From 752b3cbab9f202873948b7249a44dad1e409484f Mon Sep 17 00:00:00 2001 From: Kaushik Ghose Date: Tue, 5 Jan 2021 10:04:11 -0500 Subject: [PATCH] Update tests for PR #16 This swaps the order of class and cwlVersion Closes #15 --- tests/cwl/expected-exploded-atac-seq.cwl | 6 +- .../map.cwl | 4 +- .../map.cwl.steps/bam_idxstats.cwl | 4 +- .../map.cwl.steps/bowtie-se.cwl | 4 +- .../execute_pcr_bottleneck_coef.cwl | 4 +- .../bedtools_genomecov.cwl | 4 +- .../compute_pbc.cwl | 4 +- .../map.cwl.steps/extract_basename_1.cwl | 4 +- .../map.cwl.steps/extract_basename_2.cwl | 4 +- .../map.cwl.steps/filter-unmapped.cwl | 4 +- .../map.cwl.steps/filtered2sorted.cwl | 4 +- .../map.cwl.steps/index_bams.cwl | 4 +- .../map.cwl.steps/index_dedup_bams.cwl | 4 +- .../map.cwl.steps/index_dups_marked_bams.cwl | 4 +- .../map.cwl.steps/index_filtered_bam.cwl | 4 +- .../mapped_filtered_reads_count.cwl | 4 +- .../map.cwl.steps/mapped_reads_count.cwl | 4 +- .../map.cwl.steps/mark_duplicates.cwl | 4 +- .../percent_mitochondrial_reads.cwl | 4 +- .../map.cwl.steps/percent_uniq_reads.cwl | 4 +- .../map.cwl.steps/preseq-c-curve.cwl | 4 +- .../map.cwl.steps/remove_duplicates.cwl | 4 +- .../map.cwl.steps/sam2bam.cwl | 4 +- .../map.cwl.steps/sort_bams.cwl | 4 +- .../map.cwl.steps/sort_dedup_bams.cwl | 4 +- .../map.cwl.steps/sort_dups_marked_bams.cwl | 4 +- .../peak_call.cwl | 4 +- .../peak_call.cwl.steps/count-peaks.cwl | 4 +- .../count-reads-filtered.cwl | 4 +- .../extract-count-reads-in-peaks.cwl | 4 +- .../extract-peak-frag-length.cwl | 4 +- .../filter-reads-in-peaks.cwl | 4 +- .../peak_call.cwl.steps/peak-calling.cwl | 4 +- .../peaks-bed-to-bigbed.cwl | 4 +- .../peak_call.cwl.steps/spp.cwl | 4 +- .../peak_call.cwl.steps/trunk-peak-score.cwl | 4 +- .../qc.cwl | 4 +- .../qc.cwl.steps/compare_read_counts.cwl | 4 +- .../qc.cwl.steps/count_fastqc_reads.cwl | 4 +- .../qc.cwl.steps/count_raw_reads.cwl | 4 +- .../qc.cwl.steps/extract_basename.cwl | 4 +- .../qc.cwl.steps/extract_fastqc_data.cwl | 4 +- .../qc.cwl.steps/fastqc.cwl | 4 +- .../overrepresented_sequence_extract.cwl | 4 +- .../quant.cwl | 4 +- .../quant.cwl.steps/bamcoverage.cwl | 4 +- .../quant.cwl.steps/bdg2bw-raw.cwl | 4 +- .../quant.cwl.steps/bedsort_genomecov.cwl | 4 +- .../quant.cwl.steps/bedtools_genomecov.cwl | 4 +- .../trimm.cwl | 4 +- .../trimm.cwl.steps/count_fastq_reads.cwl | 4 +- .../trimm.cwl.steps/extract_basename.cwl | 4 +- .../trimm.cwl.steps/trimmomatic.cwl | 4 +- tests/cwl/formatted-atac-seq-pipeline.cwl | 106 +++++++++--------- tests/cwl/formatted-commented.cwl | 2 +- tests/cwl/formatted-no-comment.cwl | 2 +- tests/cwl/formatted-other-runner.cwl | 2 +- 57 files changed, 215 insertions(+), 111 deletions(-) diff --git a/tests/cwl/expected-exploded-atac-seq.cwl b/tests/cwl/expected-exploded-atac-seq.cwl index f4c8e61..f6a059b 100644 --- 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 index 536b0ac..cf0b709 100644 --- 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 index 57ca7a7..b39e702 100644 --- 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 index 037c20b..9ee13b0 100644 --- 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 index b6405cb..0b059c3 100644 --- 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/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/execute_pcr_bottleneck_coef.cwl.steps/bedtools_genomecov.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/execute_pcr_bottleneck_coef.cwl.steps/bedtools_genomecov.cwl index 33859d6..7715c6e 100644 --- a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/execute_pcr_bottleneck_coef.cwl.steps/bedtools_genomecov.cwl +++ b/tests/cwl/expected-exploded-atac-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/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/execute_pcr_bottleneck_coef.cwl.steps/compute_pbc.