mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
Merge branch 'nf-core:master' into busco
This commit is contained in:
Priyanka Surana
GitHub
commit
c20f836450
594 changed files with 7836 additions and 4867 deletions
12
.github/workflows/code-linting.yml
vendored
12
.github/workflows/code-linting.yml
vendored
|
|
@ -12,9 +12,7 @@ jobs:
|
|||
steps:
|
||||
- uses: actions/checkout@v2
|
||||
|
||||
- uses: actions/setup-node@v1
|
||||
with:
|
||||
node-version: "10"
|
||||
- uses: actions/setup-node@v2
|
||||
|
||||
- name: Install markdownlint
|
||||
run: npm install -g markdownlint-cli
|
||||
|
|
@ -27,9 +25,7 @@ jobs:
|
|||
steps:
|
||||
- uses: actions/checkout@v2
|
||||
|
||||
- uses: actions/setup-node@v1
|
||||
with:
|
||||
node-version: "10"
|
||||
- uses: actions/setup-node@v2
|
||||
|
||||
- name: Install editorconfig-checker
|
||||
run: npm install -g editorconfig-checker
|
||||
|
|
@ -44,9 +40,7 @@ jobs:
|
|||
uses: actions/checkout@v2
|
||||
|
||||
- name: Install NodeJS
|
||||
uses: actions/setup-node@v1
|
||||
with:
|
||||
node-version: "10"
|
||||
uses: actions/setup-node@v2
|
||||
|
||||
- name: Install yaml-lint
|
||||
run: npm install -g yaml-lint
|
||||
|
|
|
|||
|
|
@ -1,14 +1,14 @@
|
|||
image: nfcore/gitpod:latest
|
||||
|
||||
vscode:
|
||||
extensions: # based on nf-core.nf-core-extensionpack
|
||||
extensions: # based on nf-core.nf-core-extensionpack
|
||||
- codezombiech.gitignore # Language support for .gitignore files
|
||||
# - cssho.vscode-svgviewer # SVG viewer
|
||||
# - cssho.vscode-svgviewer # SVG viewer
|
||||
- davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code
|
||||
- eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
|
||||
- EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
|
||||
- Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
|
||||
- mechatroner.rainbow-csv # Highlight columns in csv files in different colors
|
||||
# - nextflow.nextflow # Nextflow syntax highlighting
|
||||
# - nextflow.nextflow # Nextflow syntax highlighting
|
||||
- oderwat.indent-rainbow # Highlight indentation level
|
||||
- streetsidesoftware.code-spell-checker # Spelling checker for source code
|
||||
|
|
|
|||
|
|
@ -8,4 +8,4 @@ header-increment: false
|
|||
no-duplicate-header:
|
||||
siblings_only: true
|
||||
ul-indent:
|
||||
indent: 4
|
||||
indent: 4
|
||||
|
|
|
|||
5
.yamllint.yml
Normal file
5
.yamllint.yml
Normal file
|
|
@ -0,0 +1,5 @@
|
|||
extends: default
|
||||
|
||||
rules:
|
||||
document-start: disable
|
||||
line-length: disable
|
||||
|
|
@ -14,7 +14,7 @@ tools:
|
|||
documentation: http://abacas.sourceforge.net/documentation.html
|
||||
tool_dev_url: None
|
||||
doi: "10.1093/bioinformatics/btp347"
|
||||
licence: ['GPL v2-or-later']
|
||||
licence: ["GPL v2-or-later"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
34
modules/abricate/run/main.nf
Normal file
34
modules/abricate/run/main.nf
Normal file
|
|
@ -0,0 +1,34 @@
|
|||
process ABRICATE_RUN {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1':
|
||||
'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(assembly)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.txt"), emit: report
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
abricate \\
|
||||
$assembly \\
|
||||
$args \\
|
||||
--threads $task.cpus > ${prefix}.txt
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
43
modules/abricate/run/meta.yml
Normal file
43
modules/abricate/run/meta.yml
Normal file
|
|
@ -0,0 +1,43 @@
|
|||
name: abricate_run
|
||||
description: Screen assemblies for antimicrobial resistance against multiple databases
|
||||
keywords:
|
||||
- bacteria
|
||||
- assembly
|
||||
- antimicrobial reistance
|
||||
tools:
|
||||
- abricate:
|
||||
description: Mass screening of contigs for antibiotic resistance genes
|
||||
homepage: https://github.com/tseemann/abricate
|
||||
documentation: https://github.com/tseemann/abricate
|
||||
tool_dev_url: https://github.com/tseemann/abricate
|
||||
doi: ""
|
||||
licence: ['GPL v2', 'GPL v2']
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- assembly:
|
||||
type: file
|
||||
description: FASTA, GenBank or EMBL formatted file
|
||||
pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- report:
|
||||
type: file
|
||||
description: Tab-delimited report of results
|
||||
pattern: "*.{txt}"
|
||||
|
||||
authors:
|
||||
- "@rpetit3"
|
||||
33
modules/abricate/summary/main.nf
Normal file
33
modules/abricate/summary/main.nf
Normal file
|
|
@ -0,0 +1,33 @@
|
|||
process ABRICATE_SUMMARY {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1':
|
||||
'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reports)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.txt"), emit: report
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
abricate \\
|
||||
--summary \\
|
||||
$reports > ${prefix}.txt
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
43
modules/abricate/summary/meta.yml
Normal file
43
modules/abricate/summary/meta.yml
Normal file
|
|
@ -0,0 +1,43 @@
|
|||
name: abricate_summary
|
||||
description: Screen assemblies for antimicrobial resistance against multiple databases
|
||||
keywords:
|
||||
- bacteria
|
||||
- assembly
|
||||
- antimicrobial reistance
|
||||
tools:
|
||||
- abricate:
|
||||
description: Mass screening of contigs for antibiotic resistance genes
|
||||
homepage: https://github.com/tseemann/abricate
|
||||
documentation: https://github.com/tseemann/abricate
|
||||
tool_dev_url: https://github.com/tseemann/abricate
|
||||
doi: ""
|
||||
licence: ['GPL v2', 'GPL v2']
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- assembly:
|
||||
type: file
|
||||
description: FASTA, GenBank or EMBL formatted file
|
||||
pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- summary:
|
||||
type: file
|
||||
description: Tab-delimited report of aggregated results
|
||||
pattern: "*.{txt}"
|
||||
|
||||
authors:
|
||||
- "@rpetit3"
|
||||
|
|
@ -1,50 +1,50 @@
|
|||
name: adapterremoval
|
||||
description: Trim sequencing adapters and collapse overlapping reads
|
||||
keywords:
|
||||
- trimming
|
||||
- adapters
|
||||
- merging
|
||||
- fastq
|
||||
- trimming
|
||||
- adapters
|
||||
- merging
|
||||
- fastq
|
||||
tools:
|
||||
- adapterremoval:
|
||||
description: The AdapterRemoval v2 tool for merging and clipping reads.
|
||||
homepage: https://github.com/MikkelSchubert/adapterremoval
|
||||
documentation: https://adapterremoval.readthedocs.io
|
||||
licence: ['GPL v3']
|
||||
- adapterremoval:
|
||||
description: The AdapterRemoval v2 tool for merging and clipping reads.
|
||||
homepage: https://github.com/MikkelSchubert/adapterremoval
|
||||
documentation: https://adapterremoval.readthedocs.io
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false, collapse:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
pattern: "*.{fq,fastq,fg.gz,fastq.gz}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false, collapse:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
pattern: "*.{fq,fastq,fg.gz,fastq.gz}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input adapter trimmed FastQ files of size 1 or 2 for
|
||||
single-end or collapsed data and paired-end data, respectively.
|
||||
pattern: "*.{fastq.gz}"
|
||||
- log:
|
||||
type: file
|
||||
description: AdapterRemoval log file
|
||||
pattern: "*.log"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input adapter trimmed FastQ files of size 1 or 2 for
|
||||
single-end or collapsed data and paired-end data, respectively.
|
||||
pattern: "*.{fastq.gz}"
|
||||
- log:
|
||||
type: file
|
||||
description: AdapterRemoval log file
|
||||
pattern: "*.log"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
|
||||
authors:
|
||||
- "@maxibor"
|
||||
- "@maxibor"
|
||||
|
|
|
|||
|
|
@ -11,7 +11,7 @@ tools:
|
|||
documentation: https://github.com/VishnuRaghuram94/AgrVATE
|
||||
tool_dev_url: https://github.com/VishnuRaghuram94/AgrVATE
|
||||
doi: ""
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -24,7 +24,7 @@ tools:
|
|||
documentation: "https://github.com/keyfm/amps"
|
||||
tool_dev_url: "https://github.com/keyfm/amps"
|
||||
doi: "10.1186/s13059-019-1903-0"
|
||||
licence: ['GPL >=3']
|
||||
licence: ["GPL >=3"]
|
||||
|
||||
input:
|
||||
- maltextract_results:
|
||||
|
|
|
|||
55
modules/amrfinderplus/run/main.nf
Normal file
55
modules/amrfinderplus/run/main.nf
Normal file
|
|
@ -0,0 +1,55 @@
|
|||
process AMRFINDERPLUS_RUN {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.23" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus%3A3.10.23--h17dc2d4_0':
|
||||
'quay.io/biocontainers/ncbi-amrfinderplus:3.10.23--h17dc2d4_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fasta)
|
||||
path db
|
||||
|
||||
output:
|
||||
tuple val(meta), path("${prefix}.tsv") , emit: report
|
||||
tuple val(meta), path("${prefix}-mutations.tsv"), emit: mutation_report, optional: true
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def is_compressed = fasta.getName().endsWith(".gz") ? true : false
|
||||
prefix = task.ext.prefix ?: "${meta.id}"
|
||||
organism_param = meta.containsKey("organism") ? "--organism ${meta.organism} --mutation_all ${prefix}-mutations.tsv" : ""
|
||||
fasta_name = fasta.getName().replace(".gz", "")
|
||||
fasta_param = "-n"
|
||||
if (meta.containsKey("is_proteins")) {
|
||||
if (meta.is_proteins) {
|
||||
fasta_param = "-p"
|
||||
}
|
||||
}
|
||||
"""
|
||||
if [ "$is_compressed" == "true" ]; then
|
||||
gzip -c -d $fasta > $fasta_name
|
||||
fi
|
||||
|
||||
mkdir amrfinderdb
|
||||
tar xzvf $db -C amrfinderdb
|
||||
|
||||
amrfinder \\
|
||||
$fasta_param $fasta_name \\
|
||||
$organism_param \\
|
||||
$args \\
|
||||
--database amrfinderdb \\
|
||||
--threads $task.cpus > ${prefix}.tsv
|
||||
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
amrfinderplus: \$(amrfinder --version)
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
51
modules/amrfinderplus/run/meta.yml
Normal file
51
modules/amrfinderplus/run/meta.yml
Normal file
|
|
@ -0,0 +1,51 @@
|
|||
name: amrfinderplus_run
|
||||
description: Identify antimicrobial resistance in gene or protein sequences
|
||||
keywords:
|
||||
- bacteria
|
||||
- fasta
|
||||
- antibiotic resistance
|
||||
tools:
|
||||
- amrfinderplus:
|
||||
description: AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.
|
||||
homepage: https://github.com/ncbi/amr/wiki
|
||||
documentation: https://github.com/ncbi/amr/wiki
|
||||
tool_dev_url: https://github.com/ncbi/amr
|
||||
doi: "10.1038/s41598-021-91456-0"
|
||||
licence: ['Public Domain']
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: Nucleotide or protein sequences in FASTA format
|
||||
pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
|
||||
- db:
|
||||
type: file
|
||||
description: A compressed tarball of the AMRFinderPlus database to query
|
||||
pattern: "*.tar.gz"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- report:
|
||||
type: file
|
||||
description: AMRFinder+ final report
|
||||
pattern: "*.tsv"
|
||||
- mutation_report:
|
||||
type: file
|
||||
description: Report of organism-specific point-mutations
|
||||
pattern: "*-mutations.tsv"
|
||||
|
||||
authors:
|
||||
- "@rpetit3"
|
||||
29
modules/amrfinderplus/update/main.nf
Normal file
29
modules/amrfinderplus/update/main.nf
Normal file
|
|
@ -0,0 +1,29 @@
|
|||
process AMRFINDERPLUS_UPDATE {
|
||||
tag "update"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.23" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus%3A3.10.23--h17dc2d4_0':
|
||||
'quay.io/biocontainers/ncbi-amrfinderplus:3.10.23--h17dc2d4_0' }"
|
||||
|
||||
output:
|
||||
path "amrfinderdb.tar.gz", emit: db
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
"""
|
||||
mkdir amrfinderdb
|
||||
amrfinder_update -d amrfinderdb
|
||||
tar czvf amrfinderdb.tar.gz -C \$(readlink amrfinderdb/latest) ./
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
amrfinderplus: \$(amrfinder --version)
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
37
modules/amrfinderplus/update/meta.yml
Normal file
37
modules/amrfinderplus/update/meta.yml
Normal file
|
|
@ -0,0 +1,37 @@
|
|||
name: amrfinderplus_update
|
||||
description: Identify antimicrobial resistance in gene or protein sequences
|
||||
keywords:
|
||||
- bacteria
|
||||
- fasta
|
||||
- antibiotic resistance
|
||||
tools:
|
||||
- amrfinderplus:
|
||||
description: AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.
