/
transform_mirna.cwl
862 lines (791 loc) · 21.5 KB
/
transform_mirna.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: InlineJavascriptRequirement
- class: MultipleInputFeatureRequirement
- class: ScatterFeatureRequirement
- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement
inputs:
- id: input_bam
type: File
- id: known_snp
type: File
- id: reference_sequence
type: File
- id: thread_count
type: long
- id: job_uuid
type: string
outputs:
- id: picard_markduplicates_output
type: File
outputSource: picard_markduplicates/OUTPUT
- id: merge_all_sqlite_destination_sqlite
type: File
outputSource: merge_all_sqlite/destination_sqlite
- id: mirna_profiling_mirna_adapter_report_sorted_output
type: File
outputSource: mirna_profiling/mirna_adapter_report_sorted_output
- id: mirna_profiling_mirna_alignment_stats_features
type: Directory
outputSource: mirna_profiling/mirna_alignment_stats_features
- id: mirna_profiling_mirna_expression_matrix_expn_matrix_txt
type: File
outputSource: mirna_profiling/mirna_expression_matrix_expn_matrix_txt
- id: mirna_profiling_mirna_expression_matrix_expn_matrix_norm_txt
type: File
outputSource: mirna_profiling/mirna_expression_matrix_expn_matrix_norm_txt
- id: mirna_profiling_mirna_expression_matrix_expn_matrix_norm_log_txt
type: File
outputSource: mirna_profiling/mirna_expression_matrix_expn_matrix_norm_log_txt
- id: mirna_profiling_mirna_expression_matrix_mimat_expn_matrix_mimat_txt
type: File
outputSource: mirna_profiling/mirna_expression_matrix_mimat_expn_matrix_mimat_txt
- id: mirna_profiling_mirna_expression_matrix_mimat_expn_matrix_mimat_norm_txt
type: File
outputSource: mirna_profiling/mirna_expression_matrix_mimat_expn_matrix_mimat_norm_txt
- id: mirna_profiling_mirna_expression_matrix_mimat_expn_matrix_mimat_norm_log_txt
type: File
outputSource: mirna_profiling/mirna_expression_matrix_mimat_expn_matrix_mimat_norm_log_txt
- id: mirna_profiling_mirna_graph_libs_jpgs
type: Directory
outputSource: mirna_profiling/mirna_graph_libs_jpgs
- id: mirna_profiling_mirna_tcga_isoforms_quant
type: File
outputSource: mirna_profiling/mirna_tcga_isoforms_quant
- id: mirna_profiling_mirna_tcga_mirnas_quant
type: File
outputSource: mirna_profiling/mirna_tcga_mirnas_quant
steps:
- id: samtools_bamtobam
run: ../../tools/samtools_bamtobam.cwl
in:
- id: INPUT
source: input_bam
out:
- id: OUTPUT
- id: picard_validatesamfile_original
run: ../../tools/picard_validatesamfile.cwl
in:
- id: INPUT
source: samtools_bamtobam/OUTPUT
- id: VALIDATION_STRINGENCY
valueFrom: "LENIENT"
out:
- id: OUTPUT
# need eof and dup QNAME detection
- id: picard_validatesamfile_original_to_sqlite
run: ../../tools/picard_validatesamfile_to_sqlite.cwl
in:
- id: bam
source: input_bam
valueFrom: $(self.basename)
- id: input_state
valueFrom: "original"
- id: metric_path
source: picard_validatesamfile_original/OUTPUT
- id: job_uuid
source: job_uuid
out:
- id: sqlite
- id: biobambam_bamtofastq
run: ../../tools/biobambam2_bamtofastq.cwl