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/execute_pcr_bottleneck_coef.cwl.steps/compute_pbc.cwl index 0fdc4f7..0ade455 100644 --- a/tests/cwl/expected-exploded-atac-seq.cwl.steps/map.cwl.steps/execute_pcr_bottleneck_coef.cwl.steps/compute_pbc.cwl +++ b/tests/cwl/expected-exploded-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 index 11d4529..20d0f2d 100644 --- 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 index bc3f196..15f1bf6 100644 --- 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 index 972f535..dac2b42 100644 --- 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 index 58ace72..23d32b2 100644 --- 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 index 5b95d4a..4d5ff8a 100644 --- 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 index 5b95d4a..4d5ff8a 100644 --- 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 index 5b95d4a..4d5ff8a 100644 --- 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 index 5b95d4a..4d5ff8a 100644 --- 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 index 3d04775..7847e7a 100644 --- 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 index eb6aa0d..394f764 100644 --- 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 index 764cad3..6a260bd 100644 --- 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 index 1a9ab7f..6cd30b1 100644 --- 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 index 36e35be..a09125d 100644 --- 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 index 09e466a..c3298a4 100644 --- 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] 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 index 4424c8f..6028e5f 100644 --- 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 index c1a880a..ebdded5 100644 --- 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 index 58ace72..23d32b2 100644 --- 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 index 58ace72..23d32b2 100644 --- 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 index 58ace72..23d32b2 100644 --- 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 index a2fdc91..d807c5b 100644 --- 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 index 3d83a5c..da2fff2 100644 --- 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 index 6aea7f3..dc7d050 100644 --- 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/tests/cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/extract-count-reads-in-peaks.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/extract-count-reads-in-peaks.cwl index 3d04775..7847e7a 100644 --- a/tests/cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/extract-count-reads-in-peaks.cwl +++ b/tests/cwl/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/tests/cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/extract-peak-frag-length.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/extract-peak-frag-length.cwl index 0e7d874..3790f9a 100644 --- a/tests/cwl/expected-exploded-atac-seq.cwl.steps/peak_call.cwl.steps/extract-peak-frag-length.cwl +++ b/tests/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 index 86dd99e..22bebec 100644 --- 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 index b2ca67e..01263aa 100644 --- 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 index e436c81..9a766b9 100644 --- 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 index 4231824..34b1733 100644 --- 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 index 4a54e29..0254b99 100644 --- 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 index 30cfbb4..d1f8e92 100644 --- 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 index 210d4c7..e77e3a4 100644 --- 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 index d6ab8c1..df88c79 100644 --- 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 index 044aedd..5324e47 100644 --- 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 index 11d4529..20d0f2d 100644 --- 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 index ce258d3..100fc36 100644 --- 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 index 012087c..b16e4a4 100644 --- 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: {} diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/qc.cwl.steps/overrepresented_sequence_extract.