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Analysis of variation within individual COVID-19 samples using bowtie2, bwa, fastp, multiqc , picard ,samtools, snpEff Workflow, tools and data are available on https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2/tree/master/Variation This worklow was ported into CWL from a Galaxy Workflow ( https://github.com/galaxyproject/SARS-CoV-2/tree/master/genomics/4-Variation migrated to CWL).

Inputs

ID Name Description Type
reads_reverse n/a n/a File[]
reads_forward n/a n/a File[]
reference_in n/a n/a File
unqualified_phred_quality n/a n/a int?
threads n/a n/a int?
qualified_phred_quality n/a n/a int?
min_length_required n/a n/a int?
force_polyg_tail_trimming n/a n/a boolean?
disable_trim_poly_g n/a n/a boolean?
base_correction n/a n/a boolean?
sort_order n/a n/a {"type"=>"enum", "symbols"=>["queryname", "coordinate", "duplicate"]} (Optional)
validation_stringency n/a n/a {"type"=>"enum", "symbols"=>["STRICT", "LENIENT", "SILENT"]} (Optional)
exclude_unmapped n/a n/a boolean?
count n/a n/a boolean
alignments_are_sorted n/a n/a boolean
remove_duplicates n/a n/a boolean
validation_stringency_1 n/a n/a {"type"=>"enum", "symbols"=>["STRICT", "LENIENT", "SILENT"]} (Optional)
comment n/a n/a string[]?
duplicate_scoring_strategy n/a n/a {"type"=>"enum", "symbols"=>["SUM_OF_BASE_QUALITIES", "TOTAL_MAPPED_REFERENCE_LENGTH", "RANDOM"]} (Optional)
optical_duplicate_pixel_distance n/a n/a int?
barcode_tag n/a n/a string?
keepflags n/a n/a boolean?
defqual n/a n/a int?
bq2_handling n/a n/a {"type"=>"enum", "symbols"=>["keep", "dynamic", "fixed"]} (Optional)
bed n/a n/a File?
bonferroni n/a n/a string?
call_indels n/a n/a boolean?
def_alt_bq n/a n/a int?
def_alt_jq n/a n/a int?
del_baq n/a n/a boolean?
enable_source_qual n/a n/a boolean?
ignore_vcf n/a n/a File[]?
illumina_1_3 n/a n/a boolean?
max_depth_cov n/a n/a int?
max_mapping_quality n/a n/a int?
min_bq n/a n/a int?
min_cov n/a n/a int?
min_mq n/a n/a int?
use_orphan n/a n/a boolean?
threads_lf_call n/a n/a int?
replace_non_match n/a n/a int?
region n/a n/a string?
pvalue_cutoff n/a n/a float?
only_indels n/a n/a boolean?
no_idaq n/a n/a boolean?
no_default_filter n/a n/a boolean?
no_baq n/a n/a boolean?
no_mapping_quality n/a n/a boolean?
no_ext_base_alignment_quality n/a n/a boolean?
min_jq n/a n/a int?
min_alt_jq n/a n/a int?
min_alt_bq n/a n/a int?
genome_reference n/a n/a string
udLength n/a n/a int
transcripts n/a n/a File?
strict n/a n/a boolean?
spliceSiteSize n/a n/a int?
spliceRegionIntronMin n/a n/a int?
spliceRegionIntronMax n/a n/a int?
spliceRegionExonSize n/a n/a int?
sequenceOntology n/a n/a boolean?
outputFormat n/a n/a {"type"=>"enum", "symbols"=>["vcf", "bed", "gatk", "bedAnn"]} (Optional)
onlyReg n/a n/a boolean?
onlyProtein n/a n/a boolean?
oicr n/a n/a boolean?
noStats n/a n/a boolean?
noShiftHgvs n/a n/a boolean?
noNextProt n/a n/a boolean?
noMotif n/a n/a boolean?
bankfile n/a n/a File?
cancer n/a n/a boolean?
cancerSamples n/a n/a File?
canon n/a n/a boolean?
classic n/a n/a boolean?
csvFile n/a n/a boolean?
filterInterval n/a n/a File[]?
hgvs n/a n/a boolean?
formatEff n/a n/a boolean?
html_report_1 n/a n/a boolean?
importGenome n/a n/a boolean
interval n/a n/a File[]?
lof n/a n/a boolean?
motif n/a n/a boolean?
nextProt n/a n/a boolean?
no_downstream n/a n/a boolean?
no_EffectType n/a n/a boolean?
no_intergenic n/a n/a boolean?
no_intron n/a n/a boolean?
no_upstream n/a n/a boolean?
no_utr n/a n/a boolean?
noGenome n/a n/a boolean?
noHgvs n/a n/a boolean?
noLof n/a n/a boolean?
geneId n/a n/a boolean?
separator n/a n/a string?
empty_text n/a n/a string?
extractFields n/a n/a string[]?
IndexName n/a n/a string

Steps

ID Name Description
fastp
multiqc_fastp
samtools_view_filter
picard_sortsam
picard__mark_duplicates
multiqc_markdups
lofreq_viterbi
samtools_sort
samtools_faidx
samtool_index
bwa_index_cwl
get_secondaryfiles
get_tab
bwa_mem
samtools_stats
multiqc_stats
lofreq_call LoFreq Call Variants
snpeff_build_ann
snpsift_extract

Outputs

ID Name Description Type
multiqc_fastp n/a n/a File
stats_bam n/a n/a File[]
multiqc_markdups n/a n/a File
multiqc_samtoolsstats n/a n/a File
statsFile_snpeff n/a n/a File[]
out_snpsift n/a n/a File[]
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Views: 81   Downloads: 5

Created: 8th Jun 2020 at 15:57

Last updated: 30th Jun 2020 at 08:58

Last used: 5th Jul 2020 at 09:51

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