Workflow Type: Common Workflow Language
Stable

StructuralVariants Workflow

Inputs

ID Name Description Type
fastq1 n/a FASTQ 1 list of files
  • File[]
fastq2 n/a FASTQ 2 list of files
  • File[]
generate_bwa_indexes n/a enable generation of reference genome indexes
  • boolean?
reference_fasta n/a reference genome
  • File
reference_fai n/a fai index for reference genome
  • File?
reference_amb n/a amb index for reference genome
  • File?
reference_ann n/a ann index for reference genome
  • File?
reference_bwt n/a bwt index for reference genome
  • File?
reference_pac n/a pac index reference genome
  • File?
reference_sa n/a sa index reference genome
  • File?
bed n/a capture kit
  • File
samples n/a TXT file mapping cases ID, samples ID and batch
  • File
threads_fastqc n/a number of threads for fastqc
  • int?
threads_fastp n/a number of threads for fastp
  • int?
threads_bwa_mem n/a number of threads for bwa-mem
  • int?
threads_samtools n/a number of threads for samtools
  • int?
threads_gridss n/a number of threads for GRIDSS
  • int?
bwt_algorithm n/a BWT construction algorithm: bwtsw or is (Default: auto)
  • string?
read_group n/a FASTA read group (used to fix BAM files)
  • string?
min_mapping_quality n/a skip alignments with MAPQ smaller than this minimum
  • int
bits_set n/a skip output alignments with this bits set
  • int
manta_exome n/a provide appropriate settings for WES
  • boolean
manta_min_len n/a minimum CNV lenght for MANTA
  • string
manta_max_len n/a maximum CNV lenght for MANTA
  • string
manta_min_q n/a minimum CNV quality for MANTA
  • string
blacklist n/a BED file containing regions to ignore
  • File?
gridss_min_len n/a minimum CNV lenght for GRIDSS
  • string
gridss_max_len n/a maximum CNV lenght for GRIDSS
  • string
gridss_min_q n/a minimum CNV quality for GRIDSS
  • string
exomeDepth_min_len n/a minimum CNV lenght for EXOME_DEPTH
  • string
exomeDepth_max_len n/a maximum CNV lenght for EXOME_DEPTH
  • string
exomeDepth_min_bf n/a minimum CNV Bayes factor for EXOME_DEPTH
  • string
codex_min_len n/a minimum CNV lenght for CODEX
  • string
codex_max_len n/a maximum CNV lenght for CODEX
  • string
codex_min_lratio n/a minimum CNV lratio for CODEX
  • string
enable_manta n/a execute MANTA predictions
  • boolean
enable_gridss n/a execute GRIDSS predictions
  • boolean
enable_exomeDepth n/a execute EXOME_DEPTH predictions
  • boolean
enable_codex n/a execute CODEX predictions
  • boolean

Steps

ID Name Description
bwa_index n/a n/a
trimmed_fastq n/a n/a
bwa_mem n/a n/a
samtools_view_sam2bam n/a n/a
samtools_sort n/a n/a
samtools_merge n/a n/a
samtools_index n/a n/a
picard_markduplicates n/a n/a
bam_filtering n/a n/a
cnv_manta n/a n/a
cnv_gridss n/a n/a
cnv_exomedepth n/a n/a
cnv_codex n/a n/a
final_filtering n/a n/a

Outputs

ID Name Description Type
fastqc_raw_zip n/a n/a
  • File[]
fastqc_raw_html n/a n/a
  • File[]
html_report n/a n/a
  • File[]
json_report n/a n/a
  • File[]
fastqc_paired_zip n/a n/a
  • File[]
fastqc_paired_html n/a n/a
  • File[]
output_bam_filtering n/a n/a
  • File[]
output_manta n/a n/a
  • File?
output_gridss n/a n/a
  • File?
output_exomedepth n/a n/a
  • File?
output_codex n/a n/a
  • File?
output_all n/a n/a
  • File

Version History

1.1.3 (latest) Created 11th Oct 2022 at 12:04 by Laura Rodriguez-Navas

deleted cnvChr channel


Frozen 1.1.3 93fbc4e

1.1.0 Created 9th Sep 2022 at 11:27 by Laura Rodriguez-Navas

minor changes in main.nf


Frozen 1.1.0 6f16906

1.0.9 Created 30th Jun 2022 at 14:07 by Laura Rodriguez-Navas

minor change in main of CWL workflow


Frozen 1.0.9 b62c7bf

1.0.8 Created 30th Jun 2022 at 13:00 by Laura Rodriguez-Navas

add support for input BED to exomeDepth (CWL)


Frozen 1.0.8 a478446

1.0.7 Created 1st Jun 2022 at 18:26 by Laura Rodriguez-Navas

add gunzip in bwa-index subworkflow


Frozen 1.0.7 94bcf49

1.0.6 Created 11th May 2022 at 15:27 by Laura Rodriguez-Navas

update r-base container


Frozen 1.0.6 32a040f

1.0.5 Created 10th May 2022 at 10:04 by Laura Rodriguez-Navas

added new steps to control optionality for reference fasta input


Frozen 1.0.5 a4a3547

1.0.4 Created 25th Apr 2022 at 08:30 by Laura Rodriguez-Navas

read group param as default


Frozen 1.0.4 9ac2d15

1.0.3 Created 23rd Mar 2022 at 14:19 by Laura Rodriguez-Navas

update algoType parameter on bwa index process (CWL), updating abstract too


Frozen 1.0.3 26ae491

1.0.2 Created 14th Mar 2022 at 15:00 by Laura Rodriguez-Navas

rename json and html reports of fastp CWL tool


Frozen 1.0.2 13e8e65

1.0.1 (earliest) Created 14th Mar 2022 at 12:07 by Laura Rodriguez-Navas

Merge branch 'master' into 'master'

Updated abstracts

See merge request lrodrig1/structuralvariants_poc!3


Frozen 1.0.1 27011e8
help Creators and Submitter
Creator
Additional credit

Daniel López-López

Submitter
Activity

Views: 1269

Created: 14th Mar 2022 at 12:07

Last updated: 30th Jun 2022 at 13:00

Last used: 5th Dec 2022 at 08:10

help Attributions

None

Total size: 264 KB
Powered by
(v.1.12.3)
Copyright © 2008 - 2022 The University of Manchester and HITS gGmbH

By continuing to use this site you agree to the use of cookies