in:
- id: filename
source: samtools_bamtobam/OUTPUT
out:
- id: output_fastq1
- id: output_fastq2
- id: output_fastq_o1
- id: output_fastq_o2
- id: output_fastq_s
- id: remove_duplicate_fastq1
run: ../../tools/fastq_remove_duplicate_qname.cwl
scatter: INPUT
in:
- id: INPUT
source: biobambam_bamtofastq/output_fastq1
out:
- id: OUTPUT
- id: remove_duplicate_fastq2
run: ../../tools/fastq_remove_duplicate_qname.cwl
scatter: INPUT
in:
- id: INPUT
source: biobambam_bamtofastq/output_fastq2
out:
- id: OUTPUT
- id: remove_duplicate_fastq_o1
run: ../../tools/fastq_remove_duplicate_qname.cwl
scatter: INPUT
in:
- id: INPUT
source: biobambam_bamtofastq/output_fastq_o1
out:
- id: OUTPUT
- id: remove_duplicate_fastq_o2
run: ../../tools/fastq_remove_duplicate_qname.cwl
scatter: INPUT
in:
- id: INPUT
source: biobambam_bamtofastq/output_fastq_o2
out:
- id: OUTPUT
- id: remove_duplicate_fastq_s
run: ../../tools/fastq_remove_duplicate_qname.cwl
scatter: INPUT
in:
- id: INPUT
source: biobambam_bamtofastq/output_fastq_s
out:
- id: OUTPUT
- id: sort_scattered_fastq1
run: ../../tools/sort_scatter_expression.cwl
in:
- id: INPUT
source: remove_duplicate_fastq1/OUTPUT
out:
- id: OUTPUT
- id: sort_scattered_fastq2
run: ../../tools/sort_scatter_expression.cwl
in:
- id: INPUT
source: remove_duplicate_fastq2/OUTPUT
out:
- id: OUTPUT
- id: sort_scattered_fastq_o1
run: ../../tools/sort_scatter_expression.cwl
in:
- id: INPUT
source: remove_duplicate_fastq_o1/OUTPUT
out:
- id: OUTPUT
- id: sort_scattered_fastq_o2
run: ../../tools/sort_scatter_expression.cwl
in:
- id: INPUT
source: remove_duplicate_fastq_o2/OUTPUT
out:
- id: OUTPUT
- id: sort_scattered_fastq_s
run: ../../tools/sort_scatter_expression.cwl
in:
- id: INPUT
source: remove_duplicate_fastq_s/OUTPUT
out:
- id: OUTPUT
- id: bam_readgroup_to_json
run: ../../tools/bam_readgroup_to_json.cwl
in:
- id: INPUT
source: samtools_bamtobam/OUTPUT
- id: MODE
valueFrom: "lenient"
out:
- id: OUTPUT
- id: readgroup_json_db
run: ../../tools/readgroup_json_db.cwl
scatter: json_path
in:
- id: json_path
source: bam_readgroup_to_json/OUTPUT
- id: job_uuid
source: job_uuid
out:
- id: log
- id: output_sqlite
- id: merge_readgroup_json_db
run: ../../tools/merge_sqlite.cwl
in:
- id: source_sqlite
source: readgroup_json_db/output_sqlite
- id: job_uuid
source: job_uuid
out:
- id: destination_sqlite
- id: log
- id: fastqc1
run: ../../tools/fastqc.cwl
scatter: INPUT
in:
- id: INPUT
source: sort_scattered_fastq1/OUTPUT
- id: threads
source: thread_count
out:
- id: OUTPUT
- id: fastqc2
run: ../../tools/fastqc.cwl
scatter: INPUT
in:
- id: INPUT
source: sort_scattered_fastq2/OUTPUT
- id: threads
source: thread_count
out:
- id: OUTPUT
- id: fastqc_s
run: ../../tools/fastqc.cwl
scatter: INPUT
in:
- id: INPUT
source: sort_scattered_fastq_s/OUTPUT
- id: threads
source: thread_count
out:
- id: OUTPUT
- id: fastqc_o1
run: ../../tools/fastqc.cwl
scatter: INPUT
in:
- id: INPUT
source: sort_scattered_fastq_o1/OUTPUT
