Exome-alignment Workflow

public public 1yr ago Version: Version 1 0 bookmarks
View Workflow
Report
exome-alignment
exome-alignment
exome-alignment
exome-alignment
exome-alignment
View Workflow

Exome Alignment Workflow

Code Snippets

16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
baseCommand: ["bwa", "index"]

inputs:
  algorithm:
    type: string?
    inputBinding:
      prefix: -a

  reference_genome:
    type: File
    inputBinding:
      position: 4

  block_size:
    type: int?
    inputBinding:
      position: 2
      prefix: -b
CWL BWA From line 16 of tools/bwa-index.cwl 
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
baseCommand: ["bwa" , "mem", "-M", "-p"]

inputs:
  trimmed_fastq:
    type: File
    inputBinding:
      position: 4

  reference_genome:
    type: File
    inputBinding:
      position: 3
    secondaryFiles:
      - .amb
      - .ann
      - .bwt
      - .pac
      - .sa

  sample_name:
    type: string

  threads:
    type: string?
    default: '2'
    inputBinding:
      position: 1
      prefix: '-t'

  read_group:
    type: string
    default: '@RG\\tID:H947YADXX\\tSM:NA12878\\tPL:ILLUMINA'
    inputBinding:
      position: 2
      prefix: '-R'
CWL BWA From line 17 of tools/bwa-mem.cwl 
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
baseCommand: ["cutadapt", "--interleaved"]

arguments:
  - position: 1
    prefix: '-j'
    valueFrom: '0'
  - position: 2
    prefix: '--error-rate'
    valueFrom: '0.2'
  - position: 3
    prefix: '--overlap'
    valueFrom: '6'
  - position: 4
    prefix: '-o'
    valueFrom: '$(inputs.raw_sequences[0].basename + ".trimmed.fastq.gz")'

inputs:
  raw_sequences:
    type: File[]
    inputBinding:
      position: 20
      prefix: ''
      separate: false

  adaptors_file:
    type: File?
    inputBinding:
      position: 10
      prefix: '-a'
CWL Cutadapt From line 17 of tools/cutadapt.cwl 
16
17
18
19
20
21
22
23
24
baseCommand: ["gunzip"]

arguments: ["-c", "-v"]

inputs:
  reference_genome:
    type: File
    inputBinding:
      position: 2
CWL From line 16 of tools/gunzip.cwl 
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
baseCommand: ["picard", "CreateSequenceDictionary"]

inputs:
  reference_genome:
    type: File
    inputBinding:
      position: 1
      prefix: 'R='
      separate: false

arguments:
  - position: 2
    prefix: 'O='
    separate: false
    valueFrom: $(inputs.reference_genome.nameroot).dict
CWL Picard From line 16 of tools/picard_dictionary.cwl 
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
baseCommand: ["picard", "MarkDuplicates"]

inputs:
  alignments:
    type: File
    inputBinding:
      position: 2
      prefix: 'INPUT='
      separate: false

arguments:
  - position: 0
    prefix: OPTICAL_DUPLICATE_PIXEL_DISTANCE=
    valueFrom: '100'
    separate: false
  - position: 0
    prefix: TAGGING_POLICY=
    valueFrom: 'All'
    separate: false
  - position: 0
    prefix: CREATE_INDEX=
    valueFrom: 'true'
    separate: false
  - position: 0
    prefix: REMOVE_DUPLICATES=
    valueFrom: 'true'
    separate: false
  - position: 0
    prefix: TAG_DUPLICATE_SET_MEMBERS=
    valueFrom: 'true'
    separate: false
  - position: 0
    prefix: ASSUME_SORT_ORDER=
    valueFrom: 'coordinate'
    separate: false
  - position: 1
    prefix: 'METRICS_FILE='
    valueFrom: $(inputs.alignments.nameroot).metrics.txt
    separate: false
  - position: 3
    prefix: 'OUTPUT='
    valueFrom: $(inputs.alignments.nameroot).md.bam
    separate: false
CWL Picard From line 16 of tools/picard_markduplicates.cwl 
18
19
20
21
22
23
24
baseCommand: ["samtools", "faidx"]