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/qc.cwl.steps/overrepresented_sequence_extract.cwl index 64fcad3..d20e7b5 100644 --- a/tests/cwl/expected-exploded-atac-seq.cwl.steps/qc.cwl.steps/overrepresented_sequence_extract.cwl +++ b/tests/cwl/expected-exploded-atac-seq.cwl.steps/qc.cwl.steps/overrepresented_sequence_extract.cwl @@ -1,5 +1,7 @@ -class: CommandLineTool +#!/usr/bin/env cwl-runner + cwlVersion: v1.0 +class: CommandLineTool inputs: default_adapters_file: diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/quant.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/quant.cwl index 2723d68..4bbf5c4 100644 --- a/tests/cwl/expected-exploded-atac-seq.cwl.steps/quant.cwl +++ b/tests/cwl/expected-exploded-atac-seq.cwl.steps/quant.cwl @@ -1,5 +1,7 @@ -class: Workflow +#!/usr/bin/env cwl-runner + cwlVersion: v1.0 +class: Workflow doc: ATAC-seq - Quantification requirements: diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/quant.cwl.steps/bamcoverage.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/quant.cwl.steps/bamcoverage.cwl index 729df34..c03ab41 100644 --- a/tests/cwl/expected-exploded-atac-seq.cwl.steps/quant.cwl.steps/bamcoverage.cwl +++ b/tests/cwl/expected-exploded-atac-seq.cwl.steps/quant.cwl.steps/bamcoverage.cwl @@ -1,5 +1,7 @@ -class: CommandLineTool +#!/usr/bin/env cwl-runner + cwlVersion: v1.0 +class: CommandLineTool doc: | usage: An example usage is:$ bamCoverage -b reads.bam -o coverage.bw diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/quant.cwl.steps/bdg2bw-raw.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/quant.cwl.steps/bdg2bw-raw.cwl index df11692..e5887c9 100644 --- a/tests/cwl/expected-exploded-atac-seq.cwl.steps/quant.cwl.steps/bdg2bw-raw.cwl +++ b/tests/cwl/expected-exploded-atac-seq.cwl.steps/quant.cwl.steps/bdg2bw-raw.cwl @@ -1,5 +1,7 @@ -class: CommandLineTool +#!/usr/bin/env cwl-runner + cwlVersion: v1.0 +class: CommandLineTool doc: 'Tool: bedGraphToBigWig v 4 - Convert a bedGraph file to bigWig format.' requirements: diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/quant.cwl.steps/bedsort_genomecov.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/quant.cwl.steps/bedsort_genomecov.cwl index d505f8e..64c9d79 100644 --- a/tests/cwl/expected-exploded-atac-seq.cwl.steps/quant.cwl.steps/bedsort_genomecov.cwl +++ b/tests/cwl/expected-exploded-atac-seq.cwl.steps/quant.cwl.steps/bedsort_genomecov.cwl @@ -1,5 +1,7 @@ -class: CommandLineTool +#!/usr/bin/env cwl-runner + cwlVersion: v1.0 +class: CommandLineTool doc: | bedSort - Sort a .bed file by chrom,chromStart usage: diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/quant.cwl.steps/bedtools_genomecov.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/quant.cwl.steps/bedtools_genomecov.cwl index 33859d6..7715c6e 100644 --- a/tests/cwl/expected-exploded-atac-seq.cwl.steps/quant.cwl.steps/bedtools_genomecov.cwl +++ b/tests/cwl/expected-exploded-atac-seq.cwl.steps/quant.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/tests/cwl/expected-exploded-atac-seq.cwl.steps/trimm.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/trimm.cwl index ab16b3f..0e31ce2 100644 --- a/tests/cwl/expected-exploded-atac-seq.cwl.steps/trimm.cwl +++ b/tests/cwl/expected-exploded-atac-seq.cwl.steps/trimm.cwl @@ -1,5 +1,7 @@ -class: Workflow +#!/usr/bin/env cwl-runner + cwlVersion: v1.0 +class: Workflow doc: 'ATAC-seq 02 trimming - reads: SE' requirements: diff --git a/tests/cwl/expected-exploded-atac-seq.cwl.steps/trimm.cwl.steps/count_fastq_reads.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/trimm.cwl.steps/count_fastq_reads.cwl index 044aedd..5324e47 100644 --- a/tests/cwl/expected-exploded-atac-seq.cwl.steps/trimm.cwl.steps/count_fastq_reads.cwl +++ b/tests/cwl/expected-exploded-atac-seq.cwl.steps/trimm.cwl.steps/count_fastq_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/trimm.cwl.steps/extract_basename.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/trimm.cwl.steps/extract_basename.cwl index 11d4529..20d0f2d 100644 --- a/tests/cwl/expected-exploded-atac-seq.cwl.steps/trimm.cwl.steps/extract_basename.cwl +++ b/tests/cwl/expected-exploded-atac-seq.cwl.steps/trimm.