- id: threads
source: thread_count
out:
- id: OUTPUT
- id: fastqc_o2
run: ../../tools/fastqc.cwl
scatter: INPUT
in:
- id: INPUT
source: sort_scattered_fastq_o2/OUTPUT
- id: threads
source: thread_count
out:
- id: OUTPUT
- id: fastqc_db1
run: ../../tools/fastqc_db.cwl
scatter: INPUT
in:
- id: INPUT
source: fastqc1/OUTPUT
- id: job_uuid
source: job_uuid
out:
- id: LOG
- id: OUTPUT
- id: fastqc_db2
run: ../../tools/fastqc_db.cwl
scatter: INPUT
in:
- id: INPUT
source: fastqc2/OUTPUT
- id: job_uuid
source: job_uuid
out:
- id: LOG
- id: OUTPUT
- id: fastqc_db_s
run: ../../tools/fastqc_db.cwl
scatter: INPUT
in:
- id: INPUT
source: fastqc_s/OUTPUT
- id: job_uuid
source: job_uuid
out:
- id: LOG
- id: OUTPUT
- id: fastqc_db_o1
run: ../../tools/fastqc_db.cwl
scatter: INPUT
in:
- id: INPUT
source: fastqc_o1/OUTPUT
- id: job_uuid
source: job_uuid
out:
- id: LOG
- id: OUTPUT
- id: fastqc_db_o2
run: ../../tools/fastqc_db.cwl
scatter: INPUT
in:
- id: INPUT
source: fastqc_o2/OUTPUT
- id: job_uuid
source: job_uuid
out:
- id: LOG
- id: OUTPUT
- id: merge_fastqc_db1_sqlite
run: ../../tools/merge_sqlite.cwl
in:
- id: source_sqlite
source: fastqc_db1/OUTPUT
- id: job_uuid
source: job_uuid
out:
- id: destination_sqlite
- id: log
- id: merge_fastqc_db2_sqlite
run: ../../tools/merge_sqlite.cwl
in:
- id: source_sqlite
source: fastqc_db2/OUTPUT
- id: job_uuid
source: job_uuid
out:
- id: destination_sqlite
- id: log
- id: merge_fastqc_db_s_sqlite
run: ../../tools/merge_sqlite.cwl
in:
- id: source_sqlite
source: fastqc_db_s/OUTPUT
- id: job_uuid
source: job_uuid
out:
- id: destination_sqlite
- id: log
- id: merge_fastqc_db_o1_sqlite
run: ../../tools/merge_sqlite.cwl
in:
- id: source_sqlite
source: fastqc_db_o1/OUTPUT
- id: job_uuid
source: job_uuid
out:
- id: destination_sqlite
- id: log
- id: merge_fastqc_db_o2_sqlite
run: ../../tools/merge_sqlite.cwl
in:
- id: source_sqlite
source: fastqc_db_o2/OUTPUT
- id: job_uuid
source: job_uuid
out:
- id: destination_sqlite
- id: log
- id: fastqc_pe_basicstats_json
run: ../../tools/fastqc_basicstatistics_json.cwl
in:
- id: sqlite_path
source: merge_fastqc_db1_sqlite/destination_sqlite
out:
- id: OUTPUT
- id: fastqc_se_basicstats_json
run: ../../tools/fastqc_basicstatistics_json.cwl
in:
- id: sqlite_path
source: merge_fastqc_db_s_sqlite/destination_sqlite
out:
- id: OUTPUT
- id: fastqc_o1_basicstats_json
run: ../../tools/fastqc_basicstatistics_json.cwl
in:
- id: sqlite_path
source: merge_fastqc_db_o1_sqlite/destination_sqlite
out:
- id: OUTPUT
- id: fastqc_o2_basicstats_json
run: ../../tools/fastqc_basicstatistics_json.cwl
in:
- id: sqlite_path
source: merge_fastqc_db_o2_sqlite/destination_sqlite
out:
- id: OUTPUT
- id: decider_bwa_pe
run: ../../tools/decider_bwa_expression.cwl
in:
- id: fastq_path
source: sort_scattered_fastq1/OUTPUT
- id: readgroup_path
source: bam_readgroup_to_json/OUTPUT
out:
- id: output_readgroup_paths
- id: decider_bwa_se
run: ../../tools/decider_bwa_expression.cwl
