mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
Merge branch 'master' into haplocheck
This commit is contained in:
commit
a2e2d50494
207 changed files with 4361 additions and 586 deletions
68
modules/antismash/antismashlite/main.nf
Normal file
68
modules/antismash/antismashlite/main.nf
Normal file
|
@ -0,0 +1,68 @@
|
|||
process ANTISMASH_ANTISMASHLITE {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' :
|
||||
'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }"
|
||||
|
||||
containerOptions {
|
||||
workflow.containerEngine == 'singularity' ?
|
||||
"-B $antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" :
|
||||
workflow.containerEngine == 'docker' ?
|
||||
"-v \$PWD/$antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" :
|
||||
''
|
||||
}
|
||||
|
||||
input:
|
||||
tuple val(meta), path(sequence_input)
|
||||
path(databases)
|
||||
path(antismash_dir) // Optional input: AntiSMASH installation folder. It is not needed for using this module with conda, but required for docker/singularity (see meta.yml).
|
||||
path(gff)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("${prefix}/clusterblast/*_c*.txt") , optional: true, emit: clusterblast_file
|
||||
tuple val(meta), path("${prefix}/{css,images,js}") , emit: html_accessory_files
|
||||
tuple val(meta), path("${prefix}/knownclusterblast/region*/ctg*.html") , optional: true, emit: knownclusterblast_html
|
||||
tuple val(meta), path("${prefix}/knownclusterblast/*_c*.txt") , optional: true, emit: knownclusterblast_txt
|
||||
tuple val(meta), path("${prefix}/svg/clusterblast*.svg") , optional: true, emit: svg_files_clusterblast
|
||||
tuple val(meta), path("${prefix}/svg/knownclusterblast*.svg") , optional: true, emit: svg_files_knownclusterblast
|
||||
tuple val(meta), path("${prefix}/*.gbk") , emit: gbk_input
|
||||
tuple val(meta), path("${prefix}/*.json") , emit: json_results
|
||||
tuple val(meta), path("${prefix}/*.log") , emit: log
|
||||
tuple val(meta), path("${prefix}/*.zip") , emit: zip
|
||||
tuple val(meta), path("${prefix}/*region*.gbk") , emit: gbk_results
|
||||
tuple val(meta), path("${prefix}/clusterblastoutput.txt") , optional: true, emit: clusterblastoutput
|
||||
tuple val(meta), path("${prefix}/index.html") , emit: html
|
||||
tuple val(meta), path("${prefix}/knownclusterblastoutput.txt") , optional: true, emit: knownclusterblastoutput
|
||||
tuple val(meta), path("${prefix}/regions.js") , emit: json_sideloading
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
|
||||
gff_flag = "--genefinding-gff3 ${gff}"
|
||||
|
||||
"""
|
||||
## We specifically do not include annotations (--genefinding-tool none) as
|
||||
## this should be run as a separate module for versioning purposes
|
||||
antismash \\
|
||||
$args \\
|
||||
$gff_flag \\
|
||||
-c $task.cpus \\
|
||||
--output-dir $prefix \\
|
||||
--genefinding-tool none \\
|
||||
--logfile $prefix/${prefix}.log \\
|
||||
--databases $databases \\
|
||||
$sequence_input
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
antismash-lite: \$(antismash --version | sed 's/antiSMASH //')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
128
modules/antismash/antismashlite/meta.yml
Normal file
128
modules/antismash/antismashlite/meta.yml
Normal file
|
@ -0,0 +1,128 @@
|
|||
name: antismash_antismashlite
|
||||
description: |
|
||||
antiSMASH allows the rapid genome-wide identification, annotation
|
||||
and analysis of secondary metabolite biosynthesis gene clusters.
|
||||
keywords:
|
||||
- secondary metabolites
|
||||
- BGC
|
||||
- biosynthetic gene cluster
|
||||
- genome mining
|
||||
- NRPS
|
||||
- RiPP
|
||||
- antibiotics
|
||||
- prokaryotes
|
||||
- bacteria
|
||||
- eukaryotes
|
||||
- fungi
|
||||
- antismash
|
||||
|
||||
tools:
|
||||
- antismashlite:
|
||||
description: "antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell"
|
||||
homepage: "https://docs.antismash.secondarymetabolites.org"
|
||||
documentation: "https://docs.antismash.secondarymetabolites.org"
|
||||
tool_dev_url: "https://github.com/antismash/antismash"
|
||||
doi: "10.1093/nar/gkab335"
|
||||
licence: "['AGPL v3']"
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- sequence_input:
|
||||
type: file
|
||||
description: nucleotide sequence file (annotated)
|
||||
pattern: "*.{gbk, gb, gbff, genbank, embl, fasta, fna}"
|
||||
- databases:
|
||||
type: directory
|
||||
description: downloaded AntiSMASH databases e.g. data/databases
|
||||
pattern: "*/"
|
||||
- antismash_dir:
|
||||
type: directory
|
||||
description: |
|
||||
A local copy of an AntiSMASH installation folder. This is required when running with
|
||||
docker and singularity (not required for conda), due to attempted 'modifications' of
|
||||
files during database checks in the installation directory, something that cannot
|
||||
be done in immutable docker/singularity containers. Therefore, a local installation
|
||||
directory needs to be mounted (including all modified files from the downloading step)
|
||||
to the container as a workaround.
|
||||
pattern: "*/"
|
||||
- gff:
|
||||
type: file
|
||||
pattern: "*.gff"
|
||||
|
||||
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"
|
||||
- clusterblast_file:
|
||||
type: file
|
||||
description: Output of ClusterBlast algorithm
|
||||
pattern: "clusterblast/*_c*.txt"
|
||||
- html_accessory_files:
|
||||
type: directory
|
||||
description: Accessory files for the HTML output
|
||||
pattern: "{css/,images/,js/}"
|
||||
- knownclusterblast_html:
|
||||
type: file
|
||||
description: Tables with MIBiG hits in HTML format
|
||||
pattern: "knownclusterblast/region*/ctg*.html"
|
||||
- knownclusterblast_txt:
|
||||
type: file
|
||||
description: Tables with MIBiG hits
|
||||
pattern: "knownclusterblast/*_c*.txt"
|
||||
- svg_files_clusterblast:
|
||||
type: file
|
||||
description: SVG images showing the % identity of the aligned hits against their queries
|
||||
pattern: "svg/clusterblast*.svg"
|
||||
- svg_files_knownclusterblast:
|
||||
type: file
|
||||
description: SVG images showing the % identity of the aligned hits against their queries
|
||||
pattern: "svg/knownclusterblast*.svg"
|
||||
- gbk_input:
|
||||
type: file
|
||||
description: Nucleotide sequence and annotations in GenBank format; converted from input file
|
||||
pattern: "*.gbk"
|
||||
- json_results:
|
||||
type: file
|
||||
description: Nucleotide sequence and annotations in JSON format; converted from GenBank file (gbk_input)
|
||||
pattern: "*.json"
|
||||
- log:
|
||||
type: file
|
||||
description: Contains all the logging output that antiSMASH produced during its run
|
||||
pattern: "*.log"
|
||||
- zip:
|
||||
type: file
|
||||
description: Contains a compressed version of the output folder in zip format
|
||||
pattern: "*.zip"
|
||||
- gbk_results:
|
||||
type: file
|
||||
description: Nucleotide sequence and annotations in GenBank format; one file per antiSMASH hit
|
||||
pattern: "*region*.gbk"
|
||||
- clusterblastoutput:
|
||||
type: file
|
||||
description: Raw BLAST output of known clusters previously predicted by antiSMASH using the built-in ClusterBlast algorithm
|
||||
pattern: "clusterblastoutput.txt"
|
||||
- html:
|
||||
type: file
|
||||
description: Graphical web view of results in HTML format
|
||||
patterN: "index.html"
|
||||
- knownclusterblastoutput:
|
||||
type: file
|
||||
description: Raw BLAST output of known clusters of the MIBiG database
|
||||
pattern: "knownclusterblastoutput.txt"
|
||||
- json_sideloading:
|
||||
type: file
|
||||
description: Sideloaded annotations of protoclusters and/or subregions (see antiSMASH documentation "Annotation sideloading")
|
||||
pattern: "regions.js"
|
||||
|
||||
authors:
|
||||
- "@jasmezz"
|
|
@ -42,7 +42,6 @@ output:
|
|||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
## TODO nf-core: Delete / customise this example output
|
||||
- out:
|
||||
type: file
|
||||
description: The data in the asked format (bed, fasta, fastq, json, pileup, sam, yaml)
|
||||
|
|
|
@ -8,7 +8,7 @@ process BCFTOOLS_CONCAT {
|
|||
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcfs)
|
||||
tuple val(meta), path(vcfs), path(tbi)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.gz"), emit: vcf
|
||||
|
|
|
@ -25,6 +25,11 @@ input:
|
|||
description: |
|
||||
List containing 2 or more vcf files
|
||||
e.g. [ 'file1.vcf', 'file2.vcf' ]
|
||||
- tbi:
|
||||
type: files
|
||||
description: |
|
||||
List containing 2 or more index files (optional)
|
||||
e.g. [ 'file1.tbi', 'file2.tbi' ]
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
|
|
61
modules/bcftools/roh/main.nf
Normal file
61
modules/bcftools/roh/main.nf
Normal file
|
@ -0,0 +1,61 @@
|
|||
process BCFTOOLS_ROH {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0':
|
||||
'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(tbi)
|
||||
path af_file
|
||||
path genetic_map
|
||||
path regions_file
|
||||
path samples_file
|
||||
path targets_file
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.roh"), emit: roh
|
||||
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}"
|
||||
def af_read = af_file ? "--AF-file ${af_file}" : ''
|
||||
def gen_map = genetic_map ? "--genetic-map ${genetic_map}" : ''
|
||||
def reg_file = regions_file ? "--regions-file ${regions_file}" : ''
|
||||
def samp_file = samples_file ? "--samples-file ${samples_file}" : ''
|
||||
def targ_file = targets_file ? "--targets-file ${targets_file}" : ''
|
||||
"""
|
||||
bcftools \\
|
||||
roh \\
|
||||
$args \\
|
||||
$af_read \\
|
||||
$gen_map \\
|
||||
$reg_file \\
|
||||
$samp_file \\
|
||||
$targ_file \\
|
||||
-o ${prefix}.roh \\
|
||||
$vcf
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
|
||||
stub:
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
touch ${prefix}.roh
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
55
modules/bcftools/roh/meta.yml
Normal file
55
modules/bcftools/roh/meta.yml
Normal file
|
@ -0,0 +1,55 @@
|
|||
name: "bcftools_roh"
|
||||
description: A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered.
