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example.config.yaml
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example.config.yaml
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input_data_1: rawdata/sample_data/SRR622461_1.fastq
input_data_2: rawdata/sample_data/SRR622461_2.fastq
search_chr: -r 'chr10'
reference_data: rawdata/reference/GCA_000001405.15_GRCh38_full_analysis_set.fna
conda_envs:
working_dir: './'
samtool_thread: 4
analysis:
QC_1_fastqc:
output_list: [
QC_1_fastqc/SRR622461_1_fastqc.html,
QC_1_fastqc/SRR622461_1_fastqc.zip,
QC_1_fastqc/SRR622461_2_fastqc.zip,
QC_1_fastqc/SRR622461_2_fastqc.html
]
s1_trimmomatic:
paired_output: [
s1_trimmomatic/SRR622461_1.paired.trimmed.fastq,
s1_trimmomatic/SRR622461_2.paired.trimmed.fastq
]
unpaired_output: [
s1_trimmomatic/SRR622461_1.unpaired.trimmed.fastq,
s1_trimmomatic/SRR622461_2.unpaired.trimmed.fastq
]
threads: -threads 4
tlog: -trimlog ./trim.log
lead: LEADING:10
trail: TRAILING:10
sliding: SLIDINGWINDOW:4:20
mlen: MINLEN:36
QC_2_fastqc:
output_list: [
QC_2_fastqc/SRR622461_1.paired.trimmed_fastqc.zip,
QC_2_fastqc/SRR622461_1.paired.trimmed_fastqc.html,
QC_2_fastqc/SRR622461_1.unpaired.trimmed_fastqc.zip,
QC_2_fastqc/SRR622461_1.unpaired.trimmed_fastqc.html,
QC_2_fastqc/SRR622461_2.paired.trimmed_fastqc.zip,
QC_2_fastqc/SRR622461_2.paired.trimmed_fastqc.html,
QC_2_fastqc/SRR622461_2.unpaired.trimmed_fastqc.zip,
QC_2_fastqc/SRR622461_2.unpaired.trimmed_fastqc.html
]
QC_3_multiqc:
output: QC_3_multiqc/multiqc_report.html
s2_ref_index:
output_list: [
rawdata/reference/GCA_000001405.15_GRCh38_full_analysis_set.fna.amb,
rawdata/reference/GCA_000001405.15_GRCh38_full_analysis_set.fna.ann,
rawdata/reference/GCA_000001405.15_GRCh38_full_analysis_set.fna.bwt,
rawdata/reference/GCA_000001405.15_GRCh38_full_analysis_set.fna.pac,
rawdata/reference/GCA_000001405.15_GRCh38_full_analysis_set.fna.sa
]
s3_alignment:
output: s3_alignment/SRR622461_GRCh38.aligned.bam
s4_sortbam:
output: s4_sortbam/SRR622461_GRCh38.aligned.sort.bam
s5_index_bam:
output: s4_sortbam/SRR622461_GRCh38.aligned.sort.bam.bai
s6_mrkdupes:
output: s6_mrkdupes/SRR622461_GRCh38.al.s.mkdup.bam
mrkd_output: s6_mrkdupes/marked_dupes_metrics.txt
s7_align_metrics:
output: s7_align_metrics/output.txt
s8_picard_dict:
output: rawdata/reference/GCA_000001405.15_GRCh38_full_analysis_set.dict
s9_GATK_vcf:
output: s9_GATK_vcf/SRR622461_GRCh38.asmrkd.vcf.gz
s10_excise_gene:
output: s10_excise_gene/chr10.vcf
s11_filter_qual:
output: s11_filter_qual/chr10.filtered.vcf
qual: 'QUAL>20'
s12_annotate_vcf:
output: s12_annotate_vcf/chr10.filt.annotated.vcf
output_csv: s12_annotate_vcf/snpEff.csv
s13_bgzip_index:
output_bg: s13_bgzip_index/chr10.filt.annotated.vcf.gz
output_tbi: s13_bgzip_index/chr10.filt.annotated.vcf.gz.tbi