Verified with cwltool version
3.1.20221201130942
1. Convert input SRA file into pair of upsrtream and downstream FASTQ files (run fastq-dump)
2. Analyze quality of FASTQ files (run fastqc with each of the FASTQ files)
3. If any of the following fields in fastqc generated report is marked as failed for at least one of input FASTQ files:
\"Per base sequence quality\",
\"Per sequence quality scores\",
\"Overrepresented sequences\",
\"Adapter Content\",
- trim adapters (run trimmomatic)
4. Align original or trimmed FASTQ files to reference genome (run Bowtie2)
5. Sort and index generated by Bowtie2 BAM file (run samtools sort, samtools index)
6. Remove duplicates in sorted BAM file (run picard)
7. Sort and index BAM file after duplicates removing (run samtools sort, samtools index)
8. Count mapped reads number in sorted BAM file (run bamtools stats)
9. Generate genome coverage BED file (run bedtools genomecov)
10. Sort genearted BED file (run sort)
11. Generate genome coverage bigWig file from BED file (run bedGraphToBigWig)
Fetched 2023-01-13 23:24:31 GMT