|
||||
keywords:
|
||||
- roh
|
||||
tools:
|
||||
- "roh":
|
||||
description: "A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered."
|
||||
homepage: https://www.htslib.org/
|
||||
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,.vcf.gz}"
|
||||
- af_file:
|
||||
type: file
|
||||
description: "Read allele frequencies from a tab-delimited file containing the columns: CHROM\tPOS\tREF,ALT\tAF."
|
||||
- genetic_map:
|
||||
type: file
|
||||
description: "Genetic map in the format required also by IMPUTE2."
|
||||
- regions_file:
|
||||
type: file
|
||||
description: "Regions can be specified either on command line or in a VCF, BED, or tab-delimited file (the default)."
|
||||
- samples_file:
|
||||
type: file
|
||||
description: "File of sample names to include or exclude if prefixed with '^'."
|
||||
- targets_file:
|
||||
type: file
|
||||
description: "Targets can be specified either on command line or in a VCF, BED, or tab-delimited file (the default)."
|
||||
|
||||
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"
|
||||
- roh:
|
||||
type: file
|
||||
description: Contains site-specific and/or per-region runs of homo/autozygosity calls.
|
||||
pattern: "*.{roh}"
|
||||
|
||||
authors:
|
||||
- "@ramprasadn"
|
38
modules/bedtools/split/main.nf
Normal file
38
modules/bedtools/split/main.nf
Normal file
|
@ -0,0 +1,38 @@
|
|||
process BEDTOOLS_SPLIT {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h468198e_3':
|
||||
'quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_2' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bed)
|
||||
val(number_of_files)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.bed"), emit: beds
|
||||
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}"
|
||||
|
||||
"""
|
||||
bedtools \\
|
||||
split \\
|
||||
$args \\
|
||||
-i $bed \\
|
||||
-p $prefix \\
|
||||
-n $number_of_files
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
41
modules/bedtools/split/meta.yml
Normal file
41
modules/bedtools/split/meta.yml
Normal file
|
@ -0,0 +1,41 @@
|
|||
name: "bedtools_split"
|
||||
description: Split BED files into several smaller BED files
|
||||
keywords:
|
||||
- sort
|
||||
tools:
|
||||
- "bedtools":
|
||||
description: "A powerful toolset for genome arithmetic"
|
||||
documentation: "https://bedtools.readthedocs.io/en/latest/content/tools/sort.html"
|
||||
licence: "['MIT', 'GPL v2']"
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: BED file
|
||||
pattern: "*.bed"
|
||||
- bed:
|
||||
type: value
|
||||
description: The number of files to split the BED into
|
||||
|
||||
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"
|
||||
- beds:
|
||||
type: file
|
||||
description: list of split BED files
|
||||
pattern: "*.bed"
|
||||
|
||||
authors:
|
||||
- "@nvnieuwk"
|
38
modules/biobambam/bammerge/main.nf
Normal file
38
modules/biobambam/bammerge/main.nf
Normal file
|
@ -0,0 +1,38 @@
|
|||
process BIOBAMBAM_BAMMERGE {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1':
|
||||
'quay.io/biocontainers/biobambam:2.0.183--h9f5acd7_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("${prefix}.bam") ,emit: bam
|
||||
tuple val(meta), path("*.bai") ,optional:true, emit: bam_index
|
||||
tuple val(meta), path("*.md5") ,optional:true, emit: checksum
|
||||
path "versions.yml" ,emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def input_string = bam.join(" I=")
|
||||
|
||||
"""
|
||||
bammerge \\
|
||||
I=${input_string} \\
|
||||
$args \\
|
||||
> ${prefix}.bam
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
bammerge: \$( bammerge --version |& sed '1!d; s/.*version //; s/.\$//' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
46
modules/biobambam/bammerge/meta.yml
Normal file
46
modules/biobambam/bammerge/meta.yml
Normal file
|
@ -0,0 +1,46 @@
|
|||
name: biobambam_bammerge
|
||||
description: Merge a list of sorted bam files
|
||||
keywords:
|
||||
- merge
|
||||
- bam
|
||||
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: List containing 1 or more bam files
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: Merged BAM file
|
||||
pattern: "*.bam"
|
||||
- bam_index:
|
||||
type: file
|
||||
description: BAM index file
|
||||
pattern: "*"
|
||||
- checksum:
|
||||
type: file
|
||||
description: Checksum file
|
||||
pattern: "*"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
authors:
|
||||
- "@matthdsm"
|
|
@ -11,6 +11,7 @@ process BOWTIE2_ALIGN {
|
|||
tuple val(meta), path(reads)
|
||||
path index
|
||||
val save_unaligned
|
||||
val sort_bam
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.bam") , emit: bam
|
||||
|
@ -36,8 +37,7 @@ process BOWTIE2_ALIGN {
|
|||
reads_args = "-1 ${reads[0]} -2 ${reads[1]}"
|
||||
}
|
||||
|
||||
def samtools_command = "samtools view -@ $task.cpus --bam --with-header ${args2} > ${prefix}.bam"
|
||||
|
||||
def samtools_command = sort_bam ? 'sort' : 'view'
|
||||
|
||||
"""
|
||||
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/.rev.1.bt2//"`
|
||||
|
@ -51,7 +51,7 @@ process BOWTIE2_ALIGN {
|
|||
$unaligned \\
|
||||
$args \\
|
||||
2> ${prefix}.bowtie2.log \\
|
||||
| $samtools_command
|
||||
| samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -
|
||||
|
||||
if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
|
||||
mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
|
||||
|
|
|
@ -29,6 +29,15 @@ input:
|
|||
type: file
|
||||
description: Bowtie2 genome index files
|
||||
pattern: "*.ebwt"
|
||||
- save_unaligned:
|
||||
type: boolean
|
||||
description: |
|
||||
Save reads that do not map to the reference (true) or discard them (false)
|
||||
(default: false)
|
||||
- sort_bam:
|
||||
type: boolean
|
||||
description: use samtools sort (true) or samtools view (false)
|
||||
pattern: "true or false"
|
||||
output:
|
||||
- bam:
|
||||
type: file
|
||||
|
|
36
modules/cnvkit/antitarget/main.nf
Normal file
36
modules/cnvkit/antitarget/main.nf
Normal file
|
@ -0,0 +1,36 @@
|
|||
process CNVKIT_ANTITARGET {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0':
|
||||
'quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(targets)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.bed"), emit: bed
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
||||
"""
|
||||
cnvkit.py \\
|
||||
antitarget \\
|
||||
$targets \\
|
||||
--output ${prefix}.antitarget.bed \\
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
44
modules/cnvkit/antitarget/meta.yml
Normal file
44
modules/cnvkit/antitarget/meta.yml
Normal file
|
@ -0,0 +1,44 @@
|
|||
name: cnvkit_antitarget
|
||||
description:
|
||||
keywords:
|
||||
- cvnkit
|
||||
- antitarget
|
||||
tools:
|
||||
- cnvkit:
|
||||
description: |
|
||||
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
|
||||
tool_dev_url: "https://github.com/etal/cnvkit"
|
||||
doi: 10.1371/journal.pcbi.1004873
|
