: CreateReferenceDictionary.ref_dict_output
     type: File
   - id: BuildCembaReferences.reference_fasta_index
-    outputSource: CreateReferenceFastaIndex/ref_index_output
+    outputSource: CreateReferenceFastaIndex.ref_index_output
     type: File
   - id: BuildCembaReferences.fwd_converted_reference_fasta
-    outputSource: Convert/fwd_converted_reference_fasta_output
+    outputSource: Convert.fwd_converted_reference_fasta_output
     type: File
   - id: BuildCembaReferences.rev_converted_reference_fasta
-    outputSource: Convert/rev_converted_reference_fasta_output
+    outputSource: Convert.rev_converted_reference_fasta_output
     type: File
   - id: BuildCembaReferences.fwd_bowtie2_index_files
-    outputSource: IndexForward/bowtie2_index_files
+    outputSource: IndexForward.bowtie2_index_files
     type:
         items: File
         type: array
   - id: BuildCembaReferences.rev_bowtie2_index_files
-    outputSource: IndexReverse/bowtie2_index_files
+    outputSource: IndexReverse.bowtie2_index_files
     type:
         items: File
         type: array

wdl2cwl/tests/cwl_files/align_and_count.cwl

@@ -133,11 +133,11 @@ steps:
           - script.bash
 outputs:
   - id: align_and_count_report.report
-    outputSource: align_and_count/report
+    outputSource: align_and_count.report
     type: File
   - id: align_and_count_report.report_top_hits
-    outputSource: align_and_count/report_top_hits
+    outputSource: align_and_count.report_top_hits
     type: File
   - id: align_and_count_report.viral_core_version
-    outputSource: align_and_count/viralngs_version
+    outputSource: align_and_count.viralngs_version
     type: string

wdl2cwl/tests/cwl_files/align_and_count_multiple_report.cwl

@@ -274,11 +274,11 @@ steps:
                 contain at least one item.";} else { return "";}}
 outputs:
   - id: align_and_count_multiple_report.report
-    outputSource: align_and_count_summary/count_summary
+    outputSource: align_and_count_summary.count_summary
     type: File
   - id: align_and_count_multiple_report.report_top_hits
-    outputSource: align_and_count_summary_top_hits/count_summary
+    outputSource: align_and_count_summary_top_hits.count_summary
     type: File
   - id: align_and_count_multiple_report.viral_core_version
-    outputSource: align_and_count_summary/viralngs_version
+    outputSource: align_and_count_summary.viralngs_version
     type: string

wdl2cwl/tests/cwl_files/gwas.cwl

@@ -188,8 +188,8 @@ steps:
           - script.bash
 outputs:
   - id: gwas.logistic
-    outputSource: run_gwas/logistic
+    outputSource: run_gwas.logistic
     type: File
   - id: gwas.manhattan_plot
-    outputSource: create_plot/manhattan_plot
+    outputSource: create_plot.manhattan_plot
     type: File

wdl2cwl/tests/cwl_files/merge_svs.cwl

@@ -574,17 +574,17 @@ steps:
           - script.bash
 outputs:
   - id: mergeSvs.bcftools_merged_sv_vcf
-    outputSource: filterBlocklistBcftools/filtered_sv_vcf
+    outputSource: filterBlocklistBcftools.filtered_sv_vcf
     type: File
   - id: mergeSvs.bcftools_merged_annotated_tsv
-    outputSource: bcftoolsAnnotateVariants/sv_variants_tsv
+    outputSource: bcftoolsAnnotateVariants.sv_variants_tsv
     type: File
   - id: mergeSvs.bcftools_merged_filtered_annotated_tsv
-    outputSource: bcftoolsAnnotsvFilter/filtered_tsv
+    outputSource: bcftoolsAnnotsvFilter.filtered_tsv
     type: File
   - id: mergeSvs.survivor_merged_sv_vcf
-    outputSource: filterBlocklistSurvivor/filtered_sv_vcf
+    outputSource: filterBlocklistSurvivor.filtered_sv_vcf
     type: File
   - id: mergeSvs.survivor_merged_annotated_tsv
-    outputSource: survivorAnnotateVariants/sv_variants_tsv
+    outputSource: survivorAnnotateVariants.sv_variants_tsv
     type: File

wdl2cwl/tests/cwl_files/workflow_inputs.cwl

@@ -79,14 +79,14 @@ steps:
         stdout: _stdout
 outputs:
   - id: foo.first_result
-    outputSource: first
+    outputSource: inputs.first
     type: string
   - id: foo.third_result
-    outputSource: third
+    outputSource: inputs.third
     type: float
   - id: foo.echo_out
-    outputSource: echo/out
+    outputSource: echo.out
     type: string
   - id: foo.echo_result
-    outputSource: echo/result
+    outputSource: echo.result
     type: string