|
||||
homepage: https://github.com/ncbi/amr/wiki
|
||||
documentation: https://github.com/ncbi/amr/wiki
|
||||
tool_dev_url: https://github.com/ncbi/amr
|
||||
doi: "10.1038/s41598-021-91456-0"
|
||||
licence: ['Public Domain']
|
||||
|
||||
input:
|
||||
- input_not_required:
|
||||
type: null
|
||||
description: module does not have an input
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- db:
|
||||
type: file
|
||||
description: The latest AMRFinder+ database in a compressed tarball
|
||||
pattern: "*.tar.gz"
|
||||
|
||||
authors:
|
||||
- "@rpetit3"
|
||||
|
|
@ -10,7 +10,7 @@ tools:
|
|||
documentation: https://arriba.readthedocs.io/en/latest/
|
||||
tool_dev_url: https://github.com/suhrig/arriba
|
||||
doi: "10.1101/gr.257246.119"
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -11,7 +11,7 @@ tools:
|
|||
documentation: https://artic.readthedocs.io/en/latest/
|
||||
tool_dev_url: https://github.com/artic-network/fieldbioinformatics
|
||||
doi: ""
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -13,7 +13,8 @@ process ARTIC_MINION {
|
|||
path sequencing_summary
|
||||
path ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.reference.fasta")
|
||||
path ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.scheme.bed")
|
||||
path medaka_model
|
||||
path medaka_model_file
|
||||
val medaka_model_string
|
||||
val scheme
|
||||
val scheme_version
|
||||
|
||||
|
|
@ -44,7 +45,7 @@ process ARTIC_MINION {
|
|||
if (args.tokenize().contains('--medaka')) {
|
||||
fast5 = ""
|
||||
summary = ""
|
||||
model = file(medaka_model).exists() ? "--medaka-model ./$medaka_model" : "--medaka-model $medaka_model"
|
||||
model = medaka_model_file ? "--medaka-model ./$medaka_model_file" : "--medaka-model $medaka_model_string"
|
||||
}
|
||||
def hd5_plugin_path = task.ext.hd5_plugin_path ? "export HDF5_PLUGIN_PATH=" + task.ext.hd5_plugin_path : "export HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin"
|
||||
"""
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
name: artic_minion
|
||||
description: |
|
||||
Run the alignment/variant-call/consensus logic of the artic pipeline
|
||||
Run the alignment/variant-call/consensus logic of the artic pipeline
|
||||
keywords:
|
||||
- artic
|
||||
- aggregate
|
||||
|
|
@ -12,7 +12,7 @@ tools:
|
|||
documentation: https://artic.readthedocs.io/en/latest/
|
||||
tool_dev_url: https://github.com/artic-network/fieldbioinformatics
|
||||
doi: ""
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
|
|
@ -21,11 +21,11 @@ input:
|
|||
e.g. [ id:'test', single_end:false ]
|
||||
- fastq:
|
||||
type: file
|
||||
description: FastQ file containing reads
|
||||
description: FastQ file containing reads
|
||||
pattern: "*.{fastq.gz}"
|
||||
- fast5_dir:
|
||||
type: directory
|
||||
description: Directory containing MinION FAST5 files
|
||||
description: Directory containing MinION FAST5 files
|
||||
pattern: "*"
|
||||
- sequencing_summary:
|
||||
type: file
|
||||
|
|
@ -42,11 +42,16 @@ input:
|
|||
bed files containing coordinates of each primer in the scheme,
|
||||
relative to the reference genome
|
||||
pattern: "*.{scheme.bed}"
|
||||
- medaka_model:
|
||||
- medaka_model_file:
|
||||
type: file
|
||||
description: |
|
||||
Medaka model to use (if option --medaka is set)
|
||||
pattern: "*.*"
|
||||
Medaka model file to use (if option --medaka is set)
|
||||
pattern: "*.hdf5"
|
||||
- medaka_model_string:
|
||||
type: value
|
||||
description: |
|
||||
Medaka model string to use (if option --medaka is set)
|
||||
pattern: "*"
|
||||
- scheme:
|
||||
type: value
|
||||
description: Name of the primer scheme
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@ tools:
|
|||
documentation: https://github.com/rpetit3/assembly-scan
|
||||
tool_dev_url: https://github.com/rpetit3/assembly-scan
|
||||
doi: ""
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -9,7 +9,7 @@ tools:
|
|||
documentation: https://github.com/ParkerLab/ataqv/blob/master/README.rst
|
||||
tool_dev_url: https://github.com/ParkerLab/ataqv
|
||||
doi: "https://doi.org/10.1016/j.cels.2020.02.009"
|
||||
licence: ['GPL v3']
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process BAKTA {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bakta=1.2.2" : null)
|
||||
conda (params.enable_conda ? "bioconda::bakta=1.3.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bakta:1.2.2--pyhdfd78af_0' :
|
||||
'quay.io/biocontainers/bakta:1.2.2--pyhdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/bakta:1.3.1--pyhdfd78af_0' :
|
||||
'quay.io/biocontainers/bakta:1.3.1--pyhdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fasta)
|
||||
|
|
@ -23,6 +23,7 @@ process BAKTA {
|
|||
tuple val(meta), path("${prefix}.hypotheticals.tsv"), emit: hypotheticals_tsv
|
||||
tuple val(meta), path("${prefix}.hypotheticals.faa"), emit: hypotheticals_faa
|
||||
tuple val(meta), path("${prefix}.tsv") , emit: tsv
|
||||
tuple val(meta), path("${prefix}.txt") , emit: txt
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
|
|
@ -61,6 +62,7 @@ process BAKTA {
|
|||
touch ${prefix}.hypotheticals.tsv
|
||||
touch ${prefix}.hypotheticals.faa
|
||||
touch ${prefix}.tsv
|
||||
touch ${prefix}.txt
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
|
|||
|
|
@ -1,17 +1,17 @@
|
|||
name: bakta
|
||||
description: Rapid annotation of bacterial genomes & plasmids.
|
||||
description: Annotation of bacterial genomes (isolates, MAGs) and plasmids
|
||||
keywords:
|
||||
- annotation
|
||||
- fasta
|
||||
- prokaryote
|
||||
- bacteria
|
||||
tools:
|
||||
- bakta:
|
||||
description: Rapid & standardized annotation of bacterial genomes & plasmids.
|
||||
description: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids.
|
||||
homepage: https://github.com/oschwengers/bakta
|
||||
documentation: https://github.com/oschwengers/bakta
|
||||
tool_dev_url: https://github.com/oschwengers/bakta
|
||||
doi: "10.1099/mgen.0.000685"
|
||||
licence: ['GPL v3']
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
@ -29,7 +29,7 @@ input:
|
|||
Path to the Bakta database
|
||||
- proteins:
|
||||
type: file
|
||||
description: FASTA file of trusted proteins to first annotate from (optional)
|
||||
description: FASTA/GenBank file of trusted proteins to first annotate from (optional)
|
||||
- prodigal_tf:
|
||||
type: file
|
||||
description: Training file to use for Prodigal (optional)
|
||||
|
|
@ -44,6 +44,10 @@ output:
|
|||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- txt:
|
||||
type: file
|
||||
description: genome statistics and annotation summary
|
||||
pattern: "*.txt"
|
||||
- tsv:
|
||||
type: file
|
||||
description: annotations as simple human readble tab separated values
|
||||
|
|
@ -83,3 +87,4 @@ output:
|
|||
|
||||
authors:
|
||||
- "@rpetit3"
|
||||
- "@oschwengers"
|
||||
|
|
|
|||
|
|
@ -8,7 +8,7 @@ tools:
|
|||
homepage: https://github.com/maxibor/bamAlignCleaner
|
||||
documentation: https://github.com/maxibor/bamAlignCleaner
|
||||
tool_dev_url: https://github.com/maxibor/bamAlignCleaner
|
||||
licence: ['GPL v3']
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -10,14 +10,15 @@ keywords:
|
|||
|
||||
tools:
|
||||
- bamcmp:
|
||||
description: Bamcmp is a tool for deconvolving host and graft reads, using two bam files. Reads should be mapped to two genomes, and the mapped,
|
||||
sorted bam files supplied to the tool. It is highly recommended to use the "-s as" option not the "-s mapq" option, else
|
||||
reads which multimap to the contamination genome will be spuriously kept.
|
||||
description:
|
||||
Bamcmp is a tool for deconvolving host and graft reads, using two bam files. Reads should be mapped to two genomes, and the mapped,
|
||||
sorted bam files supplied to the tool. It is highly recommended to use the "-s as" option not the "-s mapq" option, else
|
||||
reads which multimap to the contamination genome will be spuriously kept.
|
||||
homepage: https://github.com/CRUKMI-ComputationalBiology/bamcmp
|
||||
documentation: https://github.com/CRUKMI-ComputationalBiology/bamcmp
|
||||
tool_dev_url: https://github.com/CRUKMI-ComputationalBiology/bamcmp
|
||||
doi: "10.1158/1541-7786.MCR-16-0431"
|
||||
licence: ['GPL v3']
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -19,7 +19,7 @@ tools:
|
|||
documentation: https://github.com/pezmaster31/bamtools/wiki
|
||||
tool_dev_url: http://github.com/pezmaster31/bamtools
|
||||
doi: ""
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@ tools:
|
|||
documentation: https://github.com/pezmaster31/bamtools/wiki
|
||||
tool_dev_url: http://github.com/pezmaster31/bamtools
|
||||
doi: ""
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@ tools:
|
|||
documentation: https://genome.sph.umich.edu/wiki/BamUtil:_trimBam
|
||||
tool_dev_url: https://github.com/statgen/bamUtil
|
||||
doi: "10.1101/gr.176552.114"
|
||||
licence: ['GPL v3']
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -1,44 +1,44 @@
|
|||
name: bandage_image
|
||||
description: Render an assembly graph in GFA 1.0 format to PNG and SVG image formats
|
||||
keywords:
|
||||
- gfa
|
||||
- graph
|
||||
- assembly
|
||||
- visualisation
|
||||
- gfa
|
||||
- graph
|
||||
- assembly
|
||||
- visualisation
|
||||
tools:
|
||||
- bandage:
|
||||
description: |
|
||||
Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
|
||||
homepage: https://github.com/rrwick/Bandage
|
||||
documentation: https://github.com/rrwick/Bandage
|
||||
licence: ['GPL-3.0-or-later']
|
||||
- bandage:
|
||||
description: |
|
||||
Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
|
||||
homepage: https://github.com/rrwick/Bandage
|
||||
documentation: https://github.com/rrwick/Bandage
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- gfa:
|
||||
type: file
|
||||
description: Assembly graph in GFA 1.0 format
|
||||
pattern: "*.gfa"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- gfa:
|
||||
type: file
|
||||
description: Assembly graph in GFA 1.0 format
|
||||
pattern: "*.gfa"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- png:
|
||||
type: file
|
||||
description: Bandage image in PNG format
|
||||
pattern: "*.png"
|
||||
- svg:
|
||||
type: file
|
||||
description: Bandage image in SVG format
|
||||
pattern: "*.svg"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- png:
|
||||
type: file
|
||||
description: Bandage image in PNG format
|
||||
pattern: "*.png"
|
||||
- svg:
|
||||
type: file
|
||||
description: Bandage image in SVG format
|
||||
pattern: "*.svg"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@heuermh"
|
||||
- "@heuermh"
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@ tools:
|
|||
documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
|
||||
tool_dev_url: None
|
||||
doi: ""
|
||||
licence: ['UC-LBL license (see package)']
|
||||
licence: ["UC-LBL license (see package)"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
@ -24,14 +24,14 @@ input:
|
|||
- fastq:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- ref:
|
||||
type: file
|
||||
description: |
|
||||
Either "ref" a directory containing an index, the name of another directory
|
||||
with a "ref" subdirectory containing an index or the name of a fasta formatted
|
||||
nucleotide file containg the reference to map to.