||||
licence: ["Apache-2.0"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- targets:
|
||||
type: file
|
||||
description: File containing genomic regions
|
||||
pattern: "*.{bed}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: File containing off-target regions
|
||||
pattern: "*.{bed}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
|
||||
authors:
|
||||
- "@SusiJo"
|
|
@ -2,14 +2,15 @@ process CNVKIT_BATCH {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9' : null)
|
||||
conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9 bioconda::samtools=1.15.1' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0' :
|
||||
'quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0' :
|
||||
'quay.io/biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(tumor), path(normal)
|
||||
path fasta
|
||||
path fasta_fai
|
||||
path targets
|
||||
path reference
|
||||
|
||||
|
@ -18,6 +19,8 @@ process CNVKIT_BATCH {
|
|||
tuple val(meta), path("*.cnn"), emit: cnn, optional: true
|
||||
tuple val(meta), path("*.cnr"), emit: cnr, optional: true
|
||||
tuple val(meta), path("*.cns"), emit: cns, optional: true
|
||||
tuple val(meta), path("*.pdf"), emit: pdf, optional: true
|
||||
tuple val(meta), path("*.png"), emit: png, optional: true
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
|
@ -25,31 +28,168 @@ process CNVKIT_BATCH {
|
|||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def normal_args = normal ? "--normal $normal" : ""
|
||||
def fasta_args = fasta ? "--fasta $fasta" : ""
|
||||
|
||||
def tumor_exists = tumor ? true : false
|
||||
def normal_exists = normal ? true : false
|
||||
|
||||
// execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow
|
||||
def tumor_cram = tumor_exists && tumor.Extension == "cram" ? true : false
|
||||
def normal_cram = normal_exists && normal.Extension == "cram" ? true : false
|
||||
def tumor_bam = tumor_exists && tumor.Extension == "bam" ? true : false
|
||||
def normal_bam = normal_exists && normal.Extension == "bam" ? true : false
|
||||
|
||||
def tumor_out = tumor_cram ? tumor.BaseName + ".bam" : "${tumor}"
|
||||
|
||||
// tumor_only mode does not need fasta & target
|
||||
// instead it requires a pre-computed reference.cnn which is built from fasta & target
|
||||
def (normal_out, normal_args, fasta_args) = ["", "", ""]
|
||||
def fai_reference = fasta_fai ? "--fai-reference ${fasta_fai}" : ""
|
||||
|
||||
if (normal_exists){
|
||||
def normal_prefix = normal.BaseName
|
||||
normal_out = normal_cram ? "${normal_prefix}" + ".bam" : "${normal}"
|
||||
fasta_args = fasta ? "--fasta $fasta" : ""
|
||||
|
||||
// germline mode
|
||||
// normal samples must be input without a flag
|
||||
// requires flag --normal to be empty []
|
||||
if(!tumor_exists){
|
||||
tumor_out = "${normal_prefix}" + ".bam"
|
||||
normal_args = "--normal "
|
||||
}
|
||||
// somatic mode
|
||||
else {
|
||||
normal_args = normal_prefix ? "--normal $normal_out" : ""
|
||||
}
|
||||
}
|
||||
|
||||
def target_args = targets ? "--targets $targets" : ""
|
||||
def reference_args = reference ? "--reference $reference" : ""
|
||||
|
||||
def target_args = ""
|
||||
if (args.contains("--method wgs") || args.contains("-m wgs")) {
|
||||
target_args = targets ? "--targets $targets" : ""
|
||||
}
|
||||
else {
|
||||
target_args = "--targets $targets"
|
||||
}
|
||||
"""
|
||||
cnvkit.py \\
|
||||
batch \\
|
||||
$tumor \\
|
||||
$normal_args \\
|
||||
$fasta_args \\
|
||||
$reference_args \\
|
||||
$target_args \\
|
||||
--processes $task.cpus \\
|
||||
$args
|
||||
// somatic_mode cram_input
|
||||
if (tumor_cram && normal_cram){
|
||||
"""
|
||||
samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out
|
||||
samtools view -T $fasta $fai_reference $normal -@ $task.cpus -o $normal_out
|
||||
|
||||
cnvkit.py \\
|
||||
batch \\
|
||||
$tumor_out \\
|
||||
$normal_args \\
|
||||
$fasta_args \\
|
||||
$reference_args \\
|
||||
$target_args \\
|
||||
--processes $task.cpus \\
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
// somatic_mode bam_input
|
||||
else if (tumor_bam && normal_bam){
|
||||
"""
|
||||
cnvkit.py \\
|
||||
batch \\
|
||||
$tumor_out \\
|
||||
$normal_args \\
|
||||
$fasta_args \\
|
||||
$reference_args \\
|
||||
$target_args \\
|
||||
--processes $task.cpus \\
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
// tumor_only_mode cram_input
|
||||
else if(tumor_cram && !normal_exists){
|
||||
"""
|
||||
samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out
|
||||
|
||||
cnvkit.py \\
|
||||
batch \\
|
||||
$tumor_out \\
|
||||
$normal_args \\
|
||||
$fasta_args \\
|
||||
$reference_args \\
|
||||
$target_args \\
|
||||
--processes $task.cpus \\
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
// tumor_only bam_input
|
||||
else if(tumor_bam && !normal_exists){
|
||||
"""
|
||||
cnvkit.py \\
|
||||
batch \\
|
||||
$tumor_out \\
|
||||
$normal_args \\
|
||||
$fasta_args \\
|
||||
$reference_args \\
|
||||
$target_args \\
|
||||
--processes $task.cpus \\
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
// germline mode cram_input
|
||||
// normal_args must be --normal []
|
||||
else if (normal_cram && !tumor_exists){
|
||||
"""
|
||||
samtools view -T $fasta $fai_reference $normal -@ $task.cpus -o $tumor_out
|
||||
|
||||
cnvkit.py \\
|
||||
batch \\
|
||||
$tumor_out \\
|
||||
$normal_args \\
|
||||
$fasta_args \\
|
||||
$reference_args \\
|
||||
$target_args \\
|
||||
--processes $task.cpus \\
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
// germline mode bam_input
|
||||
else if (normal_bam && !tumor_exists){
|
||||
"""
|
||||
cnvkit.py \\
|
||||
batch \\
|
||||
$tumor_out \\
|
||||
$normal_args \\
|
||||
$fasta_args \\
|
||||
$reference_args \\
|
||||
$target_args \\
|
||||
--processes $task.cpus \\
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
@ -11,27 +11,6 @@ tools:
|
|||
homepage: https://cnvkit.readthedocs.io/en/stable/index.html
|
||||
documentation: https://cnvkit.readthedocs.io/en/stable/index.html
|
||||
licence: ["Apache-2.0"]
|
||||
params:
|
||||
- outdir:
|
||||
type: string
|
||||
description: |
|
||||
The pipeline's output directory. By default, the module will
|
||||
output files into `$params.outdir/<SOFTWARE>`
|
||||
- publish_dir_mode:
|
||||
type: string
|
||||
description: |
|
||||
Value for the Nextflow `publishDir` mode parameter.
|
||||
Available: symlink, rellink, link, copy, copyNoFollow, move.
|
||||
- enable_conda:
|
||||
type: boolean
|
||||
description: |
|
||||
Run the module with Conda using the software specified
|
||||
via the `conda` directive
|
||||
- singularity_pull_docker_container:
|
||||
type: boolean
|
||||
description: |
|
||||
Instead of directly downloading Singularity images for use with Singularity,
|
||||
force the workflow to pull and convert Docker containers instead.
