Update tests for PR #16

This swaps the order of class and cwlVersion Closes #15
rabix · Jan 5, 2021 · 752b3cb · 752b3cb
1 parent 480044c
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diff --git a/tests/cwl/expected-exploded-atac-seq.cwl b/tests/cwl/expected-exploded-atac-seq.cwl
@@ -1,9 +1,11 @@
 #!/usr/bin/env cwl-runner
 
-class: Workflow
 cwlVersion: v1.0
+class: Workflow
 label: ATAC-seq-pipeline-se
 doc: 'ATAC-seq pipeline - reads: SE'
+$namespaces:
+  sbg: https://sevenbridges.com
 
 requirements:
 - class: ScatterFeatureRequirement
@@ -249,8 +251,6 @@ steps:
     - output_trimmed_fastq_read_count
 id: |-
   https://api.sbgenomics.com/v2/apps/kghosesbg/sbpla-31744/ATAC-seq-pipeline-se/2/raw/
-$namespaces:
-  sbg: https://sevenbridges.com
 sbg:appVersion:
 - v1.0
 sbg:content_hash: ad9474546d1d7aba5aa20e3c7a03b5429e5f8ec1d18be92cbab7315600a6bce48

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl
@@ -1,5 +1,7 @@
-class: Workflow
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: Workflow
 doc: 'ATAC-seq 03 mapping - reads: SE'
 
 requirements:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/bam_idxstats.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/bam_idxstats.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 
 requirements:
   InitialWorkDirRequirement:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/bowtie-se.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/bowtie-se.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 
 requirements:
   InlineJavascriptRequirement: {}

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/execute_pcr_bottleneck_coef.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/execute_pcr_bottleneck_coef.cwl
@@ -1,5 +1,7 @@
-class: Workflow
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: Workflow
 doc: ChIP-seq - map - PCR Bottleneck Coefficients
 
 requirements:

diff --git a/...-seq.cwl.steps/map.cwl.steps/execute_pcr_bottleneck_coef.cwl.steps/bedtools_genomecov.cwl b/...-seq.cwl.steps/map.cwl.steps/execute_pcr_bottleneck_coef.cwl.steps/bedtools_genomecov.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 doc: |-
   Tool:    bedtools genomecov (aka genomeCoverageBed)
   Version: v2.25.0

diff --git a/...ed-atac-seq.cwl.steps/map.cwl.steps/execute_pcr_bottleneck_coef.cwl.steps/compute_pbc.cwl b/...ed-atac-seq.cwl.steps/map.cwl.steps/execute_pcr_bottleneck_coef.cwl.steps/compute_pbc.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 doc: Compute PCR Bottleneck Coeficient from BedGraph file.
 
 inputs:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/extract_basename_1.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/extract_basename_1.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 doc: Extracts the base name of a file
 
 requirements:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/extract_basename_2.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/extract_basename_2.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 doc: Extracts the base name of a file
 
 inputs:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/filter-unmapped.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/filter-unmapped.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 
 requirements:
   InlineJavascriptRequirement: {}

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/filtered2sorted.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/filtered2sorted.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 
 requirements:
   InlineJavascriptRequirement: {}

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/index_bams.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/index_bams.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 
 requirements:
   InitialWorkDirRequirement:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/index_dedup_bams.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/index_dedup_bams.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 
 requirements:
   InitialWorkDirRequirement:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/index_dups_marked_bams.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/index_dups_marked_bams.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 
 requirements:
   InitialWorkDirRequirement:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/index_filtered_bam.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/index_filtered_bam.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 
 requirements:
   InitialWorkDirRequirement:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/mapped_filtered_reads_count.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/mapped_filtered_reads_count.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 doc: Extract mapped reads from BAM file using Samtools flagstat command
 
 requirements:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/mapped_reads_count.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/mapped_reads_count.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 doc: Get number of processed reads from Bowtie log.
 
 requirements:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/mark_duplicates.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/mark_duplicates.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 
 requirements:
   InlineJavascriptRequirement: {}