|
||||
Either "ref" a directory containing an index, the name of another directory
|
||||
with a "ref" subdirectory containing an index or the name of a fasta formatted
|
||||
nucleotide file containg the reference to map to.
|
||||
|
||||
output:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -11,7 +11,7 @@ tools:
|
|||
documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
|
||||
tool_dev_url: None
|
||||
doi: ""
|
||||
licence: ['UC-LBL license (see package)']
|
||||
licence: ["UC-LBL license (see package)"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
@ -20,14 +20,14 @@ input:
|
|||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- contaminants:
|
||||
type: file
|
||||
description: |
|
||||
Reference files containing adapter and/or contaminant sequences for sequence kmer matching
|
||||
type: file
|
||||
description: |
|
||||
Reference files containing adapter and/or contaminant sequences for sequence kmer matching
|
||||
|
||||
output:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -12,7 +12,7 @@ tools:
|
|||
documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
|
||||
tool_dev_url: None
|
||||
doi: ""
|
||||
licence: ['UC-LBL license (see package)']
|
||||
licence: ["UC-LBL license (see package)"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -11,7 +11,7 @@ tools:
|
|||
documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
|
||||
tool_dev_url: None
|
||||
doi: ""
|
||||
licence: ['UC-LBL license (see package)']
|
||||
licence: ["UC-LBL license (see package)"]
|
||||
|
||||
input:
|
||||
- fasta:
|
||||
|
|
|
|||
|
|
@ -1,43 +1,43 @@
|
|||
name: bcftools_concat
|
||||
description: Concatenate VCF files
|
||||
keywords:
|
||||
- variant calling
|
||||
- concat
|
||||
- bcftools
|
||||
- VCF
|
||||
- variant calling
|
||||
- concat
|
||||
- bcftools
|
||||
- VCF
|
||||
|
||||
tools:
|
||||
- concat:
|
||||
description: |
|
||||
Concatenate VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- concat:
|
||||
description: |
|
||||
Concatenate VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcfs:
|
||||
type: files
|
||||
description: |
|
||||
List containing 2 or more vcf files
|
||||
e.g. [ 'file1.vcf', 'file2.vcf' ]
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcfs:
|
||||
type: files
|
||||
description: |
|
||||
List containing 2 or more vcf files
|
||||
e.g. [ 'file1.vcf', 'file2.vcf' ]
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF concatenated output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF concatenated output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@abhi18av"
|
||||
|
|
|
|||
|
|
@ -1,49 +1,49 @@
|
|||
name: bcftools_consensus
|
||||
description: Compresses VCF files
|
||||
keywords:
|
||||
- variant calling
|
||||
- consensus
|
||||
- VCF
|
||||
- variant calling
|
||||
- consensus
|
||||
- VCF
|
||||
tools:
|
||||
- consensus:
|
||||
description: |
|
||||
Create consensus sequence by applying VCF variants to a reference fasta file.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- consensus:
|
||||
description: |
|
||||
Create consensus sequence by applying VCF variants to a reference fasta file.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF file
|
||||
pattern: "*.{vcf}"
|
||||
- tbi:
|
||||
type: file
|
||||
description: tabix index file
|
||||
pattern: "*.{tbi}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA reference file
|
||||
pattern: "*.{fasta,fa}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF file
|
||||
pattern: "*.{vcf}"
|
||||
- tbi:
|
||||
type: file
|
||||
description: tabix index file
|
||||
pattern: "*.{tbi}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA reference file
|
||||
pattern: "*.{fasta,fa}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA reference consensus file
|
||||
pattern: "*.{fasta,fa}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA reference consensus file
|
||||
pattern: "*.{fasta,fa}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -1,41 +1,41 @@
|
|||
name: bcftools_filter
|
||||
description: Filters VCF files
|
||||
keywords:
|
||||
- variant calling
|
||||
- filtering
|
||||
- VCF
|
||||
- variant calling
|
||||
- filtering
|
||||
- VCF
|
||||
tools:
|
||||
- filter:
|
||||
description: |
|
||||
Apply fixed-threshold filters to VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- filter:
|
||||
description: |
|
||||
Apply fixed-threshold filters to VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF input file
|
||||
pattern: "*.{vcf}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF input file
|
||||
pattern: "*.{vcf}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF filtered output file
|
||||
pattern: "*.{vcf}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF filtered output file
|
||||
pattern: "*.{vcf}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@ tools:
|
|||
documentation: https://samtools.github.io/bcftools/howtos/index.html
|
||||
tool_dev_url: https://github.com/samtools/bcftools
|
||||
doi: "10.1093/gigascience/giab008"
|
||||
licence: ['MIT', 'GPL-3.0-or-later']
|
||||
licence: ["MIT", "GPL-3.0-or-later"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -1,49 +1,49 @@
|
|||
name: bcftools_isec
|
||||
description: Apply set operations to VCF files
|
||||
keywords:
|
||||
- variant calling
|
||||
- intersect
|
||||
- union
|
||||
- complement
|
||||
- VCF
|
||||
- variant calling
|
||||
- intersect
|
||||
- union
|
||||
- complement
|
||||
- VCF
|
||||
tools:
|
||||
- isec:
|
||||
description: |
|
||||
Computes intersections, unions and complements of VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- isec:
|
||||
description: |
|
||||
Computes intersections, unions and complements of VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcfs:
|
||||
type: files
|
||||
description: |
|
||||
List containing 2 or more vcf files
|
||||
e.g. [ 'file1.vcf', 'file2.vcf' ]
|
||||
- tbis:
|
||||
type: files
|
||||
description: |
|
||||
List containing the tbi index files corresponding to the vcfs input files
|
||||
e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcfs:
|
||||
type: files
|
||||
description: |
|
||||
List containing 2 or more vcf files
|
||||
e.g. [ 'file1.vcf', 'file2.vcf' ]
|
||||
- tbis:
|
||||
type: files
|
||||
description: |
|
||||
List containing the tbi index files corresponding to the vcfs input files
|
||||
e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- results:
|
||||
type: directory
|
||||
description: Folder containing the set operations results perform on the vcf files
|
||||
pattern: "${prefix}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- results:
|
||||
type: directory
|
||||
description: Folder containing the set operations results perform on the vcf files
|
||||
pattern: "${prefix}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -1,47 +1,47 @@
|
|||
name: bcftools_merge
|
||||
description: Merge VCF files
|
||||
keywords:
|
||||
- variant calling
|
||||
- merge
|
||||
- VCF
|
||||
- variant calling
|
||||
- merge
|
||||
- VCF
|
||||
tools:
|
||||
- merge:
|
||||
description: |
|
||||
Merge VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- merge:
|
||||
description: |
|
||||
Merge VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcfs:
|
||||
type: files
|
||||
description: |
|
||||
List containing 2 or more vcf files
|
||||
e.g. [ 'file1.vcf', 'file2.vcf' ]
|
||||
- tbis:
|
||||
type: files
|
||||
description: |
|
||||
List containing the tbi index files corresponding to the vcfs input files
|
||||
e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcfs:
|
||||
type: files
|
||||
description: |
|
||||
List containing 2 or more vcf files
|
||||
e.g. [ 'file1.vcf', 'file2.vcf' ]
|
||||
- tbis:
|
||||
type: files
|
||||
description: |
|
||||
List containing the tbi index files corresponding to the vcfs input files
|
||||
e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF merged output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF merged output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -1,57 +1,57 @@
|
|||
name: bcftools_mpileup
|
||||
description: Compresses VCF files
|
||||
keywords:
|
||||
- variant calling
|
||||
- mpileup
|
||||
- VCF
|
||||
- variant calling
|
||||
- mpileup
|
||||
- VCF
|
||||
tools:
|
||||
- mpileup:
|
||||
description: |
|
||||
Generates genotype likelihoods at each genomic position with coverage.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- mpileup:
|
||||
description: |
|
||||
Generates genotype likelihoods at each genomic position with coverage.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Input BAM file
|
||||
pattern: "*.{bam}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA reference file
|
||||
pattern: "*.{fasta,fa}"
|
||||
- save_mpileup:
|
||||
type: boolean
|
||||
description: Save mpileup file generated by bcftools mpileup
|
||||
patter: "*.mpileup"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Input BAM file
|
||||
pattern: "*.{bam}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA reference file
|
||||
pattern: "*.{fasta,fa}"
|
||||
- save_mpileup:
|
||||
type: boolean
|
||||
description: Save mpileup file generated by bcftools mpileup
|
||||
patter: "*.mpileup"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF gzipped output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- tbi:
|
||||
type: file
|
||||
description: tabix index file
|
||||
pattern: "*.{tbi}"
|
||||
- stats:
|
||||
type: file
|
||||
description: Text output file containing stats
|
||||
pattern: "*{stats.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF gzipped output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- tbi:
|
||||
type: file
|
||||
description: tabix index file
|
||||
pattern: "*.{tbi}"
|
||||
- stats:
|
||||
type: file
|
||||
description: Text output file containing stats
|
||||
pattern: "*{stats.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -6,41 +6,41 @@ keywords:
|
|||
- variant calling
|
||||
- VCF
|
||||
tools:
|
||||
- norm:
|
||||
description: |
|
||||
Normalize VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- norm:
|
||||
description: |
|
||||
Normalize VCF files.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: |
|
||||
The vcf file to be normalized
|
||||
e.g. 'file1.vcf'
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA reference file
|
||||
pattern: "*.{fasta,fa}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: |
|
||||
The vcf file to be normalized
|
||||
e.g. 'file1.vcf'
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA reference file
|
||||
pattern: "*.{fasta,fa}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF normalized output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF normalized output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@abhi18av"
|
||||
- "@abhi18av"
|
||||
|
|
|
|||
|
|
@ -6,56 +6,56 @@ keywords:
|
|||
- bcftools
|
||||
- VCF
|
||||
tools:
|
||||
- query:
|
||||
description: |
|
||||
Extracts fields from VCF or BCF files and outputs them in user-defined format.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- query:
|
||||
description: |
|
||||
Extracts fields from VCF or BCF files and outputs them in user-defined format.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: |
|
||||
The vcf file to be qeuried.
|
||||
pattern: "*.{vcf.gz, vcf}"
|
||||
- tbi:
|
||||
type: file
|
||||
description: |
|
||||
The tab index for the VCF file to be inspected.
|
||||
pattern: "*.tbi"
|
||||
- regions:
|
||||
type: file
|
||||
description: |
|
||||
Optionally, restrict the operation to regions listed in this file.
|
||||
- targets:
|
||||
type: file
|
||||
description: |
|
||||
Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
|
||||
- samples:
|
||||
type: file
|
||||
description: |
|
||||
Optional, file of sample names to be included or excluded.
|
||||
e.g. 'file.tsv'
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: |
|
||||
The vcf file to be qeuried.
|
||||
pattern: "*.{vcf.gz, vcf}"
|
||||
- tbi:
|
||||
type: file
|
||||
description: |
|
||||
The tab index for the VCF file to be inspected.
|
||||
pattern: "*.tbi"
|
||||
- regions:
|
||||
type: file
|
||||
description: |
|
||||
Optionally, restrict the operation to regions listed in this file.
|
||||
- targets:
|
||||
type: file
|
||||
description: |
|
||||
Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
|
||||
- samples:
|
||||
type: file
|
||||
description: |
|
||||
Optional, file of sample names to be included or excluded.
