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xenbase-fastq-bowtie-bigwig-se-pe.cwl
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xenbase-fastq-bowtie-bigwig-se-pe.cwl
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cwlVersion: v1.0
class: Workflow
requirements:
- class: SubworkflowFeatureRequirement
inputs:
upstream_fastq:
type: File
downstream_fastq:
type: File?
bowtie2_indices_folder:
type: Directory
chr_length_file:
type: File
paired:
type: boolean?
threads:
type: int?
outputs:
bowtie2_log:
type: File
outputSource: bowtie2_aligner/output_log
picard_metrics:
type: File
outputSource: remove_dup_picard/metrics_file
bam_file:
type: File
outputSource: samtools_sort_index_after_dup_removing/bam_bai_pair
bamtools_log:
type: File
outputSource: bamtools_stats/log_file
bed:
type: File
outputSource: bam_to_bigwig/bedgraph_file
bigwig:
type: File
outputSource: bam_to_bigwig/bigwig_file
steps:
bowtie2_aligner:
run: ../tools/bowtie2.cwl
in:
filelist: upstream_fastq
filelist_mates: downstream_fastq
indices_folder: bowtie2_indices_folder
threads: threads
out: [output, output_log]
samtools_sort_index:
run: ../tools/samtools-sort-index.cwl
in:
sort_input: bowtie2_aligner/output
threads: threads
out: [bam_bai_pair]
remove_dup_picard:
run: ../tools/picard-markduplicates.cwl
in:
input_file: samtools_sort_index/bam_bai_pair
remove_dup:
default: true
out:
- output_file
- metrics_file
samtools_sort_index_after_dup_removing:
run: ../tools/samtools-sort-index.cwl
in:
sort_input: remove_dup_picard/output_file
threads: threads
out: [bam_bai_pair]
bamtools_stats:
run: ../tools/bamtools-stats.cwl
in:
bam_file: samtools_sort_index_after_dup_removing/bam_bai_pair
out:
- mapped_reads_number
- log_file
bam_to_bigwig:
run: bam-bedgraph-bigwig.cwl
in:
bam_file: samtools_sort_index_after_dup_removing/bam_bai_pair
chrom_length_file: chr_length_file
mapped_reads_number: bamtools_stats/mapped_reads_number
pairchip: paired
out:
- bigwig_file
- bedgraph_file