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
|
@ -49,7 +28,11 @@ input:
|
|||
- fasta:
|
||||
type: file
|
||||
description: |
|
||||
Input reference genome fasta file
|
||||
Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided)
|
||||
- fasta_fai:
|
||||
type: file
|
||||
description: |
|
||||
Input reference genome fasta index (optional, but recommended for cram_input)
|
||||
- targetfile:
|
||||
type: file
|
||||
description: |
|
||||
|
@ -80,6 +63,14 @@ output:
|
|||
type: file
|
||||
description: File containing copy number segment information
|
||||
pattern: "*.{cns}"
|
||||
- pdf:
|
||||
type: file
|
||||
description: File with plot of copy numbers or segments on chromosomes
|
||||
pattern: "*.{pdf}"
|
||||
- png:
|
||||
type: file
|
||||
description: File with plot of bin-level log2 coverages and segmentation calls
|
||||
pattern: "*.{png}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
|
@ -91,3 +82,4 @@ authors:
|
|||
- "@drpatelh"
|
||||
- "@fbdtemme"
|
||||
- "@lassefolkersen"
|
||||
- "@SusiJo"
|
||||
|
|
40
modules/cnvkit/reference/main.nf
Normal file
40
modules/cnvkit/reference/main.nf
Normal file
|
@ -0,0 +1,40 @@
|
|||
process CNVKIT_REFERENCE {
|
||||
tag "$fasta"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::cnvkit=0.9.9" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0':
|
||||
'quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }"
|
||||
|
||||
input:
|
||||
path fasta
|
||||
path targets
|
||||
path antitargets
|
||||
|
||||
output:
|
||||
path "*.cnn" , emit: cnn
|
||||
path "versions.yml", emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: targets.BaseName
|
||||
|
||||
"""
|
||||
cnvkit.py \\
|
||||
reference \\
|
||||
--fasta $fasta \\
|
||||
--targets $targets \\
|
||||
--antitargets $antitargets \\
|
||||
--output ${prefix}.reference.cnn \\
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
47
modules/cnvkit/reference/meta.yml
Normal file
47
modules/cnvkit/reference/meta.yml
Normal file
|
@ -0,0 +1,47 @@
|
|||
name: cnvkit_reference
|
||||
description:
|
||||
keywords:
|
||||
- cnvkit
|
||||
- reference
|
||||
tools:
|
||||
- cnvkit:
|
||||
description: |
|
||||
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
|
||||
tool_dev_url: https://github.com/etal/cnvkit
|
||||
doi: 10.1371/journal.pcbi.1004873
|
||||
licence: ["Apache-2.0"]
|
||||
|
||||
input:
|
||||
- fasta:
|
||||
type: file
|
||||
description: File containing reference genome
|
||||
pattern: "*.{fasta}"
|
||||
- targets:
|
||||
type: file
|
||||
description: File containing genomic regions
|
||||
pattern: "*.{bed}"
|
||||
- antitargets:
|
||||
type: file
|
||||
description: File containing off-target genomic regions
|
||||
pattern: "*.{bed}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reference:
|
||||
type: file
|
||||
description: File containing a copy-number reference (required for CNV calling in tumor_only mode)
|
||||
pattern: "*.{cnn}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
|
||||
authors:
|
||||
- "@SusiJo"
|
|
@ -2,13 +2,15 @@ process DEEPTOOLS_BAMCOVERAGE {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::deeptools=3.5.1" : null)
|
||||
conda (params.enable_conda ? "bioconda::deeptools=3.5.1 bioconda::samtools=1.15.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0':
|
||||
'quay.io/biocontainers/deeptools:3.5.1--py_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0':
|
||||
'quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index)
|
||||
path(fasta)
|
||||
path(fasta_fai)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.bigWig") , emit: bigwig, optional: true
|
||||
|
@ -22,16 +24,44 @@ process DEEPTOOLS_BAMCOVERAGE {
|
|||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}.bigWig"
|
||||
|
||||
"""
|
||||
bamCoverage \\
|
||||
--bam $input \\
|
||||
$args \\
|
||||
--numberOfProcessors ${task.cpus} \\
|
||||
--outFileName ${prefix}
|
||||
// cram_input is currently not working with deeptools
|
||||
// therefore it's required to convert cram to bam first
|
||||
def is_cram = input.Extension == "cram" ? true : false
|
||||
def input_out = is_cram ? input.BaseName + ".bam" : "${input}"
|
||||
def fai_reference = fasta_fai ? "--fai-reference ${fasta_fai}" : ""
|
||||
|
||||
if (is_cram){
|
||||
"""
|
||||
samtools view -T $fasta $input $fai_reference -@ $task.cpus -o $input_out
|
||||
samtools index -b $input_out -@ $task.cpus
|
||||
|
||||
bamCoverage \\
|
||||
--bam $input_out \\
|
||||
$args \\
|
||||
--numberOfProcessors ${task.cpus} \\
|
||||
--outFileName ${prefix}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
|
||||
}
|
||||
else {
|
||||
"""
|
||||
bamCoverage \\
|
||||
--bam $input_out \\
|
||||
$args \\
|
||||
--numberOfProcessors ${task.cpus} \\
|
||||
--outFileName ${prefix}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
@ -25,6 +25,14 @@ input:
|
|||
type: file
|
||||
description: BAM/CRAM index file
|
||||
pattern: "*.{bai,crai}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Reference file the CRAM file was created with (required with CRAM input)
|
||||
pattern: "*.{fasta,fa}"
|
||||
- fasta_fai:
|
||||
type: file
|
||||
description: Index of the reference file (optional, but recommended)
|
||||
pattern: "*.{fai}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
|
@ -47,3 +55,4 @@ output:
|
|||
|
||||
authors:
|
||||
- "@FriederikeHanssen"
|
||||
- "@SusiJo"
|
||||
|
|
|
@ -11,8 +11,8 @@ RUN conda env create -f /environment.yml && conda clean -a
|
|||
# Setup default ARG variables
|
||||
ARG GENOME=GRCh38
|
||||
ARG SPECIES=homo_sapiens
|
||||
ARG VEP_VERSION=104
|
||||
ARG VEP_TAG=104.3
|
||||
ARG VEP_VERSION=105
|
||||
ARG VEP_TAG=105.0
|
||||
|
||||
# Add conda installation dir to PATH (instead of doing 'conda activate')
|
||||
ENV PATH /opt/conda/envs/nf-core-vep-${VEP_TAG}/bin:$PATH
|
||||
|
|
|
@ -20,9 +20,9 @@ build_push() {
|
|||
docker push nfcore/vep:${VEP_TAG}.${GENOME}
|
||||
}
|
||||
|
||||
build_push "GRCh37" "homo_sapiens" "104" "104.3"
|
||||
build_push "GRCh38" "homo_sapiens" "104" "104.3"
|
||||
build_push "GRCm38" "mus_musculus" "102" "104.3"
|
||||
build_push "GRCm39" "mus_musculus" "104" "104.3"
|
||||
build_push "CanFam3.1" "canis_lupus_familiaris" "104" "104.3"
|
||||
build_push "WBcel235" "caenorhabditis_elegans" "104" "104.3"
|
||||
build_push "GRCh37" "homo_sapiens" "105" "105.0"
|
||||
build_push "GRCh38" "homo_sapiens" "105" "105.0"
|
||||
build_push "GRCm38" "mus_musculus" "102" "105.0"
|
||||
build_push "GRCm39" "mus_musculus" "105" "105.0"
|
||||
build_push "CanFam3.1" "canis_lupus_familiaris" "104" "105.0"
|
||||
build_push "WBcel235" "caenorhabditis_elegans" "105" "105.0"
|
||||
|
|
|
@ -1,10 +1,10 @@
|
|||
# You can use this file to create a conda environment for this module:
|
||||
# conda env create -f environment.yml
|
||||
name: nf-core-vep-104.3
|
||||
name: nf-core-vep-105.0
|
||||
channels:
|
||||
- conda-forge
|
||||
- bioconda
|
||||
- defaults
|
||||
|
||||
dependencies:
|
||||
- bioconda::ensembl-vep=104.3
|
||||
- bioconda::ensembl-vep=105.0
|
||||
|
|
|
@ -11,7 +11,7 @@ process FILTLONG {
|
|||
tuple val(meta), path(shortreads), path(longreads)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("${meta.id}_lr_filtlong.fastq.gz"), emit: reads
|
||||
tuple val(meta), path("*.fastq.gz"), emit: reads
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
|
@ -20,13 +20,14 @@ process FILTLONG {
|
|||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def short_reads = meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
|
||||
def short_reads = !shortreads ? "" : meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
|
||||
if ("$longreads" == "${prefix}.fastq.gz") error "Longread FASTQ input and output names are the same, set prefix in module configuration to disambiguate!"
|
||||
"""
|
||||
filtlong \\
|
||||
$short_reads \\
|
||||
$args \\
|
||||
$longreads \\
|
||||
| gzip -n > ${prefix}_lr_filtlong.fastq.gz
|
||||
| gzip -n > ${prefix}.fastq.gz
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
|
@ -1,6 +1,6 @@
|
|||
def VERSION = '2.1' // Version information not provided by tool on CLI
|
||||
|
||||
process GAMMA {
|
||||
process GAMMA_GAMMA {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
|
@ -26,13 +26,24 @@ process GAMMA {
|
|||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
||||
"""
|
||||
GAMMA.py \\
|
||||
if [[ ${fasta} == *.gz ]]
|
||||
then
|
||||
FNAME=\$(basename ${fasta} .gz)
|
||||
gunzip -f ${fasta}
|
||||
GAMMA.py \\
|
||||
$args \\
|
||||
"\${FNAME}" \\
|
||||
$db \\
|
||||
$prefix
|
||||
else
|
||||
GAMMA.py \\
|
||||
$args \\
|
||||
$fasta \\
|
||||
$db \\
|
||||
$prefix
|
||||
|
||||
fi
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
gamma: $VERSION
|
|
@ -1,4 +1,4 @@
|
|||
name: "gamma"
|
||||
name: "gamma_gamma"
|
||||
description: Gene Allele Mutation Microbial Assessment
|
||||
keywords:
|
||||
- gamma
|
||||
|
@ -61,3 +61,4 @@ output:
|
|||
authors:
|
||||
- "@sateeshperi"
|
||||
- "@rastanton"
|
||||
- "@jvhagey"
|
63
modules/gatk/unifiedgenotyper/main.nf
Normal file
63
modules/gatk/unifiedgenotyper/main.nf
Normal file
|
@ -0,0 +1,63 @@
|
|||
process GATK_UNIFIEDGENOTYPER {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk=3.5" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11':
|
||||
'quay.io/biocontainers/gatk:3.5--hdfd78af_11' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(index)
|
||||
path fasta
|
||||
path fai
|
||||
path dict
|
||||
path intervals
|
||||
path contamination
|
||||
path dbsnp
|
||||
path comp
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.vcf.gz"), emit: vcf
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def contamination_file = contamination ? "-contaminationFile ${contamination}" : ""
|
||||
def dbsnp_file = dbsnp ? "--dbsnp ${dbsnp}" : ""
|
||||
def comp_file = comp ? "--comp ${comp}" : ""
|
||||
def intervals_file = intervals ? "--intervals ${intervals}" : ""
|
||||
|
||||
def avail_mem = 3
|
||||
if (!task.memory) {
|
||||
log.info '[GATK RealignerTargetCreator] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
||||
} else {
|
||||
avail_mem = task.memory.giga
|
||||
}
|
||||
|
||||
"""
|
||||
gatk3 \\
|
||||
-Xmx${avail_mem}g \\
|
||||
-nt ${task.cpus} \\
|
||||
-T UnifiedGenotyper \\
|
||||
-I ${input} \\
|
||||
-R ${fasta} \\
|
||||
${contamination_file} \\
|
||||
${dbsnp_file} \\
|
||||
${comp_file} \\
|
||||
${intervals_file} \\
|
||||
-o ${prefix}.vcf \\
|
||||
$args
|
||||
|
||||
gzip -n *.vcf
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
gatk: \$(echo \$(gatk3 --version))
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
73
modules/gatk/unifiedgenotyper/meta.yml
Normal file
73
modules/gatk/unifiedgenotyper/meta.yml
Normal file
|
@ -0,0 +1,73 @@
|
|||
name: "gatk_unifiedgenotyper"
|
||||
keywords:
|
||||
- bam
|
||||
- vcf
|
||||
- variant calling
|
||||
tools:
|
||||
- "gatk":
|
||||
description: "The full Genome Analysis Toolkit (GATK) framework, license restricted."