|
||||
e.g. 'file.tsv'
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- txt:
|
||||
type: file
|
||||
description: BCFTools query output file
|
||||
pattern: "*.txt"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- txt:
|
||||
type: file
|
||||
description: BCFTools query output file
|
||||
pattern: "*.txt"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@abhi18av"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -11,7 +11,7 @@ tools:
|
|||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://samtools.github.io/bcftools/bcftools.html#reheader
|
||||
doi: 10.1093/gigascience/giab008
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -11,7 +11,7 @@ tools:
|
|||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
tool_dev_url: https://github.com/samtools/bcftools
|
||||
doi: "10.1093/bioinformatics/btp352"
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -1,42 +1,42 @@
|
|||
name: bcftools_stats
|
||||
description: Generates stats from VCF files
|
||||
keywords:
|
||||
- variant calling
|
||||
- stats
|
||||
- VCF
|
||||
- variant calling
|
||||
- stats
|
||||
- VCF
|
||||
tools:
|
||||
- stats:
|
||||
description: |
|
||||
Parses VCF or BCF and produces text file stats which is suitable for
|
||||
machine processing and can be plotted using plot-vcfstats.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- stats:
|
||||
description: |
|
||||
Parses VCF or BCF and produces text file stats which is suitable for
|
||||
machine processing and can be plotted using plot-vcfstats.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF input file
|
||||
pattern: "*.{vcf}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF input file
|
||||
pattern: "*.{vcf}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- stats:
|
||||
type: file
|
||||
description: Text output file containing stats
|
||||
pattern: "*_{stats.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- stats:
|
||||
type: file
|
||||
description: Text output file containing stats
|
||||
pattern: "*_{stats.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -1,63 +1,63 @@
|
|||
name: bcftools_view
|
||||
description: View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
|
||||
keywords:
|
||||
- variant calling
|
||||
- view
|
||||
- bcftools
|
||||
- VCF
|
||||
- variant calling
|
||||
- view
|
||||
- bcftools
|
||||
- VCF
|
||||
|
||||
tools:
|
||||
- view:
|
||||
description: |
|
||||
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
- view:
|
||||
description: |
|
||||
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: |
|
||||
The vcf file to be inspected.
|
||||
e.g. 'file.vcf'
|
||||
- index:
|
||||
type: file
|
||||
description: |
|
||||
The tab index for the VCF file to be inspected.
|
||||
e.g. 'file.tbi'
|
||||
- regions:
|
||||
type: file
|
||||
description: |
|
||||
Optionally, restrict the operation to regions listed in this file.
|
||||
e.g. 'file.vcf'
|
||||
- targets:
|
||||
type: file
|
||||
description: |
|
||||
Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
|
||||
e.g. 'file.vcf'
|
||||
- samples:
|
||||
type: file
|
||||
description: |
|
||||
Optional, file of sample names to be included or excluded.
|
||||
e.g. 'file.tsv'
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: |
|
||||
The vcf file to be inspected.
|
||||
e.g. 'file.vcf'
|
||||
- index:
|
||||
type: file
|
||||
description: |
|
||||
The tab index for the VCF file to be inspected.
|
||||
e.g. 'file.tbi'
|
||||
- regions:
|
||||
type: file
|
||||
description: |
|
||||
Optionally, restrict the operation to regions listed in this file.
|
||||
e.g. 'file.vcf'
|
||||
- targets:
|
||||
type: file
|
||||
description: |
|
||||
Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
|
||||
e.g. 'file.vcf'
|
||||
- samples:
|
||||
type: file
|
||||
description: |
|
||||
Optional, file of sample names to be included or excluded.
|
||||
e.g. 'file.tsv'
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF normalized output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF normalized output file
|
||||
pattern: "*.{vcf.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@abhi18av"
|
||||
- "@abhi18av"
|
||||
|
|
|
|||
|
|
@ -1,38 +1,38 @@
|
|||
name: bedtools_bamtobed
|
||||
description: Converts a bam file to a bed12 file.
|
||||
keywords:
|
||||
- bam
|
||||
- bed
|
||||
- bam
|
||||
- bed
|
||||
tools:
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
|
||||
licence: ['MIT']
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Input BAM file
|
||||
pattern: "*.{bam}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Input BAM file
|
||||
pattern: "*.{bam}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Bed file containing genomic intervals.
|
||||
pattern: "*.{bed}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Bed file containing genomic intervals.
|
||||
pattern: "*.{bed}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@yuukiiwa"
|
||||
- "@drpatelh"
|
||||
- "@yuukiiwa"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -1,43 +1,43 @@
|
|||
name: bedtools_complement
|
||||
description: Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.
|
||||
keywords:
|
||||
- bed
|
||||
- complement
|
||||
- bed
|
||||
- complement
|
||||
tools:
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
|
||||
licence: ['MIT']
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Input BED file
|
||||
pattern: "*.{bed}"
|
||||
- sizes:
|
||||
type: file
|
||||
description: File which defines the chromosome lengths for a given genome
|
||||
pattern: "*.{sizes}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Input BED file
|
||||
pattern: "*.{bed}"
|
||||
- sizes:
|
||||
type: file
|
||||
description: File which defines the chromosome lengths for a given genome
|
||||
pattern: "*.{sizes}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Bed file with all genomic intervals that are not covered by at least one record from the input file.
|
||||
pattern: "*.{bed}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Bed file with all genomic intervals that are not covered by at least one record from the input file.
|
||||
pattern: "*.{bed}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -1,51 +1,51 @@
|
|||
name: bedtools_genomecov
|
||||
description: Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome.
|
||||
keywords:
|
||||
- bed
|
||||
- bam
|
||||
- genomecov
|
||||
- bed
|
||||
- bam
|
||||
- genomecov
|
||||
tools:
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
|
||||
licence: ['MIT']
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- intervals:
|
||||
type: file
|
||||
description: BAM/BED/GFF/VCF
|
||||
pattern: "*.{bam|bed|gff|vcf}"
|
||||
- scale:
|
||||
type: value
|
||||
description: Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch
|
||||
- sizes:
|
||||
type: file
|
||||
description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column
|
||||
- extension:
|
||||
type: string
|
||||
description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- intervals:
|
||||
type: file
|
||||
description: BAM/BED/GFF/VCF
|
||||
pattern: "*.{bam|bed|gff|vcf}"
|
||||
- scale:
|
||||
type: value
|
||||
description: Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch
|
||||
- sizes:
|
||||
type: file
|
||||
description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column
|
||||
- extension:
|
||||
type: string
|
||||
description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- genomecov:
|
||||
type: file
|
||||
description: Computed genome coverage file
|
||||
pattern: "*.${extension}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- genomecov:
|
||||
type: file
|
||||
description: Computed genome coverage file
|
||||
pattern: "*.${extension}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
- "@sidorov-si"
|
||||
- "@chris-cheshire"
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
- "@sidorov-si"
|
||||
- "@chris-cheshire"
|
||||
|
|
|
|||
|
|
@ -1,34 +1,34 @@
|
|||
name: bedtools_getfasta
|
||||
description: extract sequences in a FASTA file based on intervals defined in a feature file.
|
||||
keywords:
|
||||
- bed
|
||||
- fasta
|
||||
- getfasta
|
||||
- bed
|
||||
- fasta
|
||||
- getfasta
|
||||
tools:
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
|
||||
licence: ['MIT']
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- bed:
|
||||
type: file
|
||||
description: Bed feature file
|
||||
pattern: "*.{bed}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input fasta file
|
||||
pattern: "*.{fa,fasta}"
|
||||
- bed:
|
||||
type: file
|
||||
description: Bed feature file
|
||||
pattern: "*.{bed}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input fasta file
|
||||
pattern: "*.{fa,fasta}"
|
||||
|
||||
output:
|
||||
- fasta:
|
||||
type: file
|
||||
description: Output fasta file with extracted sequences
|
||||
pattern: "*.{fa}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Output fasta file with extracted sequences
|
||||
pattern: "*.{fa}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -1,47 +1,47 @@
|
|||
name: bedtools_intersect
|
||||
description: Allows one to screen for overlaps between two sets of genomic features.
|
||||
keywords:
|
||||
- bed
|
||||
- intersect
|
||||
- bed
|
||||
- intersect
|
||||
tools:
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
|
||||
licence: ['MIT']
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- intervals1:
|
||||
type: file
|
||||
description: BAM/BED/GFF/VCF
|
||||
pattern: "*.{bam|bed|gff|vcf}"
|
||||
- intervals2:
|
||||
type: file
|
||||
description: BAM/BED/GFF/VCF
|
||||
pattern: "*.{bam|bed|gff|vcf}"
|
||||
- extension:
|
||||
type: value
|
||||
description: Extension of the output file. It is set by the user and corresponds to the file format which depends on arguments (e. g., ".bed", ".bam", ".txt", etc.).
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- intervals1:
|
||||
type: file
|
||||
description: BAM/BED/GFF/VCF
|
||||
pattern: "*.{bam|bed|gff|vcf}"
|
||||
- intervals2:
|
||||
type: file
|
||||
description: BAM/BED/GFF/VCF
|
||||
pattern: "*.{bam|bed|gff|vcf}"
|
||||
- extension:
|
||||
type: value
|
||||
description: Extension of the output file. It is set by the user and corresponds to the file format which depends on arguments (e. g., ".bed", ".bam", ".txt", etc.).
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- intersect:
|
||||
type: file
|
||||
description: File containing the description of overlaps found between the two features
|
||||
pattern: "*.${extension}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- intersect:
|
||||
type: file
|
||||
description: File containing the description of overlaps found between the two features
|
||||
pattern: "*.${extension}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
- "@sidorov-si"
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
- "@sidorov-si"
|
||||
|
|
|
|||
|
|
@ -11,7 +11,7 @@ tools:
|
|||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/makewindows.html
|
||||
tool_dev_url: None
|
||||
doi: "10.1093/bioinformatics/btq033"
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
|
|
|
|||
|
|
@ -1,44 +1,44 @@
|
|||
name: bedtools_maskfasta
|
||||
description: masks sequences in a FASTA file based on intervals defined in a feature file.
|
||||
keywords:
|
||||
- bed
|
||||
- fasta
|
||||
- maskfasta
|
||||
- bed
|
||||
- fasta
|
||||
- maskfasta
|
||||
tools:
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
|
||||
licence: ['MIT']
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Bed feature file
|
||||
pattern: "*.{bed}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input fasta file
|
||||
pattern: "*.{fa,fasta}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Bed feature file
|
||||
pattern: "*.{bed}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input fasta file
|
||||
pattern: "*.{fa,fasta}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: Output masked fasta file
|
||||
pattern: "*.{fa}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: Output masked fasta file
|
||||
pattern: "*.{fa}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -1,39 +1,39 @@
|
|||
name: bedtools_merge
|
||||
description: combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features.
|
||||
keywords:
|
||||
- bed
|
||||
- merge
|
||||
- bed
|
||||
- merge
|
||||
tools:
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html
|
||||
licence: ['MIT']
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Input BED file
|
||||
pattern: "*.{bed}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Input BED file
|
||||
pattern: "*.{bed}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Overlapped bed file with combined features
|
||||
pattern: "*.{bed}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Overlapped bed file with combined features
|
||||
pattern: "*.{bed}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -1,39 +1,39 @@
|
|||
name: bedtools_slop
|
||||
description: Adds a specified number of bases in each direction (unique values may be specified for either -l or -r)
|
||||
keywords:
|
||||
- bed
|
||||
- slopBed
|
||||
- bed
|
||||
- slopBed
|
||||
tools:
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html
|
||||
licence: ['MIT']
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Input BED file
|
||||
pattern: "*.{bed}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Input BED file
|
||||
pattern: "*.{bed}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Slopped BED file
|
||||
pattern: "*.{bed}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Slopped BED file
|
||||
pattern: "*.{bed}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -1,46 +1,46 @@
|
|||
name: bedtools_sort
|
||||
description: Sorts a feature file by chromosome and other criteria.
|
||||
keywords:
|
||||
- bed
|
||||
- sort
|
||||
- bed
|
||||
- sort
|
||||
tools:
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html
|
||||
licence: ['MIT']
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- intervals:
|
||||
type: file
|
||||
description: BED/BEDGRAPH
|
||||
pattern: "*.{bed|bedGraph}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- intervals:
|
||||
type: file
|
||||
description: BED/BEDGRAPH
|
||||
pattern: "*.{bed|bedGraph}"
|
||||
|
||||
- extension:
|
||||
type: string
|
||||
description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
|
||||
- extension:
|
||||
type: string
|
||||
description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
|
||||
- sorted:
|
||||
type: file
|
||||
description: Sorted output file
|
||||
pattern: "*.${extension}"
|
||||
- sorted:
|
||||
type: file
|
||||
description: Sorted output file
|
||||
pattern: "*.${extension}"
|
||||
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
- "@chris-cheshire"
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
- "@chris-cheshire"
|
||||
|
|
|
|||
|
|
@ -1,16 +1,16 @@
|
|||
name: bedtools_subtract
|
||||
description: Finds overlaps between two sets of regions (A and B), removes the overlaps from A and reports the remaining portion of A.