in:
- id: fastq_path
source: sort_scattered_fastq_s/OUTPUT
- id: readgroup_path
source: bam_readgroup_to_json/OUTPUT
out:
- id: output_readgroup_paths
- id: decider_bwa_o1
run: ../../tools/decider_bwa_expression.cwl
in:
- id: fastq_path
source: sort_scattered_fastq_o1/OUTPUT
- id: readgroup_path
source: bam_readgroup_to_json/OUTPUT
out:
- id: output_readgroup_paths
- id: decider_bwa_o2
run: ../../tools/decider_bwa_expression.cwl
in:
- id: fastq_path
source: sort_scattered_fastq_o2/OUTPUT
- id: readgroup_path
source: bam_readgroup_to_json/OUTPUT
out:
- id: output_readgroup_paths
- id: bwa_pe
run: ../../tools/bwa_pe.cwl
scatter: [fastq1, fastq2, readgroup_json_path]
scatterMethod: "dotproduct"
in:
- id: fasta
source: reference_sequence
- id: fastq1
source: sort_scattered_fastq1/OUTPUT
- id: fastq2
source: sort_scattered_fastq2/OUTPUT
- id: readgroup_json_path
source: decider_bwa_pe/output_readgroup_paths
- id: fastqc_json_path
source: fastqc_pe_basicstats_json/OUTPUT
- id: thread_count
source: thread_count
out:
- id: OUTPUT
- id: bwa_se
run: ../../tools/bwa_se.cwl
scatter: [fastq, readgroup_json_path]
scatterMethod: "dotproduct"
in:
- id: fasta
source: reference_sequence
- id: fastq
source: sort_scattered_fastq_s/OUTPUT
- id: readgroup_json_path
source: decider_bwa_se/output_readgroup_paths
- id: fastqc_json_path
source: fastqc_se_basicstats_json/OUTPUT
- id: samse_maxOcc
valueFrom: $(5+5)
- id: thread_count
source: thread_count
out:
- id: OUTPUT
- id: bwa_o1
run: ../../tools/bwa_se.cwl
scatter: [fastq, readgroup_json_path]
scatterMethod: "dotproduct"
in:
- id: fasta
source: reference_sequence
- id: fastq
source: sort_scattered_fastq_o1/OUTPUT
- id: readgroup_json_path
source: decider_bwa_o1/output_readgroup_paths
- id: fastqc_json_path
source: fastqc_o1_basicstats_json/OUTPUT
- id: thread_count
source: thread_count
out:
- id: OUTPUT
- id: bwa_o2
run: ../../tools/bwa_se.cwl
scatter: [fastq, readgroup_json_path]
scatterMethod: "dotproduct"
in:
- id: fasta
source: reference_sequence
- id: fastq
source: sort_scattered_fastq_o2/OUTPUT
- id: readgroup_json_path
source: decider_bwa_o2/output_readgroup_paths
- id: fastqc_json_path
source: fastqc_o2_basicstats_json/OUTPUT
- id: thread_count
source: thread_count
out:
- id: OUTPUT
- id: picard_sortsam_pe
run: ../../tools/picard_sortsam.cwl
scatter: INPUT
in:
- id: INPUT
source: bwa_pe/OUTPUT
- id: OUTPUT
valueFrom: $(inputs.INPUT.basename)
out:
- id: SORTED_OUTPUT
- id: picard_sortsam_se
run: ../../tools/picard_sortsam.cwl
scatter: INPUT
in:
- id: INPUT
source: bwa_se/OUTPUT
- id: OUTPUT
valueFrom: $(inputs.INPUT.basename)
out:
- id: SORTED_OUTPUT
- id: picard_sortsam_o1
run: ../../tools/picard_sortsam.cwl
scatter: INPUT
in:
- id: INPUT
source: bwa_o1/OUTPUT
- id: OUTPUT
valueFrom: $(inputs.INPUT.basename)
out:
- id: SORTED_OUTPUT
- id: picard_sortsam_o2
run: ../../tools/picard_sortsam.cwl
scatter: INPUT
in:
- id: INPUT
source: bwa_o2/OUTPUT
- id: OUTPUT