|
||||
homepage: "https://gatk.broadinstitute.org/hc/en-us"
|
||||
documentation: "https://github.com/broadinstitute/gatk-docs"
|
||||
licence: "['https://software.broadinstitute.org/gatk/download/licensing', 'BSD', 'https://www.broadinstitute.org/gatk/about/#licensing']"
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- input:
|
||||
type: file
|
||||
description: Sorted and indexed BAM/CRAM/SAM file
|
||||
pattern: "*.bam"
|
||||
- index:
|
||||
type: file
|
||||
description: BAM index file
|
||||
pattern: "*.bai"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Reference file used to generate BAM file
|
||||
pattern: ".{fasta,fa,fna}"
|
||||
- fai:
|
||||
type: file
|
||||
description: Index of reference file used to generate BAM file
|
||||
pattern: ".fai"
|
||||
- dict:
|
||||
type: file
|
||||
description: GATK dict file for reference
|
||||
pattern: ".dict"
|
||||
- intervals:
|
||||
type: file
|
||||
description: Bed file with the genomic regions included in the library (optional)
|
||||
pattern: "*.intervals"
|
||||
- contamination:
|
||||
type: file
|
||||
description: Tab-separated file containing fraction of contamination in sequencing data (per sample) to aggressively remove
|
||||
pattern: "*"
|
||||
- dbsnps:
|
||||
type: file
|
||||
description: VCF file containing known sites (optional)
|
||||
pattern: "*"
|
||||
- comp:
|
||||
type: file
|
||||
description: Comparison VCF file (optional)
|
||||
pattern: "*"
|
||||
|
||||
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"
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF file containing called variants
|
||||
pattern: "*.vcf.gz"
|
||||
|
||||
authors:
|
||||
- "@ilight1542"
|
||||
- "@jfy133"
|
|
@ -2,10 +2,10 @@ process GATK4_APPLYBQSR {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_APPLYBQSR_SPARK {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_APPLYVQSR {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index), path(intervals)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR_SPARK {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'broadinstitute/gatk:4.2.3.0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index), path(intervals)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_BEDTOINTERVALLIST {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bed)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_CALCULATECONTAMINATION {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(pileup), path(matched)
|
||||
|
|
51
modules/gatk4/calibratedragstrmodel/main.nf
Normal file
51
modules/gatk4/calibratedragstrmodel/main.nf
Normal file
|
@ -0,0 +1,51 @@
|
|||
process GATK4_CALIBRATEDRAGSTRMODEL {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam), path(bam_index), path(intervals)
|
||||
path fasta
|
||||
path fasta_fai
|
||||
path dict
|
||||
path strtablefile
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.txt") , emit: dragstr_model
|
||||
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}"
|
||||
def intervals_command = intervals ? "--intervals $intervals" : ""
|
||||
|
||||
def avail_mem = 3
|
||||
if (!task.memory) {
|
||||
log.info '[GATK CalibrateDragstrModel] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
||||
} else {
|
||||
avail_mem = task.memory.giga
|
||||
}
|
||||
"""
|
||||
gatk --java-options "-Xmx${avail_mem}g" CalibrateDragstrModel \\
|
||||
--input $bam \\
|
||||
--output ${prefix}.txt \\
|
||||
--reference $fasta \\
|
||||
--str-table-path $strtablefile \\
|
||||
--threads $task.cpus \\
|
||||
$intervals_command \\
|
||||
--tmp-dir . \\
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
74
modules/gatk4/calibratedragstrmodel/meta.yml
Normal file
74
modules/gatk4/calibratedragstrmodel/meta.yml
Normal file
|
@ -0,0 +1,74 @@
|
|||
name: gatk4_calibratedragstrmodel
|
||||
description: estimates the parameters for the DRAGstr model
|
||||
keywords:
|
||||
- gatk4
|
||||
- bam
|
||||
- cram
|
||||
- sam
|
||||
- calibratedragstrmodel
|
||||
tools:
|
||||
- gatk4:
|
||||
description:
|
||||
Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
|
||||
with a primary focus on variant discovery and genotyping. Its powerful processing engine
|
||||
and high-performance computing features make it capable of taking on projects of any size.
|
||||
homepage: https://gatk.broadinstitute.org/hc/en-us
|
||||
documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360057441571-CalibrateDragstrModel-BETA-
|
||||
tool_dev_url: https://github.com/broadinstitute/gatk
|
||||
doi: 10.1158/1538-7445.AM2017-3590
|
||||
licence: ["Apache-2.0"]
|
||||
|
||||
input:
|
||||
# Only when we have meta
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- bam:
|
||||
type: file
|
||||
description: BAM/CRAM/SAM file
|
||||
pattern: "*.{bam,cram,sam}"
|
||||
- bam_index:
|
||||
type: file
|
||||
description: index of the BAM/CRAM/SAM file
|
||||
pattern: "*.{bai,crai,sai}"
|
||||
- intervals:
|
||||
type: file
|
||||
description: BED file or interval list containing regions (optional)
|
||||
pattern: "*.{bed,interval_list}"
|
||||
- fasta:
|
||||
type: file
|
||||
description: The reference FASTA file
|
||||
pattern: "*.{fasta,fa}"
|
||||
- fasta_fai:
|
||||
type: file
|
||||
description: The index of the reference FASTA file
|
||||
pattern: "*.fai"
|
||||
- dict:
|
||||
type: file
|
||||
description: The sequence dictionary of the reference FASTA file
|
||||
pattern: "*.dict"
|
||||
- strtablefile:
|
||||
type: file
|
||||
description: The StrTableFile zip folder of the reference FASTA file
|
||||
pattern: "*.zip"
|
||||
|
||||
output:
|
||||
#Only when we have meta
|
||||
- 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"
|
||||
- dragstr_model:
|
||||
type: file
|
||||
description: The DragSTR model
|
||||
pattern: "*.txt"
|
||||
|
||||
authors:
|
||||
- "@nvnieuwk"
|
58
modules/gatk4/cnnscorevariants/main.nf
Normal file
58
modules/gatk4/cnnscorevariants/main.nf
Normal file
|
@ -0,0 +1,58 @@
|
|||
process GATK4_CNNSCOREVARIANTS {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
//Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811
|
||||
if (params.enable_conda) {
|
||||
exit 1, "Conda environments cannot be used for GATK4/CNNScoreVariants at the moment. Please use docker or singularity containers."
|
||||
}
|
||||
container 'broadinstitute/gatk:4.2.6.1' //Biocontainers is missing a package
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(tbi), path(aligned_input), path(intervals)
|
||||
path fasta
|
||||
path fai
|
||||
path dict
|
||||
path architecture
|
||||
path weights
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*cnn.vcf.gz") , emit: vcf
|
||||
tuple val(meta), path("*cnn.vcf.gz.tbi"), emit: tbi
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def aligned_input = aligned_input ? "--input $aligned_input" : ""
|
||||
def interval_command = intervals ? "--intervals $intervals" : ""
|
||||
def architecture = architecture ? "--architecture $architecture" : ""
|
||||
def weights = weights ? "--weights $weights" : ""
|
||||
|
||||
def avail_mem = 3
|
||||
if (!task.memory) {
|
||||
log.info '[GATK CnnScoreVariants] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
||||
} else {
|
||||
avail_mem = task.memory.giga
|
||||
}
|
||||
"""
|
||||
gatk --java-options "-Xmx${avail_mem}g" CNNScoreVariants \\
|
||||
--variant $vcf \\
|
||||
--output ${prefix}.cnn.vcf.gz \\
|
||||
--reference $fasta \\
|
||||
$interval_command \\
|
||||
$aligned_input \\
|
||||
$architecture \\
|
||||
$weights \\
|
||||
--tmp-dir . \\
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
80
modules/gatk4/cnnscorevariants/meta.yml
Normal file
80
modules/gatk4/cnnscorevariants/meta.yml
Normal file
|
@ -0,0 +1,80 @@
|
|||
name: "gatk4_cnnscorevariants"
|
||||
description: Apply a Convolutional Neural Net to filter annotated variants
|
||||
keywords:
|
||||
- gatk4_cnnscorevariants
|
||||
- gatk4
|
||||
- variants
|
||||
tools:
|
||||
- gatk4:
|
||||
description: |
|
||||
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
|
||||
with a primary focus on variant discovery and genotyping. Its powerful processing engine
|
||||
and high-performance computing features make it capable of taking on projects of any size.
