Workflow Type: Common Workflow Language
Open
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).
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Inputs
ID | Name | Description | Type |
---|---|---|---|
reads_reverse | n/a | n/a |
|
reads_forward | n/a | n/a |
|
reference_in | n/a | n/a |
|
unqualified_phred_quality | n/a | n/a |
|
threads | n/a | n/a |
|
qualified_phred_quality | n/a | n/a |
|
min_length_required | n/a | n/a |
|
force_polyg_tail_trimming | n/a | n/a |
|
disable_trim_poly_g | n/a | n/a |
|
base_correction | n/a | n/a |
|
sort_order | n/a | n/a |
|
validation_stringency | n/a | n/a |
|
exclude_unmapped | n/a | n/a |
|
count | n/a | n/a |
|
alignments_are_sorted | n/a | n/a |
|
remove_duplicates | n/a | n/a |
|
validation_stringency_1 | n/a | n/a |
|
comment | n/a | n/a |
|
duplicate_scoring_strategy | n/a | n/a |
|
optical_duplicate_pixel_distance | n/a | n/a |
|
barcode_tag | n/a | n/a |
|
keepflags | n/a | n/a |
|
defqual | n/a | n/a |
|
bq2_handling | n/a | n/a |
|
bed | n/a | n/a |
|
bonferroni | n/a | n/a |
|
call_indels | n/a | n/a |
|
def_alt_bq | n/a | n/a |
|
def_alt_jq | n/a | n/a |
|
del_baq | n/a | n/a |
|
enable_source_qual | n/a | n/a |
|
ignore_vcf | n/a | n/a |
|
illumina_1_3 | n/a | n/a |
|
max_depth_cov | n/a | n/a |
|
max_mapping_quality | n/a | n/a |
|
min_bq | n/a | n/a |
|
min_cov | n/a | n/a |
|
min_mq | n/a | n/a |
|
use_orphan | n/a | n/a |
|
threads_lf_call | n/a | n/a |
|
replace_non_match | n/a | n/a |
|
region | n/a | n/a |
|
pvalue_cutoff | n/a | n/a |
|
only_indels | n/a | n/a |
|
no_idaq | n/a | n/a |
|
no_default_filter | n/a | n/a |
|
no_baq | n/a | n/a |
|
no_mapping_quality | n/a | n/a |
|
no_ext_base_alignment_quality | n/a | n/a |
|
min_jq | n/a | n/a |
|
min_alt_jq | n/a | n/a |
|
min_alt_bq | n/a | n/a |
|
genome_reference | n/a | n/a |
|
udLength | n/a | n/a |
|
transcripts | n/a | n/a |
|
strict | n/a | n/a |
|
spliceSiteSize | n/a | n/a |
|
spliceRegionIntronMin | n/a | n/a |
|
spliceRegionIntronMax | n/a | n/a |
|
spliceRegionExonSize | n/a | n/a |
|
sequenceOntology | n/a | n/a |
|
outputFormat | n/a | n/a |
|
onlyReg | n/a | n/a |
|
onlyProtein | n/a | n/a |
|
oicr | n/a | n/a |
|
noStats | n/a | n/a |
|
noShiftHgvs | n/a | n/a |
|
noNextProt | n/a | n/a |
|
noMotif | n/a | n/a |
|
bankfile | n/a | n/a |
|
cancer | n/a | n/a |
|
cancerSamples | n/a | n/a |
|
canon | n/a | n/a |
|
classic | n/a | n/a |
|
csvFile | n/a | n/a |
|
filterInterval | n/a | n/a |
|
hgvs | n/a | n/a |
|
formatEff | n/a | n/a |
|
html_report_1 | n/a | n/a |
|
importGenome | n/a | n/a |
|
interval | n/a | n/a |
|
lof | n/a | n/a |
|
motif | n/a | n/a |
|
nextProt | n/a | n/a |
|
no_downstream | n/a | n/a |
|
no_EffectType | n/a | n/a |
|
no_intergenic | n/a | n/a |
|
no_intron | n/a | n/a |
|
no_upstream | n/a | n/a |
|
no_utr | n/a | n/a |
|
noGenome | n/a | n/a |
|
noHgvs | n/a | n/a |
|
noLof | n/a | n/a |
|
geneId | n/a | n/a |
|
separator | n/a | n/a |
|
empty_text | n/a | n/a |
|
extractFields | n/a | n/a |
|
IndexName | n/a | n/a |
|
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 |
|
stats_bam | n/a | n/a |
|
multiqc_markdups | n/a | n/a |
|
multiqc_samtoolsstats | n/a | n/a |
|
statsFile_snpeff | n/a | n/a |
|
out_snpsift | n/a | n/a |
|
Version History
Version 1 (earliest) Created 8th Jun 2020 at 15:57 by Camille Juigné
Added/updated 1 files
Open
master
b355223
Creators and Submitter
Creator
Submitter
License
Activity
Views: 3029 Downloads: 804
Created: 8th Jun 2020 at 15:57
Last updated: 30th Jun 2020 at 08:58
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