valueFrom: $(inputs.INPUT.basename)
out:
- id: SORTED_OUTPUT
- id: metrics_pe
run: metrics.cwl
scatter: bam
in:
- id: bam
source: picard_sortsam_pe/SORTED_OUTPUT
- id: known_snp
source: known_snp
- id: fasta
source: reference_sequence
- id: input_state
valueFrom: "sorted_readgroup"
- id: parent_bam
source: input_bam
valueFrom: $(self.basename)
- id: thread_count
source: thread_count
- id: job_uuid
source: job_uuid
out:
- id: merge_sqlite_destination_sqlite
- id: merge_metrics_pe
run: ../../tools/merge_sqlite.cwl
in:
- id: source_sqlite
source: metrics_pe/merge_sqlite_destination_sqlite
- id: job_uuid
source: job_uuid
out:
- id: destination_sqlite
- id: log
- id: metrics_se
run: metrics.cwl
scatter: bam
in:
- id: bam
source: picard_sortsam_se/SORTED_OUTPUT
- id: known_snp
source: known_snp
- id: fasta
source: reference_sequence
- id: input_state
valueFrom: "sorted_readgroup"
- id: parent_bam
source: input_bam
valueFrom: $(self.basename)
- id: thread_count
source: thread_count
- id: job_uuid
source: job_uuid
out:
- id: merge_sqlite_destination_sqlite
- id: merge_metrics_se
run: ../../tools/merge_sqlite.cwl
in:
- id: source_sqlite
source: metrics_se/merge_sqlite_destination_sqlite
- id: job_uuid
source: job_uuid
out:
- id: destination_sqlite
- id: log
- id: picard_mergesamfiles_pe
run: ../../tools/picard_mergesamfiles.cwl
in:
- id: INPUT
source: picard_sortsam_pe/SORTED_OUTPUT
- id: OUTPUT
source: input_bam
valueFrom: $(self.basename)
out:
- id: MERGED_OUTPUT
- id: picard_mergesamfiles_se
run: ../../tools/picard_mergesamfiles.cwl
in:
- id: INPUT
source: picard_sortsam_se/SORTED_OUTPUT
- id: OUTPUT
source: input_bam
valueFrom: $(self.basename)
out:
- id: MERGED_OUTPUT
- id: picard_mergesamfiles_o1
run: ../../tools/picard_mergesamfiles.cwl
in:
- id: INPUT
source: picard_sortsam_o1/SORTED_OUTPUT
- id: OUTPUT
source: input_bam
valueFrom: $(self.basename)
out:
- id: MERGED_OUTPUT
- id: picard_mergesamfiles_o2
run: ../../tools/picard_mergesamfiles.cwl
in:
- id: INPUT
source: picard_sortsam_o2/SORTED_OUTPUT
- id: OUTPUT
source: input_bam
valueFrom: $(self.basename)
out:
- id: MERGED_OUTPUT
- id: picard_mergesamfiles
run: ../../tools/picard_mergesamfiles.cwl
in:
- id: INPUT
source: [
picard_mergesamfiles_pe/MERGED_OUTPUT,
picard_mergesamfiles_se/MERGED_OUTPUT,
picard_mergesamfiles_o1/MERGED_OUTPUT,
picard_mergesamfiles_o2/MERGED_OUTPUT
]
- id: OUTPUT
source: input_bam
valueFrom: $(self.basename.slice(0,-4) + "_gdc_realn.bam")
out:
- id: MERGED_OUTPUT
- id: bam_reheader
run: ../../tools/bam_reheader.cwl
in:
- id: input
source: picard_mergesamfiles/MERGED_OUTPUT
out:
- id: output
- id: picard_markduplicates
run: ../../tools/picard_markduplicates.cwl
in:
- id: INPUT
source: bam_reheader/output
out:
- id: OUTPUT
- id: METRICS
- id: picard_markduplicates_to_sqlite
run: ../../tools/picard_markduplicates_to_sqlite.cwl
in:
- id: bam
source: picard_markduplicates/OUTPUT
valueFrom: $(self.basename)
- id: input_state
valueFrom: "markduplicates_readgroups"