|
||||
keywords:
|
||||
- bed
|
||||
- gff
|
||||
- vcf
|
||||
- subtract
|
||||
- bed
|
||||
- gff
|
||||
- vcf
|
||||
- subtract
|
||||
tools:
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html
|
||||
licence: ['MIT']
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
38
modules/biobambam/bammarkduplicates2/main.nf
Normal file
38
modules/biobambam/bammarkduplicates2/main.nf
Normal file
|
|
@ -0,0 +1,38 @@
|
|||
process BIOBAMBAM_BAMMARKDUPLICATES2 {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::biobambam=2.0.182" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/biobambam:2.0.182--h7d875b9_0':
|
||||
'quay.io/biocontainers/biobambam:2.0.182--h7d875b9_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.bam") , emit: bam
|
||||
tuple val(meta), path("*.metrics.txt"), emit: metrics
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
bammarkduplicates2 \\
|
||||
$args \\
|
||||
I=$bam \\
|
||||
O=${prefix}.bam \\
|
||||
M=${prefix}.metrics.txt \\
|
||||
tmpfile=$prefix \\
|
||||
markthreads=$task.cpus
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
bammarkduplicates2: \$(echo \$(bammarkduplicates2 --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
44
modules/biobambam/bammarkduplicates2/meta.yml
Normal file
44
modules/biobambam/bammarkduplicates2/meta.yml
Normal file
|
|
@ -0,0 +1,44 @@
|
|||
name: biobambam_bammarkduplicates2
|
||||
description: Locate and tag duplicate reads in a BAM file
|
||||
keywords:
|
||||
- markduplicates
|
||||
- bam
|
||||
- cram
|
||||
tools:
|
||||
- biobambam:
|
||||
description: |
|
||||
biobambam is a set of tools for early stage alignment file processing.
|
||||
homepage: https://gitlab.com/german.tischler/biobambam2
|
||||
documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md
|
||||
doi: 10.1186/1751-0473-9-13
|
||||
licence: ["GPL v3"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: BAM/CRAM file
|
||||
pattern: "*.{bam,cram}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: BAM file with duplicate reads marked/removed
|
||||
pattern: "*.{bam}"
|
||||
- metrics:
|
||||
type: file
|
||||
description: Duplicate metrics file generated by biobambam
|
||||
pattern: "*.{metrics.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@muffato"
|
||||
|
|
@ -1,59 +1,59 @@
|
|||
name: bismark_align
|
||||
description: Performs alignment of BS-Seq reads using bismark
|
||||
keywords:
|
||||
- bismark
|
||||
- 3-letter genome
|
||||
- map
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- bam
|
||||
- bismark
|
||||
- 3-letter genome
|
||||
- map
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- bam
|
||||
tools:
|
||||
- bismark:
|
||||
description: |
|
||||
Bismark is a tool to map bisulfite treated sequencing reads
|
||||
and perform methylation calling in a quick and easy-to-use fashion.
|
||||
homepage: https://github.com/FelixKrueger/Bismark
|
||||
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
|
||||
doi: 10.1093/bioinformatics/btr167
|
||||
licence: ['GPL-3.0-or-later']
|
||||
- bismark:
|
||||
description: |
|
||||
Bismark is a tool to map bisulfite treated sequencing reads
|
||||
and perform methylation calling in a quick and easy-to-use fashion.
|
||||
homepage: https://github.com/FelixKrueger/Bismark
|
||||
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
|
||||
doi: 10.1093/bioinformatics/btr167
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- index:
|
||||
type: dir
|
||||
description: Bismark genome index directory
|
||||
pattern: "BismarkIndex"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- index:
|
||||
type: dir
|
||||
description: Bismark genome index directory
|
||||
pattern: "BismarkIndex"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- unmapped:
|
||||
type: file
|
||||
description: Output FastQ file(s) containing unmapped reads
|
||||
pattern: "*.{fq.gz}"
|
||||
- report:
|
||||
type: file
|
||||
description: Bismark alignment reports
|
||||
pattern: "*{report.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- unmapped:
|
||||
type: file
|
||||
description: Output FastQ file(s) containing unmapped reads
|
||||
pattern: "*.{fq.gz}"
|
||||
- report:
|
||||
type: file
|
||||
description: Bismark alignment reports
|
||||
pattern: "*{report.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@phue"
|
||||
- "@phue"
|
||||
|
|
|
|||
|
|
@ -1,52 +1,52 @@
|
|||
name: bismark_deduplicate
|
||||
description: |
|
||||
Removes alignments to the same position in the genome
|
||||
from the Bismark mapping output.
|
||||
Removes alignments to the same position in the genome
|
||||
from the Bismark mapping output.
|
||||
keywords:
|
||||
- bismark
|
||||
- 3-letter genome
|
||||
- map
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- bam
|
||||
- bismark
|
||||
- 3-letter genome
|
||||
- map
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- bam
|
||||
tools:
|
||||
- bismark:
|
||||
description: |
|
||||
Bismark is a tool to map bisulfite treated sequencing reads
|
||||
and perform methylation calling in a quick and easy-to-use fashion.
|
||||
homepage: https://github.com/FelixKrueger/Bismark
|
||||
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
|
||||
doi: 10.1093/bioinformatics/btr167
|
||||
licence: ['GPL-3.0-or-later']
|
||||
- bismark:
|
||||
description: |
|
||||
Bismark is a tool to map bisulfite treated sequencing reads
|
||||
and perform methylation calling in a quick and easy-to-use fashion.
|
||||
homepage: https://github.com/FelixKrueger/Bismark
|
||||
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
|
||||
doi: 10.1093/bioinformatics/btr167
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Deduplicated output BAM file containing read alignments
|
||||
pattern: "*.{deduplicated.bam}"
|
||||
- report:
|
||||
type: file
|
||||
description: Bismark deduplication reports
|
||||
pattern: "*.{deduplication_report.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Deduplicated output BAM file containing read alignments
|
||||
pattern: "*.{deduplicated.bam}"
|
||||
- report:
|
||||
type: file
|
||||
description: Bismark deduplication reports
|
||||
pattern: "*.{deduplication_report.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@phue"
|
||||
- "@phue"
|
||||
|
|
|
|||
|
|
@ -1,37 +1,37 @@
|
|||
name: bismark_genomepreparation
|
||||
description: |
|
||||
Converts a specified reference genome into two different bisulfite
|
||||
converted versions and indexes them for alignments.
|
||||
Converts a specified reference genome into two different bisulfite
|
||||
converted versions and indexes them for alignments.
|
||||
keywords:
|
||||
- bismark
|
||||
- 3-letter genome
|
||||
- index
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- fasta
|
||||
- bismark
|
||||
- 3-letter genome
|
||||
- index
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- fasta
|
||||
tools:
|
||||
- bismark:
|
||||
description: |
|
||||
Bismark is a tool to map bisulfite treated sequencing reads
|
||||
and perform methylation calling in a quick and easy-to-use fashion.
|
||||
homepage: https://github.com/FelixKrueger/Bismark
|
||||
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
|
||||
doi: 10.1093/bioinformatics/btr167
|
||||
licence: ['GPL-3.0-or-later']
|
||||
- bismark:
|
||||
description: |
|
||||
Bismark is a tool to map bisulfite treated sequencing reads
|
||||
and perform methylation calling in a quick and easy-to-use fashion.
|
||||
homepage: https://github.com/FelixKrueger/Bismark
|
||||
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
|
||||
doi: 10.1093/bioinformatics/btr167
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
input:
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
output:
|
||||
- index:
|
||||
type: dir
|
||||
description: Bismark genome index directory
|
||||
pattern: "BismarkIndex"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- index:
|
||||
type: dir
|
||||
description: Bismark genome index directory
|
||||
pattern: "BismarkIndex"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@phue"
|
||||
- "@phue"
|
||||
|
|
|
|||
|
|
@ -1,67 +1,67 @@
|
|||
name: bismark_methylationextractor
|
||||
description: Extracts methylation information for individual cytosines from alignments.
|
||||
keywords:
|
||||
- bismark
|
||||
- consensus
|
||||
- map
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- bam
|
||||
- bedGraph
|
||||
- bismark
|
||||
- consensus
|
||||
- map
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- bam
|
||||
- bedGraph
|
||||
tools:
|
||||
- bismark:
|
||||
description: |
|
||||
Bismark is a tool to map bisulfite treated sequencing reads
|
||||
and perform methylation calling in a quick and easy-to-use fashion.
|
||||
homepage: https://github.com/FelixKrueger/Bismark
|
||||
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
|
||||
doi: 10.1093/bioinformatics/btr167
|
||||
licence: ['GPL-3.0-or-later']
|
||||
- bismark:
|
||||
description: |
|
||||
Bismark is a tool to map bisulfite treated sequencing reads
|
||||
and perform methylation calling in a quick and easy-to-use fashion.
|
||||
homepage: https://github.com/FelixKrueger/Bismark
|
||||
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
|
||||
doi: 10.1093/bioinformatics/btr167
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- index:
|
||||
type: dir
|
||||
description: Bismark genome index directory
|
||||
pattern: "BismarkIndex"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- index:
|
||||
type: dir
|
||||
description: Bismark genome index directory
|
||||
pattern: "BismarkIndex"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bedgraph:
|
||||
type: file
|
||||
description: Bismark output file containing coverage and methylation metrics
|
||||
pattern: "*.{bedGraph.gz}"
|
||||
- methylation_calls:
|
||||
type: file
|
||||
description: Bismark output file containing strand-specific methylation calls
|
||||
pattern: "*.{txt.gz}"
|
||||
- coverage:
|
||||
type: file
|
||||
description: Bismark output file containing coverage metrics
|
||||
pattern: "*.{cov.gz}"
|
||||
- report:
|
||||
type: file
|
||||
description: Bismark splitting reports
|
||||
pattern: "*_{splitting_report.txt}"
|
||||
- mbias:
|
||||
type: file
|
||||
description: Text file containing methylation bias information
|
||||
pattern: "*.{M-bias.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bedgraph:
|
||||
type: file
|
||||
description: Bismark output file containing coverage and methylation metrics
|
||||
pattern: "*.{bedGraph.gz}"
|
||||
- methylation_calls:
|
||||
type: file
|
||||
description: Bismark output file containing strand-specific methylation calls
|
||||
pattern: "*.{txt.gz}"
|
||||
- coverage:
|
||||
type: file
|
||||
description: Bismark output file containing coverage metrics
|
||||
pattern: "*.{cov.gz}"
|
||||
- report:
|
||||
type: file
|
||||
description: Bismark splitting reports
|
||||
pattern: "*_{splitting_report.txt}"
|
||||
- mbias:
|
||||
type: file
|
||||
description: Text file containing methylation bias information
|
||||
pattern: "*.{M-bias.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@phue"
|
||||
- "@phue"
|
||||
|
|
|
|||
|
|
@ -1,60 +1,60 @@
|
|||
name: bismark_report
|
||||
description: Collects bismark alignment reports
|
||||
keywords:
|
||||
- bismark
|
||||
- qc
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- report
|
||||
- bismark
|
||||
- qc
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- report
|
||||
tools:
|
||||
- bismark:
|
||||
description: |
|
||||
Bismark is a tool to map bisulfite treated sequencing reads
|
||||
and perform methylation calling in a quick and easy-to-use fashion.
|
||||
homepage: https://github.com/FelixKrueger/Bismark
|
||||
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
|
||||
doi: 10.1093/bioinformatics/btr167
|
||||
licence: ['GPL-3.0-or-later']
|
||||
- bismark:
|
||||
description: |
|
||||
Bismark is a tool to map bisulfite treated sequencing reads
|
||||
and perform methylation calling in a quick and easy-to-use fashion.
|
||||
homepage: https://github.com/FelixKrueger/Bismark
|
||||
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
|
||||
doi: 10.1093/bioinformatics/btr167
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- align_report:
|
||||
type: file
|
||||
description: Bismark alignment reports
|
||||
pattern: "*{report.txt}"
|
||||
- splitting_report:
|
||||
type: file
|
||||
description: Bismark splitting reports
|
||||
pattern: "*{splitting_report.txt}"
|
||||
- dedup_report:
|
||||
type: file
|
||||
description: Bismark deduplication reports
|
||||
pattern: "*.{deduplication_report.txt}"
|
||||
- mbias:
|
||||
type: file
|
||||
description: Text file containing methylation bias information
|
||||
pattern: "*.{txt}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- align_report:
|
||||
type: file
|
||||
description: Bismark alignment reports
|
||||
pattern: "*{report.txt}"
|
||||
- splitting_report:
|
||||
type: file
|
||||
description: Bismark splitting reports
|
||||
pattern: "*{splitting_report.txt}"
|
||||
- dedup_report:
|
||||
type: file
|
||||
description: Bismark deduplication reports
|
||||
pattern: "*.{deduplication_report.txt}"
|
||||
- mbias:
|
||||
type: file
|
||||
description: Text file containing methylation bias information
|
||||
pattern: "*.{txt}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- report:
|
||||
type: file
|
||||
description: Bismark reports
|
||||
pattern: "*.{html,txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- report:
|
||||
type: file
|
||||
description: Bismark reports
|
||||
pattern: "*.{html,txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@phue"
|
||||
- "@phue"
|
||||
|
|
|
|||
|
|
@ -1,54 +1,54 @@
|
|||
name: bismark_summary
|
||||
description: |
|
||||
Uses Bismark report files of several samples in a run folder
|
||||
to generate a graphical summary HTML report.