inputs:
  sequences:
    type: File
    inputBinding:
      position: 1
CWL SAMtools From line 18 of tools/samtools_faidx.cwl 
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
baseCommand: ["samtools", "sort"]

inputs:
  bam_unsorted:
    type: File
    inputBinding:
      position: 2

  threads:
    type: string?
    default: "8"
    inputBinding:
      position: 1
      prefix: '--threads'

arguments:
  - position: 2
    prefix: '-o'
    valueFrom: $(inputs.bam_unsorted.nameroot).sorted.bam
CWL SAMtools From line 18 of tools/samtools_sort.cwl
ShowHide 4 more snippets with no or duplicated tags.

Login to post a comment if you would like to share your experience with this workflow.

Do you know this workflow well? If so, you can request seller status , and start supporting this workflow.

Free

Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/inab/ipc_workflows/tree/main/exome/alignment
Name: exome-alignment
Version: Version 1
Badge:
workflow icon

Insert copied code into your website to add a link to this workflow.

Downloaded: 0
Copyright: Public Domain
License: Boost Software License 1.0
  • Future updates

Related Workflows

psychip_snakemake
Show Details View Workflow
ENCODE pipeline for histone marks developed for the psychENCODE project
public

public

psychip pipeline is an improved version of the ENCODE pipeline for histone marks developed for the psychENCODE project. The o...
raw sequence reads Alignment Sequence alignment report macs2 ucsc-bedclip bedGraphToBigWig BEDTools BWA Picard SAMtools Snakemake
Free
74
ncov_2
Show Details View Workflow
Near-real time tracking of SARS-CoV-2 in Connecticut
public

public

Repository containing scripts to perform near-real time tracking of SARS-CoV-2 in Connecticut using genomic data. This pipeli...
JSON nextclade Augur Biopython FOCUS Pandas Snakemake bs4 epiweeks geopy matplotlib numpy pycountry pycountry-convert uszipcode
Free
28
cellranger-snakemake-gke
Show Details View Workflow
snakemake workflow to run cellranger on a given bucket using gke.
public

public

A Snakemake workflow for running cellranger on a given bucket using Google Kubernetes Engine. The usage of this workflow ...
macs2 ucsc-bedclip bedGraphToBigWig BEDTools BWA Picard SAMtools Snakemake
Free
74
atlas
Show Details View Workflow
ATLAS - Three commands to start analyzing your metagenome data
public

public

Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, t...
raw sequence reads Genome assembly Annotation track checkm2 gunc prodigal snakemake-wrapper-utils MEGAHIT Atlas BBMap Biopython BioRuby Bwa-mem2 cd-hit CheckM DAS Diamond eggNOG-mapper v2 MetaBAT 2 Minimap2 MMseqs MultiQC Pandas Picard pyfastx SAMtools SemiBin Snakemake SPAdes SqueezeMeta TADpole VAMB CONCOCT ete3 gtdbtk h5py networkx numpy plotly psutil utils metagenomics
Free
175
rna-seq-star-deseq2
Show Details View Workflow
RNA-seq workflow using STAR and DESeq2
public

public

This workflow performs a differential gene expression analysis with STAR and Deseq2. The usage of this workflow is described ...
raw sequence reads Gene expression profiling ID list snakemake-wrapper-utils biomaRt PCAtools BiocParallel BWA Cutadapt DESeq2 GFFutils MultiQC Pandas SAMtools Snakemake STAR cli stringr tidyverse RNA-Seq
Free
41
dna-seq-gatk-variant-calling
Show Details View Workflow
This Snakemake pipeline implements the GATK best-practices workflow
public

public

This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. The usage of thi...
VCF raw sequence reads Variant calling genetic variants gatk rust-bio-tools snakemake-wrapper-utils tabix BCFtools BWA FastQC MultiQC Pandas Picard SAMtools Snakemake Trimmomatic Variant Effect Predictor (VEP) common matplotlib numpy seaborn DNA
Free
57