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/trimm.cwl.steps/trimmomatic.cwl b/tests/cwl/expected-exploded-atac-seq.cwl.steps/trimm.cwl.steps/trimmomatic.cwl index c6f329b..3bb561a 100644 --- a/tests/cwl/expected-exploded-atac-seq.cwl.steps/trimm.cwl.steps/trimmomatic.cwl +++ b/tests/cwl/expected-exploded-atac-seq.cwl.steps/trimm.cwl.steps/trimmomatic.cwl @@ -1,5 +1,7 @@ -class: CommandLineTool +#!/usr/bin/env cwl-runner + cwlVersion: v1.0 +class: CommandLineTool doc: | Trimmomatic is a fast, multithreaded command line tool that can be used to trim and crop Illumina (FASTQ) data as well as to remove adapters. These adapters can pose a real problem diff --git a/tests/cwl/formatted-atac-seq-pipeline.cwl b/tests/cwl/formatted-atac-seq-pipeline.cwl index e76c6e7..1252f6e 100644 --- a/tests/cwl/formatted-atac-seq-pipeline.cwl +++ b/tests/cwl/formatted-atac-seq-pipeline.cwl @@ -1,7 +1,7 @@ #!/usr/bin/env cwl-runner -class: Workflow cwlVersion: v1.0 +class: Workflow label: ATAC-seq-pipeline-se doc: 'ATAC-seq pipeline - reads: SE' $namespaces: @@ -186,8 +186,8 @@ steps: picard_jar_path: picard_jar_path picard_java_opts: picard_java_opts run: - class: Workflow cwlVersion: v1.0 + class: Workflow doc: 'ATAC-seq 03 mapping - reads: SE' requirements: @@ -273,8 +273,8 @@ steps: bam: index_bams/indexed_file scatter: bam run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool requirements: InitialWorkDirRequirement: @@ -325,8 +325,8 @@ steps: - output_filename scatterMethod: dotproduct run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool requirements: InlineJavascriptRequirement: {} @@ -468,8 +468,8 @@ steps: input_bam_files: filtered2sorted/sorted_file input_output_filenames: extract_basename_2/output_path run: - class: Workflow cwlVersion: v1.0 + class: Workflow doc: ChIP-seq - map - PCR Bottleneck Coefficients requirements: @@ -497,8 +497,8 @@ steps: ibam: input_bam_files scatter: ibam run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: |- Tool: bedtools genomecov (aka genomeCoverageBed) Version: v2.25.0 @@ -749,8 +749,8 @@ steps: - output_filename scatterMethod: dotproduct run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: Compute PCR Bottleneck Coeficient from BedGraph file. inputs: @@ -780,8 +780,8 @@ steps: input_file: input_fastq_files scatter: input_file run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: Extracts the base name of a file requirements: @@ -812,8 +812,8 @@ steps: file_path: extract_basename_1/output_basename scatter: file_path run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: Extracts the base name of a file inputs: @@ -844,8 +844,8 @@ steps: - output_filename scatterMethod: dotproduct run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool requirements: InlineJavascriptRequirement: {} @@ -895,8 +895,8 @@ steps: scatter: - input_file run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool requirements: InlineJavascriptRequirement: {} @@ -951,8 +951,8 @@ steps: input_file: sort_bams/sorted_file scatter: input_file run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool requirements: InitialWorkDirRequirement: @@ -993,8 +993,8 @@ steps: scatter: - input_file run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool requirements: InitialWorkDirRequirement: @@ -1035,8 +1035,8 @@ steps: scatter: - input_file run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool requirements: InitialWorkDirRequirement: @@ -1076,8 +1076,8 @@ steps: input_file: filtered2sorted/sorted_file scatter: input_file run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool requirements: InitialWorkDirRequirement: @@ -1119,8 +1119,8 @@ steps: valueFrom: .mapped_and_filtered.read_count.txt scatter: input_bam_file run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: Extract mapped reads from BAM file using Samtools flagstat command requirements: @@ -1164,8 +1164,8 @@ steps: bowtie_log: bowtie-se/output_bowtie_log scatter: bowtie_log run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: Get number of processed reads from Bowtie log. requirements: @@ -1204,8 +1204,8 @@ steps: - output_filename scatterMethod: dotproduct run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool requirements: InlineJavascriptRequirement: {} @@ -1302,8 +1302,8 @@ steps: ${return inputs.idxstats.basename.