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/percent_mitochondrial_reads.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/percent_mitochondrial_reads.cwl
@@ -1,5 +1,7 @@
-class: ExpressionTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: ExpressionTool
 
 requirements:
   InlineJavascriptRequirement: {}

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/percent_uniq_reads.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/percent_uniq_reads.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 doc: Get number of processed reads from Bowtie log.
 
 requirements:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/preseq-c-curve.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/preseq-c-curve.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 doc: |-
   Usage: c_curve [OPTIONS] <sorted-bed-file>
 

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/remove_duplicates.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/remove_duplicates.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 
 requirements:
   InlineJavascriptRequirement: {}

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/sam2bam.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/sam2bam.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 
 requirements:
   InlineJavascriptRequirement: {}

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/sort_bams.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/sort_bams.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 
 requirements:
   InlineJavascriptRequirement: {}

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/sort_dedup_bams.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/sort_dedup_bams.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 
 requirements:
   InlineJavascriptRequirement: {}

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/sort_dups_marked_bams.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/sort_dups_marked_bams.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 
 requirements:
   InlineJavascriptRequirement: {}

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl
@@ -1,5 +1,7 @@
-class: Workflow
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: Workflow
 doc: ATAC-seq 04 quantification - SE
 
 requirements:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/count-peaks.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/count-peaks.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 doc: Counts lines in a file and returns a suffixed file with that number
 
 requirements:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/count-reads-filtered.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/count-reads-filtered.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 doc: Count number of dedup-ed reads used in peak calling
 
 requirements:

diff --git a/...expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/extract-count-reads-in-peaks.cwl b/...expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/extract-count-reads-in-peaks.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 doc: Extract mapped reads from BAM file using Samtools flagstat command
 
 requirements:

diff --git a/...cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/extract-peak-frag-length.cwl b/...cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/extract-peak-frag-length.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 doc: Extracts best fragment length from SPP output text file
 
 inputs:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/filter-reads-in-peaks.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/filter-reads-in-peaks.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 doc: Filter BAM file to only include reads overlapping with a BED file
 
 requirements:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/peak-calling.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/peak-calling.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 
 requirements:
   InlineJavascriptRequirement: {}

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/peaks-bed-to-bigbed.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/peaks-bed-to-bigbed.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 doc: |
   "bedToBigBed v. 2.7 - Convert bed file to bigBed. (BigBed version: 4)
   usage:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/spp.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/spp.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 
 requirements:
   InlineJavascriptRequirement: {}

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/trunk-peak-score.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/trunk-peak-score.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 doc: Trunk scores in ENCODE bed6+4 files
 
 inputs:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/qc.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/qc.cwl
@@ -1,5 +1,7 @@
-class: Workflow
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: Workflow
 doc: 'ATAC-seq 01 QC - reads: SE'
 
 requirements:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/qc.cwl.steps/compare_read_counts.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/qc.cwl.steps/compare_read_counts.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 doc: Compares 2 files
 
 inputs:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/qc.cwl.steps/count_fastqc_reads.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/qc.cwl.steps/count_fastqc_reads.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 doc: Extracts read count from fastqc_data.txt
 
 inputs:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/qc.cwl.steps/count_raw_reads.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/qc.cwl.steps/count_raw_reads.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 doc: Counts reads in a fastq file
 
 requirements:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/qc.cwl.steps/extract_basename.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/qc.cwl.steps/extract_basename.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 doc: Extracts the base name of a file
 
 requirements:

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/qc.cwl.steps/extract_fastqc_data.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/qc.cwl.steps/extract_fastqc_data.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 doc: |-
   Unzips a zipped fastqc report and returns the fastqc_data.txt file. Unzips the file to pipe and uses redirection
 

diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/qc.cwl.steps/fastqc.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/qc.cwl.steps/fastqc.cwl
@@ -1,5 +1,7 @@
-class: CommandLineTool
+#!/usr/bin/env cwl-runner
+
 cwlVersion: v1.0
+class: CommandLineTool
 
 requirements:
   InlineJavascriptRequirement: {}