- id: metric_path
source: picard_markduplicates/METRICS
- id: job_uuid
source: job_uuid
out:
- id: sqlite
- id: picard_validatesamfile_markduplicates
run: ../../tools/picard_validatesamfile.cwl
in:
- id: INPUT
source: picard_markduplicates/OUTPUT
- id: VALIDATION_STRINGENCY
valueFrom: "STRICT"
out:
- id: OUTPUT
#need eof and dup QNAME detection
- id: picard_validatesamfile_markdupl_to_sqlite
run: ../../tools/picard_validatesamfile_to_sqlite.cwl
in:
- id: bam
source: input_bam
valueFrom: $(self.basename)
- id: input_state
valueFrom: "markduplicates_readgroups"
- id: metric_path
source: picard_validatesamfile_markduplicates/OUTPUT
- id: job_uuid
source: job_uuid
out:
- id: sqlite
- id: metrics_markduplicates
run: mixed_library_metrics.cwl
in:
- id: bam
source: picard_markduplicates/OUTPUT
- id: known_snp
source: known_snp
- id: fasta
source: reference_sequence
- id: input_state
valueFrom: "markduplicates_readgroups"
- id: thread_count
source: thread_count
- id: job_uuid
source: job_uuid
out:
- id: merge_sqlite_destination_sqlite
- id: mirna_profiling
run: mirna_profiling.cwl
in:
- id: awk_expression
valueFrom: "{arr[length($10)]+=1} END {for (i in arr) {print i\" \"arr[i]}}"
- id: bam
source: picard_markduplicates/OUTPUT
- id: mirbase_db
valueFrom: "mirbase"
- id: species_code
valueFrom: "hsa"
- id: project_directory
valueFrom: "."
- id: ucsc_database
valueFrom: "hg38"
out:
- id: mirna_adapter_report_sorted_output
- id: mirna_alignment_stats_features
- id: mirna_expression_matrix_expn_matrix_txt
- id: mirna_expression_matrix_expn_matrix_norm_txt
- id: mirna_expression_matrix_expn_matrix_norm_log_txt
- id: mirna_expression_matrix_mimat_expn_matrix_mimat_txt
- id: mirna_expression_matrix_mimat_expn_matrix_mimat_norm_txt
- id: mirna_expression_matrix_mimat_expn_matrix_mimat_norm_log_txt
- id: mirna_graph_libs_jpgs
- id: mirna_tcga_isoforms_quant
- id: mirna_tcga_mirnas_quant
- id: integrity
run: integrity.cwl
in:
- id: bai
source: picard_markduplicates/OUTPUT
valueFrom: $(self.secondaryFiles[0])
- id: bam
source: picard_markduplicates/OUTPUT
- id: input_state
valueFrom: "markduplicates_readgroups"
- id: job_uuid
source: job_uuid
out:
- id: merge_sqlite_destination_sqlite
- id: merge_all_sqlite
run: ../../tools/merge_sqlite.cwl
in:
- id: source_sqlite
source: [
picard_validatesamfile_original_to_sqlite/sqlite,
picard_validatesamfile_markdupl_to_sqlite/sqlite,
merge_readgroup_json_db/destination_sqlite,
merge_fastqc_db1_sqlite/destination_sqlite,
merge_fastqc_db2_sqlite/destination_sqlite,
merge_fastqc_db_s_sqlite/destination_sqlite,
merge_fastqc_db_o1_sqlite/destination_sqlite,
merge_fastqc_db_o2_sqlite/destination_sqlite,
merge_metrics_pe/destination_sqlite,
merge_metrics_se/destination_sqlite,
metrics_markduplicates/merge_sqlite_destination_sqlite,
picard_markduplicates_to_sqlite/sqlite,
integrity/merge_sqlite_destination_sqlite
]
- id: job_uuid
source: job_uuid
out:
- id: destination_sqlite
- id: log