Workflow Type: Common Workflow Language
Stable

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
  • <strong>enum</strong> of: queryname, coordinate, duplicate
validation_stringency n/a n/a
  • <strong>enum</strong> of: STRICT, LENIENT, SILENT
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
  • <strong>enum</strong> of: STRICT, LENIENT, SILENT
comment n/a n/a
  • string[]?
duplicate_scoring_strategy n/a n/a
  • <strong>enum</strong> of: SUM_OF_BASE_QUALITIES, TOTAL_MAPPED_REFERENCE_LENGTH, RANDOM
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
  • <strong>enum</strong> of: keep, dynamic, fixed
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
  • <strong>enum</strong> of: vcf, bed, gatk, bedAnn
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 n/a n/a
multiqc_fastp n/a n/a
samtools_view_filter n/a n/a
picard_sortsam n/a n/a
picard__mark_duplicates n/a n/a
multiqc_markdups n/a n/a
lofreq_viterbi n/a n/a
samtools_sort n/a n/a
samtools_faidx n/a n/a
samtool_index n/a n/a
bwa_index_cwl n/a n/a
get_secondaryfiles n/a n/a
get_tab n/a n/a
bwa_mem n/a n/a
samtools_stats n/a n/a
multiqc_stats n/a n/a
lofreq_call LoFreq Call Variants n/a
snpeff_build_ann n/a n/a
snpsift_extract n/a n/a

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[]

Version History

Version 1 (earliest) Created 8th Jun 2020 at 15:57 by Camille Juigné

Added/updated 1 files


Open master b355223
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Views: 1104   Downloads: 73

Created: 8th Jun 2020 at 15:57

Last updated: 30th Jun 2020 at 08:58

Last used: 25th Jun 2022 at 14:24

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