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transform.cwl
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transform.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: MultipleInputFeatureRequirement
inputs:
- id: sqlite_file
type: File
- id: sql_count_fastq_files
type: string
- id: exp_count_fastq_files
type: int
- id: sql_count_files_output
type: string
- id: exp_count_files_output
type: int
- id: sql_count_readgroups
type: string
- id: exp_count_readgroups
type: int
- id: sql_bases_mapped_samtools_stats
type: string
- id: exp_bases_mapped_samtools_stats
type: int
- id: sql_average_quality_samtools_stats
type: string
- id: exp_average_quality_samtools_stats
type: double
- id: sql_bases_duplicated_samtools_stats
type: string
- id: exp_bases_duplicated_samtools_stats
type: int
- id: sql_pairs_diff_chr_samtools_stats
type: string
- id: exp_pairs_diff_chr_samtools_stats
type: int
- id: sql_pairs_other_orient_samtools_stats
type: string
- id: exp_pairs_other_orient_samtools_stats
type: int
- id: sql_raw_total_seq_samtools_stats
type: string
- id: exp_raw_total_seq_samtools_stats
type: int
- id: sql_reads_mq0_samtools_stats
type: string
- id: exp_reads_mq0_samtools_stats
type: int
- id: sql_reads_dup_samtools_stats
type: string
- id: exp_reads_dup_samtools_stats
type: int
- id: sql_reads_mapped_samtools_stats
type: string
- id: exp_reads_mapped_samtools_stats
type: int
- id: sql_reads_mapped_and_paired_samtools_stats
type: string
- id: exp_reads_mapped_and_paired_samtools_stats
type: int
- id: sql_reads_paired_samtool_stats
type: string
- id: exp_reads_paired_samtool_stats
type: int
- id: sql_reads_prop_paired_samtools_stats
type: string
- id: exp_reads_prop_paired_samtools_stats
type: int
- id: sql_read_unmapped_samtools_stats
type: string
- id: exp_read_unmapped_samtools_stats
type: int
- id: sql_seqs_samtools_stats
type: string
- id: exp_seqs_samtools_stats
type: int
- id: sql_total_length_samtools_stats
type: string
- id: exp_total_length_samtools_stats
type: int
- id: sql_read_pairs_picard_markduplicates
type: string
- id: exp_read_pairs_picard_markduplicates
type: int
- id: sql_read_pair_dups_picard_markduplicates
type: string
- id: exp_read_pair_dups_picard_markduplicates
type: int
outputs:
- id: tests_logical_conjunction_result
type: boolean
outputSource: tests_logical_conjunction/result
steps:
- id: sqlite_count_fastq_files
run: ../../../tools/get_int_sqlite.cwl
in:
- id: sqlite_expression
source: sql_count_fastq_files
- id: sqlite_file
source: sqlite_file
out:
- id: result
- id: sqlite_count_files_output
run: ../../../tools/get_int_sqlite.cwl
in:
- id: sqlite_expression
source: sql_count_files_output
- id: sqlite_file
source: sqlite_file
out:
- id: result
- id: sqlite_count_readgroups
run: ../../../tools/get_int_sqlite.cwl
in:
- id: sqlite_expression
source: sql_count_readgroups
- id: sqlite_file
source: sqlite_file
out:
- id: result
- id: sqlite_bases_mapped_samtools_stats
run: ../../../tools/get_int_sqlite.cwl
in:
- id: sqlite_expression
source: sql_bases_mapped_samtools_stats
- id: sqlite_file
source: sqlite_file
out:
- id: result
- id: sqlite_reads_mapped_samtools_stats
run: ../../../tools/get_int_sqlite.cwl
in:
- id: sqlite_expression
source: sql_reads_mapped_samtools_stats
- id: sqlite_file
source: sqlite_file
out:
- id: result
- id: test_count_fastq_files
run: ../../../tools/test_int.cwl
in:
- id: expected_value
source: exp_count_fastq_files
- id: test_value
source: sqlite_count_fastq_files/result
out:
- id: result
- id: test_count_files_output
run: ../../../tools/test_int.cwl
in:
- id: expected_value
source: exp_count_files_output
- id: test_value
source: sqlite_count_files_output/result
out:
- id: result
- id: test_count_readgroups
run: ../../../tools/test_int.cwl
in:
- id: expected_value
source: exp_count_readgroups
- id: test_value
source: sqlite_count_readgroups/result
out:
- id: result
- id: test_bases_mapped_samtools_stats
run: ../../../tools/test_int.cwl
in:
- id: expected_value
source: exp_bases_mapped_samtools_stats
- id: test_value
source: sqlite_bases_mapped_samtools_stats/result
out:
- id: result
- id: test_reads_mapped_samtools_stats
run: ../../../tools/test_int.cwl
in:
- id: expected_value
source: exp_reads_mapped_samtools_stats
- id: test_value
source: sqlite_reads_mapped_samtools_stats/result
out:
- id: result
- id: tests_logical_conjunction
run: ../../../tools/logical_conjunction_expression.cwl
in:
- id: values
source: [
test_count_fastq_files/result,
test_count_files_output/result,
test_count_readgroups/result,
test_bases_mapped_samtools_stats/result,
test_reads_mapped_samtools_stats/result
]
out:
- id: result