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.[^/.]+$/, '').replace(/\.[^/.]+$/, '.mitochondrial_percentage.txt')} scatter: idxstats run: - class: ExpressionTool cwlVersion: v1.0 + class: ExpressionTool requirements: InlineJavascriptRequirement: {} @@ -1360,8 +1360,8 @@ steps: preseq_c_curve_outfile: preseq-c-curve/output_file scatter: preseq_c_curve_outfile run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: Get number of processed reads from Bowtie log. requirements: @@ -1398,8 +1398,8 @@ steps: - output_file_basename scatterMethod: dotproduct run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: |- Usage: c_curve [OPTIONS] @@ -1512,8 +1512,8 @@ steps: scatter: - input_file run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool requirements: InlineJavascriptRequirement: {} @@ -1626,8 +1626,8 @@ steps: nthreads: nthreads scatter: input_file run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool requirements: InlineJavascriptRequirement: {} @@ -1679,8 +1679,8 @@ steps: nthreads: nthreads scatter: input_file run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool requirements: InlineJavascriptRequirement: {} @@ -1737,8 +1737,8 @@ steps: scatter: - input_file run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool requirements: InlineJavascriptRequirement: {} @@ -1797,8 +1797,8 @@ steps: scatter: - input_file run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool requirements: InlineJavascriptRequirement: {} @@ -1868,8 +1868,8 @@ steps: input_genome_sizes: genome_sizes_file nthreads: nthreads_peakcall run: - class: Workflow cwlVersion: v1.0 + class: Workflow doc: ATAC-seq 04 quantification - SE requirements: @@ -1945,8 +1945,8 @@ steps: valueFrom: .peak_count.within_replicate.txt scatter: input_file run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: Counts lines in a file and returns a suffixed file with that number requirements: @@ -1977,8 +1977,8 @@ steps: peak_xls_file: peak-calling/output_peak_xls_file scatter: peak_xls_file run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: Count number of dedup-ed reads used in peak calling requirements: @@ -2013,8 +2013,8 @@ steps: valueFrom: .read_count.within_replicate.txt scatter: input_bam_file run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: Extract mapped reads from BAM file using Samtools flagstat command requirements: @@ -2058,8 +2058,8 @@ steps: input_spp_txt_file: spp/output_spp_cross_corr scatter: input_spp_txt_file run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: Extracts best fragment length from SPP output text file inputs: @@ -2093,8 +2093,8 @@ steps: - input_bedfile scatterMethod: dotproduct run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: Filter BAM file to only include reads overlapping with a BED file requirements: @@ -2154,8 +2154,8 @@ steps: - treatment scatterMethod: dotproduct run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool requirements: InlineJavascriptRequirement: {} @@ -2486,8 +2486,8 @@ steps: genome_sizes: input_genome_sizes scatter: bed run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: | "bedToBigBed v. 2.7 - Convert bed file to bigBed. (BigBed version: 4) usage: @@ -2606,8 +2606,8 @@ steps: - input_bam scatterMethod: dotproduct run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool requirements: InlineJavascriptRequirement: {} @@ -2758,8 +2758,8 @@ steps: peaks: peak-calling/output_peak_file scatter: peaks run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: Trunk scores in ENCODE bed6+4 files inputs: @@ -2810,8 +2810,8 @@ steps: input_fastq_files: input_fastq_files nthreads: nthreads_qc run: - class: Workflow cwlVersion: v1.0 + class: Workflow doc: 'ATAC-seq 01 QC - reads: SE' requirements: @@ -2859,8 +2859,8 @@ steps: - file2 scatterMethod: dotproduct