Workflow Type: Common Workflow Language
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Work-in-progress
StructuralVariants Workflow
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Inputs
ID | Name | Description | Type |
---|---|---|---|
fastq1 | n/a | FASTQ 1 list of files |
|
fastq2 | n/a | FASTQ 2 list of files |
|
reference_fasta | n/a | reference genome |
|
bed | n/a | capture kit |
|
samples | n/a | TXT file mapping cases ID, samples ID and batch |
|
threads_fastqc | n/a | number of threads for fastqc |
|
threads_fastp | n/a | number of threads for fastp |
|
threads_bwa_mem | n/a | number of threads for bwa-mem |
|
threads_samtools | n/a | number of threads for samtools |
|
threads_gridss | n/a | number of threads for GRIDSS |
|
read_group | n/a | FASTA read group (used to fix BAM files) |
|
min_mapping_quality | n/a | skip alignments with MAPQ smaller than this minimum |
|
bits_set | n/a | skip output alignments with this bits set |
|
manta_exome | n/a | provide appropriate settings for WES |
|
manta_min_len | n/a | minimum CNV lenght for MANTA |
|
manta_max_len | n/a | maximum CNV lenght for MANTA |
|
manta_min_q | n/a | minimum CNV quality for MANTA |
|
blacklist | n/a | BED file containing regions to ignore |
|
gridss_min_len | n/a | minimum CNV lenght for GRIDSS |
|
gridss_max_len | n/a | maximum CNV lenght for GRIDSS |
|
gridss_min_q | n/a | minimum CNV quality for GRIDSS |
|
exomeDepth_min_len | n/a | minimum CNV lenght for EXOME_DEPTH |
|
exomeDepth_max_len | n/a | maximum CNV lenght for EXOME_DEPTH |
|
exomeDepth_min_bf | n/a | minimum CNV Bayes factor for EXOME_DEPTH |
|
chromosome | n/a | chromosome for targeted sequencing for CODEX |
|
codex_min_len | n/a | minimum CNV lenght for CODEX |
|
codex_max_len | n/a | maximum CNV lenght for CODEX |
|
codex_min_lratio | n/a | minimum CNV lratio for CODEX |
|
enable_manta | n/a | execute MANTA predictions |
|
enable_gridss | n/a | execute GRIDSS predictions |
|
enable_exomeDepth | n/a | execute EXOME_DEPTH predictions |
|
enable_codex | n/a | execute CODEX predictions |
|
Steps
ID | Name | Description |
---|---|---|
trimmed_fastq | n/a | n/a |
bwa_index | 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 |
|
fastqc_raw_html | n/a | n/a |
|
html_report | n/a | n/a |
|
json_report | n/a | n/a |
|
fastqc_paired_zip | n/a | n/a |
|
fastqc_paired_html | n/a | n/a |
|
output_bam_filtering | n/a | n/a |
|
output_manta | n/a | n/a |
|
output_gridss | n/a | n/a |
|
output_exomedepth | n/a | n/a |
|
output_codex | n/a | n/a |
|
output_all | n/a | n/a |
|
Version History
1.1.3 (latest) Created 11th Oct 2022 at 12:04 by Laura Rodriguez-Navas
deleted cnvChr channel
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1.1.3
93fbc4e
1.1.0 Created 9th Sep 2022 at 11:27 by Laura Rodriguez-Navas
minor changes in main.nf
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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
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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)
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1.0.8
a478446
1.0.7 Created 1st Jun 2022 at 18:26 by Laura Rodriguez-Navas
add gunzip in bwa-index subworkflow
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1.0.7
94bcf49
1.0.6 Created 11th May 2022 at 15:27 by Laura Rodriguez-Navas
update r-base container
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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
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1.0.5
a4a3547
1.0.4 Created 25th Apr 2022 at 08:30 by Laura Rodriguez-Navas
read group param as default
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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
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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
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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
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1.0.1
27011e8
Creators and Submitter
Creator
Additional credit
Daniel López-López
Submitter
License
Activity
Views: 6890 Downloads: 1577
Created: 14th Mar 2022 at 12:07
Last updated: 30th Jun 2022 at 13:00
Attributions
None