CNV_pipeline
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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 |
|
| generate_bwa_indexes | n/a | enable generation of reference genome indexes |
|
| reference_fasta | n/a | reference genome |
|
| reference_fai | n/a | fai index for reference genome |
|
| reference_amb | n/a | amb index for reference genome |
|
| reference_ann | n/a | ann index for reference genome |
|
| reference_bwt | n/a | bwt index for reference genome |
|
| reference_pac | n/a | pac index reference genome |
|
| reference_sa | n/a | sa index 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 |
|
| bwt_algorithm | n/a | BWT construction algorithm: bwtsw or is (Default: auto) |
|
| 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 |
|---|---|---|
| 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 |
|
| 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
Frozen
1.1.393fbc4e
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
Creators and Submitter
Views: 7151 Downloads: 1669
Created: 14th Mar 2022 at 12:07
Last updated: 30th Jun 2022 at 13:00
AttributionsNone
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