|
||||
homepage: https://gatk.broadinstitute.org/hc/en-us
|
||||
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
|
||||
doi: 10.1158/1538-7445.AM2017-3590
|
||||
licence: ["Apache-2.0"]
|
||||
|
||||
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.gz"
|
||||
- tbi:
|
||||
type: file
|
||||
description: VCF index file
|
||||
pattern: "*.vcf.gz.tbi"
|
||||
- aligned_input:
|
||||
type: file
|
||||
description: BAM/CRAM file from alignment (optional)
|
||||
pattern: "*.{bam,cram}"
|
||||
- intervals:
|
||||
type: file
|
||||
description: Bed file with the genomic regions included in the library (optional)
|
||||
- fasta:
|
||||
type: file
|
||||
description: The reference fasta file
|
||||
pattern: "*.fasta"
|
||||
- fai:
|
||||
type: file
|
||||
description: Index of reference fasta file
|
||||
pattern: "*.fasta.fai"
|
||||
- dict:
|
||||
type: file
|
||||
description: GATK sequence dictionary
|
||||
pattern: "*.dict"
|
||||
- architecture:
|
||||
type: file
|
||||
description: Neural Net architecture configuration json file (optional)
|
||||
pattern: "*.json"
|
||||
- weights:
|
||||
type: file
|
||||
description: Keras model HD5 file with neural net weights. (optional)
|
||||
pattern: "*.hd5"
|
||||
|
||||
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"
|
||||
- vcf:
|
||||
type: file
|
||||
description: Annotated VCF file
|
||||
pattern: "*.vcf"
|
||||
- tbi:
|
||||
type: file
|
||||
description: VCF index file
|
||||
pattern: "*.vcf.gz.tbi"
|
||||
|
||||
authors:
|
||||
- "@FriederikeHanssen"
|
|
@ -2,10 +2,10 @@ process GATK4_COMBINEGVCFS {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(vcf_idx)
|
||||
|
|
53
modules/gatk4/composestrtablefile/main.nf
Normal file
53
modules/gatk4/composestrtablefile/main.nf
Normal file
|
@ -0,0 +1,53 @@
|
|||
process GATK4_COMPOSESTRTABLEFILE {
|
||||
tag "$fasta"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
path(fasta)
|
||||
path(fasta_fai)
|
||||
path(dict)
|
||||
|
||||
output:
|
||||
path "*.zip" , emit: str_table
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
|
||||
def avail_mem = 6
|
||||
if (!task.memory) {
|
||||
log.info '[GATK ComposeSTRTableFile] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
|
||||
} else {
|
||||
avail_mem = task.memory.giga
|
||||
}
|
||||
"""
|
||||
gatk --java-options "-Xmx${avail_mem}g" ComposeSTRTableFile \\
|
||||
--reference $fasta \\
|
||||
--output ${fasta.baseName}.zip \\
|
||||
--tmp-dir . \\
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
|
||||
stub:
|
||||
"""
|
||||
touch test.zip
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
43
modules/gatk4/composestrtablefile/meta.yml
Normal file
43
modules/gatk4/composestrtablefile/meta.yml
Normal file
|
@ -0,0 +1,43 @@
|
|||
name: "gatk4_composestrtablefile"
|
||||
description: This tool looks for low-complexity STR sequences along the reference that are later used to estimate the Dragstr model during single sample auto calibration CalibrateDragstrModel.
|
||||
keywords:
|
||||
- gatk4
|
||||
- composestrtablefile
|
||||
tools:
|
||||
- gatk4:
|
||||
description:
|
||||
Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
|
||||
with a primary focus on variant discovery and genotyping. Its powerful processing engine
|
||||
and high-performance computing features make it capable of taking on projects of any size.
|
||||
homepage: https://gatk.broadinstitute.org/hc/en-us
|
||||
documentation: https://gatk.broadinstitute.org/hc/en-us/articles/4405451249819-ComposeSTRTableFile
|
||||
tool_dev_url: https://github.com/broadinstitute/gatk
|
||||
doi: 10.1158/1538-7445.AM2017-3590
|
||||
licence: ["Apache-2.0"]
|
||||
|
||||
input:
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA reference file
|
||||
pattern: "*.{fasta,fa}"
|
||||
- fasta_fai:
|
||||
type: file
|
||||
description: index of the FASTA reference file
|
||||
pattern: "*.fai"
|
||||
- dict:
|
||||
type: file
|
||||
description: Sequence dictionary of the FASTA reference file
|
||||
pattern: "*.dict"
|
||||
|
||||
output:
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- str_table:
|
||||
type: file
|
||||
description: A zipped folder containing the STR table files
|
||||
pattern: "*.zip"
|
||||
|
||||
authors:
|
||||
- "@nvnieuwk"
|
|
@ -2,10 +2,10 @@ process GATK4_CREATESEQUENCEDICTIONARY {
|
|||
tag "$fasta"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
path fasta
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_CREATESOMATICPANELOFNORMALS {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(genomicsdb)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_FASTQTOSAM {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_FILTERMUTECTCALLS {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(vcf_tbi), path(stats), path(orientationbias), path(segmentation), path(table), val(estimate)
|
||||
|
|
51
modules/gatk4/filtervarianttranches/main.nf
Normal file
51
modules/gatk4/filtervarianttranches/main.nf
Normal file
|
@ -0,0 +1,51 @@
|
|||
process GATK4_FILTERVARIANTTRANCHES {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(tbi), path(intervals)
|
||||
path resources
|
||||
path resources_index
|
||||
path fasta
|
||||
path fai
|
||||
path dict
|
||||
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.vcf.gz") , emit: vcf
|
||||
tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
||||
def resources = resources.collect{"--resource $it"}.join(' ')
|
||||
def avail_mem = 3
|
||||
if (!task.memory) {
|
||||
log.info '[GATK FilterVariantTranches] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
||||
} else {
|
||||
avail_mem = task.memory.giga
|
||||
}
|
||||
"""
|
||||
gatk --java-options "-Xmx${avail_mem}g" FilterVariantTranches \\
|
||||
--variant $vcf \\
|
||||
$resources \\
|
||||
--output ${prefix}.filtered.vcf.gz \\
|
||||
--tmp-dir . \\
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
68
modules/gatk4/filtervarianttranches/meta.yml
Normal file
68
modules/gatk4/filtervarianttranches/meta.yml
Normal file
|
@ -0,0 +1,68 @@
|
|||
name: "gatk4_filtervarianttranches"
|
||||
description: Apply tranche filtering
|
||||
keywords:
|
||||
- gatk4
|
||||
- filtervarianttranches
|
||||
|
||||
tools:
|
||||
- "gatk4":
|
||||
description: Genome Analysis Toolkit (GATK4)
|
||||
homepage: https://gatk.broadinstitute.org/hc/en-us
|
||||
documentation: https://gatk.broadinstitute.org/hc/en-us
|
||||
tool_dev_url: https://github.com/broadinstitute/gatk
|
||||
doi: "10.1158/1538-7445.AM2017-3590"
|
||||
licence: ["BSD-3-clause"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: a VCF file containing variants, must have info key:CNN_2D
|
||||
pattern: "*.vcf.gz"
|
||||
- tbi:
|
||||
type: file
|
||||
description: tbi file matching with -vcf
|
||||
pattern: "*.vcf.gz.tbi"
|
||||
- resources:
|
||||
type: list
|
||||
description: resource A VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary
|
||||
pattern: "*.vcf.gz"
|
||||
- resources_index:
|
||||
type: list
|
||||
description: Index of resource VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary
|
||||
pattern: "*.vcf.gz"
|
||||
- fasta:
|
||||
type: file
|
||||
description: The reference fasta file
|
||||
pattern: "*.fasta"
|
||||
- fai:
|
||||
type: file
|
||||
description: Index of reference fasta file
|
||||
pattern: "fasta.fai"
|
||||
- dict:
|
||||
|
||||
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"
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF file
|
||||
pattern: "*.vcf.gz"
|
||||
- tbi:
|
||||
type: file
|
||||
description: VCF index file
|
||||
pattern: "*.vcf.gz.tbi"
|
||||
|
||||
authors:
|
||||
- "@FriederikeHanssen"
|
|
@ -2,10 +2,10 @@ process GATK4_GATHERBQSRREPORTS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(table)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_GATHERPILEUPSUMMARIES {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
|
||||
input:
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_GENOMICSDBIMPORT {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_GENOTYPEGVCFS {
|
|||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_GETPILEUPSUMMARIES {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(index), path(intervals)
|
||||
|
@ -40,7 +40,7 @@ process GATK4_GETPILEUPSUMMARIES {
|
|||
--variant $variants \\
|
||||
--output ${prefix}.pileups.table \\
|
||||
$reference_command \\
|
||||
$sites_command \\
|
||||
$interval_command \\
|
||||
--tmp-dir . \\
|
||||
$args
|
||||
|
||||
|
|
|
@ -2,13 +2,13 @@ process GATK4_HAPLOTYPECALLER {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index), path(intervals)
|
||||
tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model)
|
||||
path fasta
|
||||
path fai
|
||||
path dict
|
||||
|
@ -28,6 +28,7 @@ process GATK4_HAPLOTYPECALLER {
|
|||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def dbsnp_command = dbsnp ? "--dbsnp $dbsnp" : ""
|
||||
def interval_command = intervals ? "--intervals $intervals" : ""
|
||||
def dragstr_command = dragstr_model ? "--dragstr-params-path $dragstr_model" : ""
|
||||
|
||||
def avail_mem = 3
|
||||
if (!task.memory) {
|
||||
|
@ -42,6 +43,7 @@ process GATK4_HAPLOTYPECALLER {
|
|||
--reference $fasta \\
|
||||
$dbsnp_command \\
|
||||
$interval_command \\
|
||||
$dragstr_command \\
|
||||
--tmp-dir . \\
|
||||
$args
|
||||
|
||||
|
|
|
@ -32,6 +32,10 @@ input:
|
|||
- intervals:
|
||||
type: file
|
||||
description: Bed file with the genomic regions included in the library (optional)
|
||||
- dragstr_model:
|
||||
type: file
|
||||
description: Text file containing the DragSTR model of the used BAM/CRAM file (optional)
|
||||
pattern: "*.txt"
|
||||
- fasta:
|
||||
type: file
|
||||
description: The reference fasta file