|
||||
Uses Bismark report files of several samples in a run folder
|
||||
to generate a graphical summary HTML report.
|
||||
keywords:
|
||||
- bismark
|
||||
- qc
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- report
|
||||
- summary
|
||||
- bismark
|
||||
- qc
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- report
|
||||
- summary
|
||||
tools:
|
||||
- bismark:
|
||||
description: |
|
||||
Bismark is a tool to map bisulfite treated sequencing reads
|
||||
and perform methylation calling in a quick and easy-to-use fashion.
|
||||
homepage: https://github.com/FelixKrueger/Bismark
|
||||
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
|
||||
doi: 10.1093/bioinformatics/btr167
|
||||
licence: ['GPL-3.0-or-later']
|
||||
- bismark:
|
||||
description: |
|
||||
Bismark is a tool to map bisulfite treated sequencing reads
|
||||
and perform methylation calling in a quick and easy-to-use fashion.
|
||||
homepage: https://github.com/FelixKrueger/Bismark
|
||||
documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
|
||||
doi: 10.1093/bioinformatics/btr167
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
input:
|
||||
- bam:
|
||||
type: file
|
||||
description: Bismark alignment
|
||||
pattern: "*.{bam}"
|
||||
- align_report:
|
||||
type: file
|
||||
description: Bismark alignment reports
|
||||
pattern: "*{report.txt}"
|
||||
- dedup_report:
|
||||
type: file
|
||||
description: Bismark deduplication reports
|
||||
pattern: "*.{deduplication_report.txt}"
|
||||
- splitting_report:
|
||||
type: file
|
||||
description: Bismark splitting reports
|
||||
pattern: "*{splitting_report.txt}"
|
||||
- mbias:
|
||||
type: file
|
||||
description: Text file containing methylation bias information
|
||||
pattern: "*.{txt}"
|
||||
- bam:
|
||||
type: file
|
||||
description: Bismark alignment
|
||||
pattern: "*.{bam}"
|
||||
- align_report:
|
||||
type: file
|
||||
description: Bismark alignment reports
|
||||
pattern: "*{report.txt}"
|
||||
- dedup_report:
|
||||
type: file
|
||||
description: Bismark deduplication reports
|
||||
pattern: "*.{deduplication_report.txt}"
|
||||
- splitting_report:
|
||||
type: file
|
||||
description: Bismark splitting reports
|
||||
pattern: "*{splitting_report.txt}"
|
||||
- mbias:
|
||||
type: file
|
||||
description: Text file containing methylation bias information
|
||||
pattern: "*.{txt}"
|
||||
output:
|
||||
- summary:
|
||||
type: file
|
||||
description: Bismark summary
|
||||
pattern: "*.{html,txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- summary:
|
||||
type: file
|
||||
description: Bismark summary
|
||||
pattern: "*.{html,txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@phue"
|
||||
- "@phue"
|
||||
|
|
|
|||
|
|
@ -1,41 +1,41 @@
|
|||
name: blast_blastn
|
||||
description: Queries a BLAST DNA database
|
||||
keywords:
|
||||
- fasta
|
||||
- blast
|
||||
- blastn
|
||||
- DNA sequence
|
||||
- fasta
|
||||
- blast
|
||||
- blastn
|
||||
- DNA sequence
|
||||
tools:
|
||||
- blast:
|
||||
description: |
|
||||
BLAST finds regions of similarity between biological sequences.
|
||||
homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
|
||||
documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
|
||||
doi: 10.1016/S0022-2836(05)80360-2
|
||||
licence: ['US-Government-Work']
|
||||
- blast:
|
||||
description: |
|
||||
BLAST finds regions of similarity between biological sequences.
|
||||
homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
|
||||
documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
|
||||
doi: 10.1016/S0022-2836(05)80360-2
|
||||
licence: ["US-Government-Work"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input fasta file containing queries sequences
|
||||
pattern: "*.{fa,fasta}"
|
||||
- db:
|
||||
type: directory
|
||||
description: Directory containing blast database
|
||||
pattern: "*"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input fasta file containing queries sequences
|
||||
pattern: "*.{fa,fasta}"
|
||||
- db:
|
||||
type: directory
|
||||
description: Directory containing blast database
|
||||
pattern: "*"
|
||||
output:
|
||||
- txt:
|
||||
type: file
|
||||
description: File containing blastn hits
|
||||
pattern: "*.{blastn.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- txt:
|
||||
type: file
|
||||
description: File containing blastn hits
|
||||
pattern: "*.{blastn.txt}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -1,31 +1,31 @@
|
|||
name: blast_makeblastdb
|
||||
description: Builds a BLAST database
|
||||
keywords:
|
||||
- fasta
|
||||
- blast
|
||||
- database
|
||||
- fasta
|
||||
- blast
|
||||
- database
|
||||
tools:
|
||||
- blast:
|
||||
description: |
|
||||
BLAST finds regions of similarity between biological sequences.
|
||||
homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
|
||||
documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
|
||||
doi: 10.1016/S0022-2836(05)80360-2
|
||||
licence: ['US-Government-Work']
|
||||
- blast:
|
||||
description: |
|
||||
BLAST finds regions of similarity between biological sequences.
|
||||
homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
|
||||
documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
|
||||
doi: 10.1016/S0022-2836(05)80360-2
|
||||
licence: ["US-Government-Work"]
|
||||
input:
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input fasta file
|
||||
pattern: "*.{fa,fasta}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input fasta file
|
||||
pattern: "*.{fa,fasta}"
|
||||
output:
|
||||
- db:
|
||||
type: directory
|
||||
description: Output directory containing blast database files
|
||||
pattern: "*"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- db:
|
||||
type: directory
|
||||
description: Output directory containing blast database files
|
||||
pattern: "*"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -1,46 +1,46 @@
|
|||
name: bowtie_align
|
||||
description: Align reads to a reference genome using bowtie
|
||||
keywords:
|
||||
- align
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
- align
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
tools:
|
||||
- bowtie:
|
||||
description: |
|
||||
bowtie is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: http://bowtie-bio.sourceforge.net/index.shtml
|
||||
documentation: http://bowtie-bio.sourceforge.net/manual.shtml
|
||||
arxiv: arXiv:1303.3997
|
||||
licence: ['Artistic-2.0']
|
||||
- bowtie:
|
||||
description: |
|
||||
bowtie is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: http://bowtie-bio.sourceforge.net/index.shtml
|
||||
documentation: http://bowtie-bio.sourceforge.net/manual.shtml
|
||||
arxiv: arXiv:1303.3997
|
||||
licence: ["Artistic-2.0"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- index:
|
||||
type: file
|
||||
description: Bowtie genome index files
|
||||
pattern: "*.ebwt"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- index:
|
||||
type: file
|
||||
description: Bowtie genome index files
|
||||
pattern: "*.ebwt"
|
||||
output:
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- fastq:
|
||||
type: file
|
||||
description: Unaligned FastQ files
|
||||
pattern: "*.fastq.gz"
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- fastq:
|
||||
type: file
|
||||
description: Unaligned FastQ files
|
||||
pattern: "*.fastq.gz"
|
||||
authors:
|
||||
- "@kevinmenden"
|
||||
- "@kevinmenden"
|
||||
|
|
|
|||
|
|
@ -1,32 +1,32 @@
|
|||
name: bowtie_build
|
||||
description: Create bowtie index for reference genome
|
||||
keywords:
|
||||
- index
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
- index
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
tools:
|
||||
- bowtie:
|
||||
description: |
|
||||
bowtie is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: http://bowtie-bio.sourceforge.net/index.shtml
|
||||
documentation: http://bowtie-bio.sourceforge.net/manual.shtml
|
||||
arxiv: arXiv:1303.3997
|
||||
licence: ['Artistic-2.0']
|
||||
- bowtie:
|
||||
description: |
|
||||
bowtie is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: http://bowtie-bio.sourceforge.net/index.shtml
|
||||
documentation: http://bowtie-bio.sourceforge.net/manual.shtml
|
||||
arxiv: arXiv:1303.3997
|
||||
licence: ["Artistic-2.0"]
|
||||
input:
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
output:
|
||||
- index:
|
||||
type: file
|
||||
description: Bowtie genome index files
|
||||
pattern: "*.ebwt"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- index:
|
||||
type: file
|
||||
description: Bowtie genome index files
|
||||
pattern: "*.ebwt"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@kevinmenden"
|
||||
- "@drpatelh"
|
||||
- "@kevinmenden"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -1,51 +1,51 @@
|
|||
name: bowtie2_align
|
||||
description: Align reads to a reference genome using bowtie2
|
||||
keywords:
|
||||
- align
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
- align
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
tools:
|
||||
- bowtie2:
|
||||
description: |
|
||||
Bowtie 2 is an ultrafast and memory-efficient tool for aligning
|
||||
sequencing reads to long reference sequences.
|
||||
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
||||
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
|
||||
doi: 10.1038/nmeth.1923
|
||||
licence: ['GPL-3.0-or-later']
|
||||
- bowtie2:
|
||||
description: |
|
||||
Bowtie 2 is an ultrafast and memory-efficient tool for aligning
|
||||
sequencing reads to long reference sequences.
|
||||
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
||||
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
|
||||
doi: 10.1038/nmeth.1923
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- index:
|
||||
type: file
|
||||
description: Bowtie2 genome index files
|
||||
pattern: "*.ebwt"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- index:
|
||||
type: file
|
||||
description: Bowtie2 genome index files
|
||||
pattern: "*.ebwt"
|
||||
output:
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- fastq:
|
||||
type: file
|
||||
description: Unaligned FastQ files
|
||||
pattern: "*.fastq.gz"
|
||||
- log:
|
||||
type: file
|
||||
description: Aligment log
|
||||
pattern: "*.log"
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- fastq:
|
||||
type: file
|
||||
description: Unaligned FastQ files
|
||||
pattern: "*.fastq.gz"
|
||||
- log:
|
||||
type: file
|
||||
description: Aligment log
|
||||
pattern: "*.log"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -1,33 +1,33 @@
|
|||
name: bowtie2_build
|
||||
description: Builds bowtie index for reference genome
|
||||
keywords:
|
||||
- build
|
||||
- index
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
- build
|
||||
- index
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
tools:
|
||||
- bowtie2:
|
||||
description: |
|
||||
Bowtie 2 is an ultrafast and memory-efficient tool for aligning
|
||||
sequencing reads to long reference sequences.
|
||||
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
||||
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
|
||||
doi: 10.1038/nmeth.1923
|
||||
licence: ['GPL-3.0-or-later']
|
||||
- bowtie2:
|
||||
description: |
|
||||
Bowtie 2 is an ultrafast and memory-efficient tool for aligning
|
||||
sequencing reads to long reference sequences.