run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: Compares 2 files inputs: @@ -2902,8 +2902,8 @@ steps: - input_basename scatterMethod: dotproduct run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: Extracts read count from fastqc_data.txt inputs: @@ -2937,8 +2937,8 @@ steps: - input_basename scatterMethod: dotproduct run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: Counts reads in a fastq file requirements: @@ -2971,8 +2971,8 @@ steps: input_file: input_fastq_files scatter: input_file run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: Extracts the base name of a file requirements: @@ -3007,8 +3007,8 @@ steps: - input_basename scatterMethod: dotproduct run: - class: CommandLineTool 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 @@ -3051,8 +3051,8 @@ steps: threads: nthreads scatter: input_fastq_file run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool requirements: InlineJavascriptRequirement: {} @@ -3112,8 +3112,8 @@ steps: - input_basename scatterMethod: dotproduct run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool inputs: default_adapters_file: @@ -3159,8 +3159,8 @@ steps: input_genome_sizes: genome_sizes_file nthreads: nthreads_quant run: - class: Workflow cwlVersion: v1.0 + class: Workflow doc: ATAC-seq - Quantification requirements: @@ -3202,8 +3202,8 @@ steps: valueFrom: .rpkm.bw scatter: bam run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: | usage: An example usage is:$ bamCoverage -b reads.bam -o coverage.bw @@ -3652,8 +3652,8 @@ steps: valueFrom: .raw.bw scatter: bed_graph run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: 'Tool: bedGraphToBigWig v 4 - Convert a bedGraph file to bigWig format.' @@ -3699,8 +3699,8 @@ steps: bed_file: bedtools_genomecov/output_bedfile scatter: bed_file run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: | bedSort - Sort a .bed file by chrom,chromStart usage: @@ -3741,8 +3741,8 @@ steps: ibam: input_bam_files scatter: ibam run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: |- Tool: bedtools genomecov (aka genomeCoverageBed) Version: v2.25.0 @@ -3993,8 +3993,8 @@ steps: trimmomatic_jar_path: trimmomatic_jar_path trimmomatic_java_opts: trimmomatic_java_opts run: - class: Workflow cwlVersion: v1.0 + class: Workflow doc: 'ATAC-seq 02 trimming - reads: SE' requirements: @@ -4044,8 +4044,8 @@ steps: - input_basename scatterMethod: dotproduct run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: Counts reads in a fastq file requirements: @@ -4078,8 +4078,8 @@ steps: input_file: trimmomatic/output_read1_trimmed_file scatter: input_file run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: Extracts the base name of a file requirements: @@ -4131,8 +4131,8 @@ steps: - input_adapters_file scatterMethod: dotproduct run: - class: CommandLineTool cwlVersion: v1.0 + class: CommandLineTool doc: | Trimmomatic is a fast, multithreaded command line tool that can be used to trim and crop Illumina (FASTQ) data as well as to remove adapters. These adapters can pose a real problem diff --git a/tests/cwl/formatted-commented.cwl b/tests/cwl/formatted-commented.cwl index bee5e71..46965ed 100644 --- a/tests/cwl/formatted-commented.cwl +++ b/tests/cwl/formatted-commented.cwl @@ -3,8 +3,8 @@ # Top comment is preserved -class: CommandLineTool cwlVersion: v1.0 +class: CommandLineTool requirements: InlineJavascriptRequirement: {} diff --git a/tests/cwl/formatted-no-comment.cwl b/tests/cwl/formatted-no-comment.cwl index dea9ebc..b12818c 100644 --- a/tests/cwl/formatted-no-comment.cwl +++ b/tests/cwl/formatted-no-comment.cwl @@ -1,7 +1,7 @@ #!/usr/bin/env cwl-runner -class: CommandLineTool cwlVersion: v1.0 +class: CommandLineTool requirements: InlineJavascriptRequirement: {} diff --git a/tests/cwl/formatted-other-runner.cwl b/tests/cwl/formatted-other-runner.cwl index 9a390d4..bcff7b9 100644 --- a/tests/cwl/formatted-other-runner.cwl +++ b/tests/cwl/formatted-other-runner.cwl @@ -1,7 +1,7 @@ #!/usr/bin/env other-runner -class: CommandLineTool cwlVersion: v1.0 +class: CommandLineTool requirements: InlineJavascriptRequirement: {}