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_INDEXFEATUREFILE {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(feature_file)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOBED {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(intervals)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOOLS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(intervals)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_LEARNREADORIENTATIONMODEL {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(f1r2)
|
||||
|
|
|
@ -1,11 +1,11 @@
|
|||
process GATK4_MARKDUPLICATES {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_MERGEBAMALIGNMENT {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(aligned), path(unmapped)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_MERGEMUTECTSTATS {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(stats)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_MERGEVCFS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
|
@ -13,6 +13,7 @@ process GATK4_MERGEVCFS {
|
|||
|
||||
output:
|
||||
tuple val(meta), path('*.vcf.gz'), emit: vcf
|
||||
tuple val(meta), path("*.tbi") , emit: tbi
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
|
|
|
@ -35,6 +35,11 @@ output:
|
|||
type: file
|
||||
description: merged vcf file
|
||||
pattern: "*.vcf.gz"
|
||||
- tbi:
|
||||
type: file
|
||||
description: index files for the merged vcf files
|
||||
pattern: "*.tbi"
|
||||
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_MUTECT2 {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index), path(intervals)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_REVERTSAM {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_SAMTOFASTQ {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_SELECTVARIANTS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(vcf_idx)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_SPLITNCIGARREADS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam), path(bai), path(intervals)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_VARIANTFILTRATION {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(tbi)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_VARIANTRECALIBRATOR {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(tbi)
|
||||
|
|
45
modules/hmtnote/main.nf
Normal file
45
modules/hmtnote/main.nf
Normal file
|
@ -0,0 +1,45 @@
|
|||
process HMTNOTE {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::hmtnote=0.7.2" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/hmtnote:0.7.2--pyhdfd78af_0':
|
||||
'quay.io/biocontainers/hmtnote:0.7.2--pyhdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*_annotated.vcf"), emit: vcf
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
||||
"""
|
||||
hmtnote \\
|
||||
annotate \\
|
||||
$vcf \\
|
||||
${prefix}_annotated.vcf \\
|
||||
$args
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote, version //; s/Using.*\$//' ))
|
||||
END_VERSIONS
|
||||
"""
|
||||
stub:
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
touch ${prefix}_annotated.vcf
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote, version //; s/Using.*\$//' ))
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
39
modules/hmtnote/meta.yml
Normal file
39
modules/hmtnote/meta.yml
Normal file
|
@ -0,0 +1,39 @@
|
|||
name: hmtnote
|
||||
description: Human mitochondrial variants annotation using HmtVar.
|
||||
keywords:
|
||||
- hmtnote mitochondria annotation
|
||||
tools:
|
||||
- hmtnote:
|
||||
description: Human mitochondrial variants annotation using HmtVar.
|
||||
homepage: https://github.com/robertopreste/HmtNote
|
||||
documentation: https://hmtnote.readthedocs.io/en/latest/usage.html
|
||||
tool_dev_url: None
|
||||
doi: "https://doi.org/10.1101/600619"
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
- vcf:
|
||||
type: file
|
||||
description: vcf file
|
||||
pattern: "*.vcf"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- vcf:
|
||||
type: file
|
||||
description: annotated vcf
|
||||
pattern: "*_annotated.vcf"
|
||||
|
||||
authors:
|
||||
- "@sysbiocoder"
|
42
modules/kat/hist/main.nf
Normal file
42
modules/kat/hist/main.nf
Normal file
|
@ -0,0 +1,42 @@
|
|||
process KAT_HIST {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::kat=2.4.2" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/kat:2.4.2--py38hfc5f9d8_2':
|
||||
'quay.io/biocontainers/kat:2.4.2--py38hfc5f9d8_2' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.hist") , emit: hist
|
||||
tuple val(meta), path("*.hist.dist_analysis.json"), emit: json
|
||||
tuple val(meta), path("*.png") , emit: png , optional: true
|
||||
tuple val(meta), path("*.ps") , emit: ps , optional: true
|
||||
tuple val(meta), path("*.pdf") , emit: pdf , optional: true
|
||||
tuple val(meta), path("*-hash.jf*") , emit: jellyfish_hash, optional: true
|
||||
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}"
|
||||
"""
|
||||
kat hist \\
|
||||
--threads $task.cpus \\
|
||||
--output_prefix ${prefix}.hist \\
|
||||
$args \\
|
||||
$reads
|
||||
|
||||
ls -l
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
kat: \$( kat hist --version | sed 's/kat //' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
64
modules/kat/hist/meta.yml
Normal file
64
modules/kat/hist/meta.yml
Normal file
|
@ -0,0 +1,64 @@
|
|||
name: "kat_hist"
|
||||
description: Creates a histogram of the number of distinct k-mers having a given frequency.
|
||||
keywords:
|
||||
- k-mer
|
||||
- histogram
|
||||
- count
|
||||
tools:
|
||||
- "kat":
|
||||
description: "KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts"
|
||||
homepage: https://www.earlham.ac.uk/kat-tools
|
||||
documentation: https://kat.readthedocs.io/en/latest/index.html
|
||||
tool_dev_url: https://github.com/TGAC/KAT
|
||||
doi: http://bioinformatics.oxfordjournals.org/content/early/2016/10/20/bioinformatics.btw663.abstract
|
||||
licence: "['GPL v3']"
|
||||
|
||||
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.
|
||||
|
||||
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"
|
||||
- hist:
|
||||
type: file
|
||||
description: KAT histogram of k-mer counts
|
||||
pattern: "*.hist"
|
||||
- json:
|
||||
type: file
|
||||
description: KAT histogram summary of distance analysis
|
||||
pattern: "*.hist.dist_analysis.json"
|
||||
- png:
|
||||
type: file
|
||||
description: KAT plot of k-mer histogram in PNG format
|
||||
pattern: "*.png"
|
||||
- ps:
|
||||
type: file
|
||||
description: KAT plot of k-mer histogram in PS format
|
||||
pattern: "*.ps"
|
||||
- pdf:
|
||||
type: file
|
||||
description: KAT plot of k-mer histogram in PDF format
|
||||
pattern: "*.pdf"
|
||||
- jellyfish_hash:
|
||||
type: file
|
||||
description: Jellyfish hash file
|
||||
pattern: "*-hist.jf*"
|
||||
|
||||
authors:
|
||||
- "@mahesh-panchal"
|
38
modules/mash/screen/main.nf
Normal file
38
modules/mash/screen/main.nf
Normal file
|
@ -0,0 +1,38 @@
|
|||
process MASH_SCREEN {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::mash=2.3" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1':
|
||||
'quay.io/biocontainers/mash:2.3--he348c14_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(query)
|
||||
path sequences_sketch
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.screen"), emit: screen
|
||||
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}"
|
||||
"""
|
||||
mash \\
|
||||
screen \\
|
||||
$args \\
|
||||
-p $task.cpus \\
|
||||
$sequences_sketch \\
|
||||
$query \\
|
||||
> ${prefix}.screen
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
mash: \$( mash --version )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
48
modules/mash/screen/meta.yml
Normal file
48
modules/mash/screen/meta.yml
Normal file
|
@ -0,0 +1,48 @@
|
|||
name: "mash_screen"
|
||||
description: Screens query sequences against large sequence databases
|
||||
keywords:
|
||||
- screen
|
||||
- containment
|
||||
- contamination
|
||||
- taxonomic assignment
|
||||
tools:
|
||||
- "mash":
|
||||
description: Fast sequence distance estimator that uses MinHash
|
||||
homepage: https://github.com/marbl/Mash
|
||||
documentation: https://mash.readthedocs.io/en/latest/sketches.html
|
||||
tool_dev_url: https://github.com/marbl/Mash
|
||||
doi: "10.1186/s13059-016-0997-x"
|
||||
licence: ["https://github.com/marbl/Mash/blob/master/LICENSE.txt"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- query:
|
||||
type: file
|
||||
description: Query sequences
|
||||
pattern: "*.fastq.gz"
|
||||
- sequence_sketch:
|
||||
type: file
|
||||
description: Sequence files to match against
|
||||
pattern: "*.msh"
|
||||
|
||||
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"
|
||||
- screen:
|
||||
type: file
|
||||
description: List of sequences from fastx_db similar to query sequences
|
||||
pattern: "*.screen"
|
||||
|
||||
authors:
|
||||
- "@mahesh-panchal"
|
37
modules/maxquant/lfq/main.nf
Normal file
37
modules/maxquant/lfq/main.nf
Normal file
|
@ -0,0 +1,37 @@
|
|||
process MAXQUANT_LFQ {
|
||||
tag "$meta.id"
|
||||
label 'process_long'
|
||||
conda (params.enable_conda ? "bioconda::maxquant=2.0.3.0=py310hdfd78af_1" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/maxquant:2.0.3.0--py310hdfd78af_1"
|
||||
} else {
|
||||
container "quay.io/biocontainers/maxquant:2.0.3.0--py310hdfd78af_1"
|
||||
}
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fasta), path(paramfile)
|
||||
path raw
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.txt"), emit: maxquant_txt
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
||||
"""
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
maxquant: \$(maxquant --version 2>&1 > /dev/null | cut -f2 -d\" \")
|
||||
END_VERSIONS
|
||||
sed \"s_<numThreads>.*_<numThreads>$task.cpus</numThreads>_\" ${paramfile} > mqpar_changed.xml
|
||||
sed -i \"s|PLACEHOLDER|\$PWD/|g\" mqpar_changed.xml
|
||||
mkdir temp
|
||||
maxquant mqpar_changed.xml
|
||||
mv combined/txt/*.txt .