|
||||
homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
||||
documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
|
||||
doi: 10.1038/nmeth.1923
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
input:
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
output:
|
||||
- index:
|
||||
type: file
|
||||
description: Bowtie2 genome index files
|
||||
pattern: "*.bt2"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- index:
|
||||
type: file
|
||||
description: Bowtie2 genome index files
|
||||
pattern: "*.bt2"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -10,30 +10,30 @@ keywords:
|
|||
- map
|
||||
- fastq
|
||||
tools:
|
||||
- bwa:
|
||||
description: |
|
||||
BWA is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: http://bio-bwa.sourceforge.net/
|
||||
documentation: http://bio-bwa.sourceforge.net/
|
||||
doi: "10.1093/bioinformatics/btp324"
|
||||
licence: ['GPL-3.0-or-later']
|
||||
- bwa:
|
||||
description: |
|
||||
BWA is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: http://bio-bwa.sourceforge.net/
|
||||
documentation: http://bio-bwa.sourceforge.net/
|
||||
doi: "10.1093/bioinformatics/btp324"
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- index:
|
||||
type: file
|
||||
description: BWA genome index files
|
||||
pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- index:
|
||||
type: file
|
||||
description: BWA genome index files
|
||||
pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -1,32 +1,32 @@
|
|||
name: bwa_index
|
||||
description: Create BWA index for reference genome
|
||||
keywords:
|
||||
- index
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
- index
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
tools:
|
||||
- bwa:
|
||||
description: |
|
||||
BWA is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: http://bio-bwa.sourceforge.net/
|
||||
documentation: http://www.htslib.org/doc/samtools.html
|
||||
arxiv: arXiv:1303.3997
|
||||
licence: ['GPL-3.0-or-later']
|
||||
- bwa:
|
||||
description: |
|
||||
BWA is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: http://bio-bwa.sourceforge.net/
|
||||
documentation: http://www.htslib.org/doc/samtools.html
|
||||
arxiv: arXiv:1303.3997
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
input:
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
output:
|
||||
- index:
|
||||
type: file
|
||||
description: BWA genome index files
|
||||
pattern: "*.{amb,ann,bwt,pac,sa}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- index:
|
||||
type: file
|
||||
description: BWA genome index files
|
||||
pattern: "*.{amb,ann,bwt,pac,sa}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@drpatelh"
|
||||
- "@maxulysse"
|
||||
- "@drpatelh"
|
||||
- "@maxulysse"
|
||||
|
|
|
|||
|
|
@ -1,50 +1,50 @@
|
|||
name: bwa_mem
|
||||
description: Performs fastq alignment to a fasta reference using BWA
|
||||
keywords:
|
||||
- mem
|
||||
- bwa
|
||||
- alignment
|
||||
- map
|
||||
- fastq
|
||||
- bam
|
||||
- sam
|
||||
- mem
|
||||
- bwa
|
||||
- alignment
|
||||
- map
|
||||
- fastq
|
||||
- bam
|
||||
- sam
|
||||
tools:
|
||||
- bwa:
|
||||
description: |
|
||||
BWA is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: http://bio-bwa.sourceforge.net/
|
||||
documentation: http://www.htslib.org/doc/samtools.html
|
||||
arxiv: arXiv:1303.3997
|
||||
licence: ['GPL-3.0-or-later']
|
||||
- bwa:
|
||||
description: |
|
||||
BWA is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: http://bio-bwa.sourceforge.net/
|
||||
documentation: http://www.htslib.org/doc/samtools.html
|
||||
arxiv: arXiv:1303.3997
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- index:
|
||||
type: file
|
||||
description: BWA genome index files
|
||||
pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
|
||||
- sort_bam:
|
||||
type: boolean
|
||||
description: use samtools sort (true) or samtools view (false)
|
||||
pattern: "true or false"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- index:
|
||||
type: file
|
||||
description: BWA genome index files
|
||||
pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
|
||||
- sort_bam:
|
||||
type: boolean
|
||||
description: use samtools sort (true) or samtools view (false)
|
||||
pattern: "true or false"
|
||||
output:
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@drpatelh"
|
||||
- "@jeremy1805"
|
||||
- "@drpatelh"
|
||||
- "@jeremy1805"
|
||||
|
|
|
|||
|
|
@ -11,14 +11,14 @@ keywords:
|
|||
- sam
|
||||
- bam
|
||||
tools:
|
||||
- bwa:
|
||||
description: |
|
||||
BWA is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: http://bio-bwa.sourceforge.net/
|
||||
documentation: http://bio-bwa.sourceforge.net/
|
||||
doi: "10.1093/bioinformatics/btp324"
|
||||
licence: ['GPL-3.0-or-later']
|
||||
- bwa:
|
||||
description: |
|
||||
BWA is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: http://bio-bwa.sourceforge.net/
|
||||
documentation: http://bio-bwa.sourceforge.net/
|
||||
doi: "10.1093/bioinformatics/btp324"
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
@ -35,9 +35,9 @@ input:
|
|||
description: SAI file specified alongside meta and reads in input channel.
|
||||
pattern: "*.sai"
|
||||
- index:
|
||||
type: directory
|
||||
description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX
|
||||
pattern: "bwa/"
|
||||
type: directory
|
||||
description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX
|
||||
pattern: "bwa/"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -12,14 +12,14 @@ keywords:
|
|||
- bam
|
||||
|
||||
tools:
|
||||
- bwa:
|
||||
description: |
|
||||
BWA is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: http://bio-bwa.sourceforge.net/
|
||||
documentation: http://bio-bwa.sourceforge.net/
|
||||
doi: "10.1093/bioinformatics/btp324"
|
||||
licence: ['GPL-3.0-or-later']
|
||||
- bwa:
|
||||
description: |
|
||||
BWA is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: http://bio-bwa.sourceforge.net/
|
||||
documentation: http://bio-bwa.sourceforge.net/
|
||||
doi: "10.1093/bioinformatics/btp324"
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
@ -36,9 +36,9 @@ input:
|
|||
description: SAI file specified alongside meta and reads in input channel.
|
||||
pattern: "*.sai"
|
||||
- index:
|
||||
type: directory
|
||||
description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX
|
||||
pattern: "bwa/"
|
||||
type: directory
|
||||
description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX
|
||||
pattern: "bwa/"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -1,30 +1,30 @@
|
|||
name: bwamem2_index
|
||||
description: Create BWA-mem2 index for reference genome
|
||||
keywords:
|
||||
- index
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
- index
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
tools:
|
||||
- bwa:
|
||||
description: |
|
||||
BWA-mem2 is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: https://github.com/bwa-mem2/bwa-mem2
|
||||
documentation: https://github.com/bwa-mem2/bwa-mem2#usage
|
||||
licence: ['MIT']
|
||||
- bwa:
|
||||
description: |
|
||||
BWA-mem2 is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: https://github.com/bwa-mem2/bwa-mem2
|
||||
documentation: https://github.com/bwa-mem2/bwa-mem2#usage
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
output:
|
||||
- index:
|
||||
type: file
|
||||
description: BWA genome index files
|
||||
pattern: "*.{0132,amb,ann,bwt.2bit.64,pac}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- index:
|
||||
type: file
|
||||
description: BWA genome index files
|
||||
pattern: "*.{0132,amb,ann,bwt.2bit.64,pac}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@maxulysse"
|
||||
- "@maxulysse"
|
||||
|
|
|
|||
|
|
@ -1,49 +1,49 @@
|
|||
name: bwamem2_mem
|
||||
description: Performs fastq alignment to a fasta reference using BWA
|
||||
keywords:
|
||||
- mem
|
||||
- bwa
|
||||
- alignment
|
||||
- map
|
||||
- fastq
|
||||
- bam
|
||||
- sam
|
||||
- mem
|
||||
- bwa
|
||||
- alignment
|
||||
- map
|
||||
- fastq
|
||||
- bam
|
||||
- sam
|
||||
tools:
|
||||
- bwa:
|
||||
description: |
|
||||
BWA-mem2 is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: https://github.com/bwa-mem2/bwa-mem2
|
||||
documentation: http://www.htslib.org/doc/samtools.html
|
||||
arxiv: arXiv:1303.3997
|
||||
licence: ['MIT']
|
||||
- bwa:
|
||||
description: |
|
||||
BWA-mem2 is a software package for mapping DNA sequences against
|
||||
a large reference genome, such as the human genome.
|
||||
homepage: https://github.com/bwa-mem2/bwa-mem2
|
||||
documentation: http://www.htslib.org/doc/samtools.html
|
||||
arxiv: arXiv:1303.3997
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- index:
|
||||
type: file
|
||||
description: BWA genome index files
|
||||
pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}"
|
||||
- sort_bam:
|
||||
type: boolean
|
||||
description: use samtools sort (true) or samtools view (false)
|
||||
pattern: "true or false"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- index:
|
||||
type: file
|
||||
description: BWA genome index files
|
||||
pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}"
|
||||
- sort_bam:
|
||||
type: boolean
|
||||
description: use samtools sort (true) or samtools view (false)
|
||||
pattern: "true or false"
|
||||
output:
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@maxulysse"
|
||||
- "@maxulysse"
|
||||
|
|
|
|||
|
|
@ -1,52 +1,52 @@
|
|||
name: bwameth_align
|
||||
description: Performs alignment of BS-Seq reads using bwameth
|
||||
keywords:
|
||||
- bwameth
|
||||
- alignment
|
||||
- 3-letter genome
|
||||
- map
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- fastq
|
||||
- bam
|
||||
- bwameth
|
||||
- alignment
|
||||
- 3-letter genome
|
||||
- map
|
||||
- methylation
|
||||
- 5mC
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- fastq
|
||||
- bam
|
||||
tools:
|
||||
- bwameth:
|
||||
description: |
|
||||
Fast and accurate alignment of BS-Seq reads
|
||||
using bwa-mem and a 3-letter genome.
|
||||
homepage: https://github.com/brentp/bwa-meth
|
||||
documentation: https://github.com/brentp/bwa-meth
|
||||
arxiv: arXiv:1401.1129
|
||||
licence: ['MIT']
|
||||
- bwameth:
|
||||
description: |
|
||||
Fast and accurate alignment of BS-Seq reads
|
||||
using bwa-mem and a 3-letter genome.
|
||||
homepage: https://github.com/brentp/bwa-meth
|
||||
documentation: https://github.com/brentp/bwa-meth
|
||||
arxiv: arXiv:1401.1129
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- index:
|
||||
type: dir
|
||||
description: Directory containing bwameth genome index
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- index:
|
||||
type: dir
|
||||
description: Directory containing bwameth genome index
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Output BAM file containing read alignments
|
||||
pattern: "*.{bam}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@phue"
|
||||
- "@phue"
|
||||
|
|
|
|||
|
|
@ -1,33 +1,33 @@
|
|||
name: bwameth_index
|
||||
description: Performs indexing of c2t converted reference genome
|
||||
keywords:
|
||||
- bwameth
|
||||
- 3-letter genome
|
||||
- index
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- fasta
|
||||
- bwameth
|
||||
- 3-letter genome
|
||||
- index
|
||||
- methylseq
|
||||
- bisulphite
|
||||
- fasta
|
||||
tools:
|
||||
- bwameth:
|
||||
description: |
|
||||
Fast and accurate alignment of BS-Seq reads
|
||||
using bwa-mem and a 3-letter genome.
|
||||
homepage: https://github.com/brentp/bwa-meth
|
||||
documentation: https://github.com/brentp/bwa-meth
|
||||
arxiv: arXiv:1401.1129
|
||||
licence: ['MIT']
|
||||
- bwameth:
|
||||
description: |
|
||||
Fast and accurate alignment of BS-Seq reads
|
||||
using bwa-mem and a 3-letter genome.
|
||||
homepage: https://github.com/brentp/bwa-meth
|
||||
documentation: https://github.com/brentp/bwa-meth
|
||||
arxiv: arXiv:1401.1129
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
- fasta:
|
||||
type: file
|
||||
description: Input genome fasta file
|
||||
output:
|
||||
- index:
|
||||
type: dir
|
||||
description: Directory containing bwameth genome index
|
||||
pattern: "index"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- index:
|
||||
type: dir
|
||||
description: Directory containing bwameth genome index
|
||||
pattern: "index"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@phue"
|
||||
- "@phue"
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@ tools:
|
|||
homepage: None
|
||||
documentation: https://man7.org/linux/man-pages/man1/cat.1.html
|
||||
tool_dev_url: None
|
||||
licence: ['GPL-3.0-or-later']
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
input:
|
||||
- files_in:
|
||||
type: file
|
||||
|
|
|
|||
|
|
@ -1,39 +1,39 @@
|
|||
name: cat_fastq
|
||||
description: Concatenates fastq files
|
||||
keywords:
|
||||
- fastq
|
||||
- concatenate
|
||||
- fastq
|
||||
- concatenate
|
||||
tools:
|
||||
- cat:
|
||||
description: |
|
||||
The cat utility reads files sequentially, writing them to the standard output.
|
||||
documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html
|
||||
licence: ['GPL-3.0-or-later']
|
||||
- cat:
|
||||
description: |
|
||||
The cat utility reads files sequentially, writing them to the standard output.
|
||||
documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html
|
||||
licence: ["GPL-3.0-or-later"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: list
|
||||
description: |
|
||||
List of input FastQ files to be concatenated.
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: list
|
||||
description: |
|
||||
List of input FastQ files to be concatenated.
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: Merged fastq file
|
||||
pattern: "*.{merged.fastq.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: Merged fastq file
|
||||
pattern: "*.{merged.fastq.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
|
||||
authors:
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -1,40 +1,40 @@
|
|||
name: cellranger_count
|
||||
description: Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Gene Expression.
|
||||
keywords:
|
||||
- align
|
||||
- count
|
||||
- reference
|
||||
- align
|
||||
- count
|
||||
- reference
|
||||
tools:
|
||||
- cellranger:
|
||||
description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
|
||||
homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
|
||||
documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
doi: ""
|
||||
licence: 10x Genomics EULA
|
||||
- cellranger:
|
||||
description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
|
||||
homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
|
||||
documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
doi: ""
|
||||
licence: 10x Genomics EULA
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- reference:
|
||||
type: folder
|
||||
description: Folder containing all the reference indices needed by Cell Ranger
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
type: file
|
||||
description: |
|
||||
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
- reference:
|
||||
type: folder
|
||||
description: Folder containing all the reference indices needed by Cell Ranger
|
||||
output:
|
||||
- outs:
|
||||
type: file
|
||||
description: Files containing the outputs of Cell Ranger
|
||||
pattern: "sample-${meta.gem}/outs/*"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "versions.yml"
|
||||
- outs:
|
||||
type: file
|
||||
description: Files containing the outputs of Cell Ranger
|
||||
pattern: "sample-${meta.gem}/outs/*"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@ggabernet"
|
||||
- "@Emiller88"
|
||||
|
|
|
|||
|
|
@ -7,31 +7,31 @@ keywords:
|
|||
- illumina
|
||||
- bcl2fastq
|
||||
tools:
|
||||
- cellranger:
|
||||
description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
|
||||
homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
|
||||
documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
doi: ""
|
||||
licence: 10x Genomics EULA
|
||||
- cellranger:
|
||||
description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
|
||||
homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
|
||||
documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
doi: ""
|
||||
licence: 10x Genomics EULA
|
||||
input:
|
||||
- bcl:
|
||||
type: file
|
||||
description: Base call files
|
||||
pattern: "*.bcl.bgzf"
|
||||
- csv:
|
||||
type: file
|
||||
description: Sample sheet
|
||||
pattern: "*.csv"
|
||||
- bcl:
|
||||
type: file
|
||||
description: Base call files
|
||||
pattern: "*.bcl.bgzf"
|
||||
- csv:
|
||||
type: file
|
||||
description: Sample sheet
|
||||
pattern: "*.csv"
|
||||
output:
|
||||
- fastq:
|
||||
type: file
|
||||
description: Unaligned FastQ files
|
||||
pattern: "*.fastq.gz"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "versions.yml"
|
||||
- fastq:
|
||||
type: file
|
||||
description: Unaligned FastQ files
|
||||
pattern: "*.fastq.gz"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@ggabernet"
|
||||
- "@Emiller88"
|
||||
|
|
|
|||
|
|
@ -1,31 +1,31 @@
|
|||
name: cellranger_mkgtf
|
||||
description: Module to build a filtered gtf needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkgtf command.
|
||||
keywords:
|
||||
- reference
|
||||
- mkref
|
||||
- index
|
||||
- reference
|
||||
- mkref
|
||||
- index
|
||||
tools:
|
||||
- cellranger:
|
||||
description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
|
||||
homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
|
||||
documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
doi: ""
|
||||
licence: 10x Genomics EULA
|
||||
- cellranger:
|
||||
description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
|
||||
homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
|
||||
documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
doi: ""
|
||||
licence: 10x Genomics EULA
|
||||
input:
|
||||
- gtf:
|
||||
type: file
|
||||
description:
|
||||
pattern: "*.gtf"
|
||||
- gtf:
|
||||
type: file
|
||||
description:
|
||||
pattern: "*.gtf"
|
||||
output:
|
||||
- gtf:
|
||||
type: folder
|
||||
description: gtf transcriptome file
|
||||
pattern: "*.filtered.gtf"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "versions.yml"
|
||||
- gtf:
|
||||
type: folder
|
||||
description: gtf transcriptome file
|
||||
pattern: "*.filtered.gtf"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@ggabernet"
|
||||
- "@Emiller88"
|
||||
|
|
|
|||
|
|
@ -1,37 +1,37 @@
|
|||
name: cellranger_mkref
|
||||
description: Module to build the reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkref command.
|
||||
keywords:
|
||||
- reference
|
||||
- mkref
|
||||
- index
|
||||
- reference
|
||||
- mkref
|
||||
- index
|
||||
tools:
|
||||
- cellranger:
|
||||
description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
|
||||
homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
|
||||
documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
doi: ""
|
||||
licence: 10x Genomics EULA
|
||||
- cellranger:
|
||||
description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
|
||||
homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
|
||||
documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
|
||||
doi: ""
|
||||
licence: 10x Genomics EULA
|
||||
input:
|
||||
- fasta:
|
||||
type: file
|
||||
description: fasta genome file
|
||||
pattern: "*.{fasta,fa}"
|
||||
- gtf:
|
||||
type: file
|
||||
description: gtf transcriptome file
|
||||
pattern: "*.gtf"
|
||||
- reference_name:
|
||||
type: val
|
||||
description: name to give the reference folder
|
||||
pattern: str
|
||||
- fasta:
|
||||
type: file
|
||||
description: fasta genome file
|
||||
pattern: "*.{fasta,fa}"
|
||||
- gtf:
|
||||
type: file
|
||||
description: gtf transcriptome file
|
||||
pattern: "*.gtf"
|
||||
- reference_name:
|
||||
type: val
|
||||
description: name to give the reference folder
|
||||
pattern: str
|
||||
output:
|
||||
- reference:
|
||||
type: folder
|
||||
description: Folder containing all the reference indices needed by Cell Ranger
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "versions.yml"
|
||||
- reference:
|
||||
type: folder
|
||||
description: Folder containing all the reference indices needed by Cell Ranger
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@ggabernet"
|
||||
|
|
|
|||
|
|
@ -19,7 +19,7 @@ tools:
|
|||
documentation: https://github.com/Ecogenomics/CheckM/wiki
|
||||
tool_dev_url: https://github.com/Ecogenomics/CheckM
|
||||
doi: "10.1101/gr.186072.114"
|
||||
licence: ['GPL v3']
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -1,19 +1,19 @@
|
|||
name: chromap_chromap
|
||||
description: |
|
||||
Performs preprocessing and alignment of chromatin fastq files to
|
||||
fasta reference files using chromap.
|
||||
Performs preprocessing and alignment of chromatin fastq files to
|
||||
fasta reference files using chromap.
|
||||
keywords:
|
||||
- chromap
|
||||
- alignment
|
||||
- map
|
||||
- fastq
|
||||
- bam
|
||||
- sam
|
||||
- hi-c
|
||||
- atac-seq
|
||||
- chip-seq
|
||||
- trimming
|
||||
- duplicate removal
|
||||
- chromap
|
||||
- alignment
|
||||
- map
|
||||
- fastq
|
||||
- bam
|
||||
- sam
|
||||
- hi-c
|
||||
- atac-seq
|
||||
- chip-seq
|
||||
- trimming
|
||||
- duplicate removal
|
||||
tools:
|
||||
- chromap:
|
||||
description: Fast alignment and preprocessing of chromatin profiles
|
||||
|
|
@ -21,7 +21,7 @@ tools:
|
|||
documentation: https://github.com/haowenz/chromap
|
||||
tool_dev_url: https://github.com/haowenz/chromap
|
||||
doi: ""
|
||||
licence: ['GPL v3']
|
||||
licence: ["GPL v3"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
name: chromap_index
|
||||
description: Indexes a fasta reference genome ready for chromatin profiling.
|
||||
keywords:
|
||||
- index
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
- index
|
||||
- fasta
|
||||
- genome
|
||||
- reference
|
||||
tools:
|
||||
- chromap:
|
||||
description: Fast alignment and preprocessing of chromatin profiles
|
||||
|
|
@ -12,7 +12,7 @@ tools:
|
|||
documentation: https://github.com/haowenz/chromap
|
||||
tool_dev_url: https://github.com/haowenz/chromap
|
||||
doi: ""
|
||||
licence: ['GPL v3']
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- fasta:
|
||||
|
|
|
|||
|
|
@ -11,7 +11,7 @@ tools:
|
|||
documentation: https://github.com/xavierdidelot/clonalframeml/wiki
|
||||
tool_dev_url: https://github.com/xavierdidelot/ClonalFrameML
|
||||
doi: "10.1371/journal.pcbi.1004041"
|
||||
licence: ['GPL v3']
|
||||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -17,7 +17,7 @@ tools:
|
|||
homepage: https://github.com/SegataLab/cmseq
|
||||
documentation: https://github.com/SegataLab/cmseq
|
||||
tool_dev_url: https://github.com/SegataLab/cmseq
|
||||
licence: ['MIT License']
|
||||
licence: ["MIT License"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@ tools:
|
|||
CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.
|
||||
homepage: https://cnvkit.readthedocs.io/en/stable/index.html
|
||||
documentation: https://cnvkit.readthedocs.io/en/stable/index.html
|
||||
licence: ['Apache-2.0']
|
||||
licence: ["Apache-2.0"]
|
||||
params:
|
||||
- outdir:
|
||||
type: string
|
||||
|
|
@ -85,9 +85,9 @@ output:
|
|||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@kaurravneet4123"
|
||||
- "@KevinMenden"
|
||||
- "@MaxUlysse"
|
||||
- "@drpatelh"
|
||||
- "@fbdtemme"
|
||||
- "@lassefolkersen"
|
||||
- "@kaurravneet4123"
|
||||
- "@KevinMenden"
|
||||
- "@MaxUlysse"
|
||||
- "@drpatelh"
|
||||
- "@fbdtemme"
|
||||
- "@lassefolkersen"
|
||||
|
|
|
|||
|
|
@ -9,7 +9,7 @@ tools:
|
|||
documentation: https://cooler.readthedocs.io/en/latest/index.html
|
||||
tool_dev_url: https://github.com/open2c/cooler
|
||||
doi: "10.1093/bioinformatics/btz540"
|
||||
licence: ['BSD-3-clause']
|
||||
licence: ["BSD-3-clause"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@ tools:
|
|||
documentation: https://cooler.readthedocs.io/en/latest/index.html
|
||||
tool_dev_url: https://github.com/open2c/cooler
|
||||
doi: "10.1093/bioinformatics/btz540"
|
||||
licence: ['BSD-3-Clause']
|
||||
licence: ["BSD-3-Clause"]
|
||||
|
||||
input:
|
||||
- fasta:
|
||||
|
|
|
|||
|
|
@ -9,7 +9,7 @@ tools:
|
|||
documentation: https://cooler.readthedocs.io/en/latest/index.html
|
||||
tool_dev_url: https://github.com/open2c/cooler
|
||||
doi: "10.1093/bioinformatics/btz540"
|
||||
licence: ['BSD-3-Clause']
|
||||
licence: ["BSD-3-Clause"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -9,7 +9,7 @@ tools:
|
|||
documentation: https://cooler.readthedocs.io/en/latest/index.html
|
||||
tool_dev_url: https://github.com/open2c/cooler
|
||||
doi: "10.1093/bioinformatics/btz540"
|
||||
licence: ['BSD-3-clause']
|
||||
licence: ["BSD-3-clause"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -9,7 +9,7 @@ tools:
|
|||
documentation: https://cooler.readthedocs.io/en/latest/index.html
|
||||
tool_dev_url: https://github.com/open2c/cooler
|
||||
doi: "10.1093/bioinformatics/btz540"
|
||||
licence: ['BSD-3-clause']
|
||||
licence: ["BSD-3-clause"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -11,7 +11,7 @@ tools:
|
|||
documentation: http://bioinf.shenwei.me/csvtk
|
||||
tool_dev_url: https://github.com/shenwei356/csvtk
|
||||
doi: ""
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
|
|||
|
|
@ -7,13 +7,13 @@ keywords:
|
|||
tools:
|
||||
- csvtk:
|
||||
description:
|
||||
CSVTK is a cross-platform, efficient and practical CSV/TSV toolkit
|
||||
that allows rapid data investigation and manipulation.
|
||||
CSVTK is a cross-platform, efficient and practical CSV/TSV toolkit
|
||||
that allows rapid data investigation and manipulation.
|
||||
homepage: https://bioinf.shenwei.me/csvtk/
|
||||
documentation: https://bioinf.shenwei.me/csvtk/
|
||||
tool_dev_url: https://github.com/shenwei356/csvtk
|
||||
doi: ""
|
||||
licence: ['MIT']
|
||||
licence: ["MIT"]
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
|
|
|
|||
Some files were not shown because too many files have changed in this diff Show more
Loading…
Reference in a new issue