|
||||
"""
|
||||
}
|
52
modules/maxquant/lfq/meta.yml
Normal file
52
modules/maxquant/lfq/meta.yml
Normal file
|
@ -0,0 +1,52 @@
|
|||
name: maxquant_lfq
|
||||
description: Run standard proteomics data analysis with MaxQuant, mostly dedicated to label-free. Paths to fasta and raw files needs to be marked by "PLACEHOLDER"
|
||||
keywords:
|
||||
- sort
|
||||
tools:
|
||||
- maxquant:
|
||||
description: MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. License restricted.
|
||||
homepage: None
|
||||
documentation: None
|
||||
tool_dev_url: None
|
||||
doi: ""
|
||||
licence: ["http://www.coxdocs.org/lib/exe/fetch.php?media=license_agreement.pdf"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
|
||||
- raw:
|
||||
type: file
|
||||
description: raw files with mass spectra
|
||||
pattern: "*.{raw,RAW,Raw}"
|
||||
|
||||
- fasta:
|
||||
type: file
|
||||
description: fasta file with protein sequences
|
||||
pattern: "*.{fasta}"
|
||||
|
||||
- parfile:
|
||||
type: file
|
||||
description: MaxQuant parameter file (XML)
|
||||
pattern: "*.{xml}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "versions.yml"
|
||||
- maxquant_txt:
|
||||
type: file
|
||||
description: tables with peptides and protein information
|
||||
pattern: "*.{txt}"
|
||||
|
||||
authors:
|
||||
- "@veitveit"
|
|
@ -10,18 +10,22 @@ process MOSDEPTH {
|
|||
input:
|
||||
tuple val(meta), path(bam), path(bai)
|
||||
path bed
|
||||
val window_size
|
||||
path fasta
|
||||
|
||||
output:
|
||||
tuple val(meta), path('*.global.dist.txt') , emit: global_txt
|
||||
tuple val(meta), path('*.region.dist.txt') , emit: regions_txt , optional:true
|
||||
tuple val(meta), path('*.summary.txt') , emit: summary_txt
|
||||
tuple val(meta), path('*.per-base.d4') , emit: d4 , optional:true
|
||||
tuple val(meta), path('*.per-base.bed.gz') , emit: per_base_bed, optional:true
|
||||
tuple val(meta), path('*.per-base.bed.gz.csi'), emit: per_base_csi, optional:true
|
||||
tuple val(meta), path('*.regions.bed.gz') , emit: regions_bed , optional:true
|
||||
tuple val(meta), path('*.regions.bed.gz.csi') , emit: regions_csi , optional:true
|
||||
path "versions.yml" , emit: versions
|
||||
tuple val(meta), path('*.global.dist.txt') , emit: global_txt
|
||||
tuple val(meta), path('*.summary.txt') , emit: summary_txt
|
||||
tuple val(meta), path('*.region.dist.txt') , optional:true, emit: regions_txt
|
||||
tuple val(meta), path('*.per-base.d4') , optional:true, emit: per_base_d4
|
||||
tuple val(meta), path('*.per-base.bed.gz') , optional:true, emit: per_base_bed
|
||||
tuple val(meta), path('*.per-base.bed.gz.csi') , optional:true, emit: per_base_csi
|
||||
tuple val(meta), path('*.regions.bed.gz') , optional:true, emit: regions_bed
|
||||
tuple val(meta), path('*.regions.bed.gz.csi') , optional:true, emit: regions_csi
|
||||
tuple val(meta), path('*.quantized.bed.gz') , optional:true, emit: quantized_bed
|
||||
tuple val(meta), path('*.quantized.bed.gz.csi') , optional:true, emit: quantized_csi
|
||||
tuple val(meta), path('*.thresholds.bed.gz') , optional:true, emit: thresholds_bed
|
||||
tuple val(meta), path('*.thresholds.bed.gz.csi'), optional:true, emit: thresholds_csi
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
@ -29,19 +33,24 @@ process MOSDEPTH {
|
|||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
if (window_size) {
|
||||
interval = "--by ${window_size}"
|
||||
} else if ( bed ) {
|
||||
interval = "--by ${bed}"
|
||||
} else {
|
||||
interval = ""
|
||||
def reference = fasta ? "--fasta ${fasta}" : ""
|
||||
def interval = bed ? "--by ${bed}" : ""
|
||||
if (bed && args.contains("--by")) {
|
||||
exit 1, "'--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition"
|
||||
}
|
||||
if (!bed && args.contains("--thresholds")) {
|
||||
exit 1, "'--thresholds' can only be specified in conjunction with '--by'"
|
||||
}
|
||||
|
||||
"""
|
||||
mosdepth \\
|
||||
--threads $task.cpus \\
|
||||
$interval \\
|
||||
$reference \\
|
||||
$args \\
|
||||
$prefix \\
|
||||
$bam
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//')
|
||||
|
@ -59,6 +68,10 @@ process MOSDEPTH {
|
|||
touch ${prefix}.per-base.bed.gz.csi
|
||||
touch ${prefix}.regions.bed.gz
|
||||
touch ${prefix}.regions.bed.gz.csi
|
||||
touch ${prefix}.quantized.bed.gz
|
||||
touch ${prefix}.quantized.bed.gz.csi
|
||||
touch ${prefix}.thresholds.bed.gz
|
||||
touch ${prefix}.thresholds.bed.gz.csi
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
|
@ -30,10 +30,10 @@ input:
|
|||
type: file
|
||||
description: BED file with intersected intervals
|
||||
pattern: "*.{bed}"
|
||||
- window_size:
|
||||
type: integer
|
||||
description: Window size
|
||||
pattern: "[0-9]+"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Reference genome FASTA file
|
||||
pattern: "*.{fa,fasta}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
|
@ -60,6 +60,10 @@ output:
|
|||
type: file
|
||||
description: Index file for BED file with per-base coverage
|
||||
pattern: "*.{per-base.bed.gz.csi}"
|
||||
- per_base_d4:
|
||||
type: file
|
||||
description: D4 file with per-base coverage
|
||||
pattern: "*.{per-base.d4}"
|
||||
- regions_bed:
|
||||
type: file
|
||||
description: BED file with per-region coverage
|
||||
|
@ -68,6 +72,22 @@ output:
|
|||
type: file
|
||||
description: Index file for BED file with per-region coverage
|
||||
pattern: "*.{regions.bed.gz.csi}"
|
||||
- quantized_bed:
|
||||
type: file
|
||||
description: BED file with binned coverage
|
||||
pattern: "*.{quantized.bed.gz}"
|
||||
- quantized_csi:
|
||||
type: file
|
||||
description: Index file for BED file with binned coverage
|
||||
pattern: "*.{quantized.bed.gz.csi}"
|
||||
- thresholds_bed:
|
||||
type: file
|
||||
description: BED file with the number of bases in each region that are covered at or above each threshold
|
||||
pattern: "*.{thresholds.bed.gz}"
|
||||
- thresholds_csi:
|
||||
type: file
|
||||
description: Index file for BED file with threshold coverage
|
||||
pattern: "*.{thresholds.bed.gz.csi}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
|
@ -76,3 +96,4 @@ authors:
|
|||
- "@joseespinosa"
|
||||
- "@drpatelh"
|
||||
- "@ramprasadn"
|
||||
- "@matthdsm"
|
||||
|
|
54
modules/motus/profile/main.nf
Normal file
54
modules/motus/profile/main.nf
Normal file
|
@ -0,0 +1,54 @@
|
|||
process MOTUS_PROFILE {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0':
|
||||
'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
path db
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.out"), emit: out
|
||||
tuple val(meta), path("*.bam"), optional: true, emit: bam
|
||||
tuple val(meta), path("*.mgc"), optional: true, emit: mgc
|
||||
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}"
|
||||
def inputs = reads[0].getExtension() == 'bam' ?
|
||||
"-i ${reads}" :
|
||||
reads[0].getExtension() == 'mgc' ? "-m $reads" :
|
||||
meta.single_end ?
|
||||
"-s $reads" : "-f ${reads[0]} -r ${reads[1]}"
|
||||
def refdb = db ? "-db ${db}" : ""
|
||||
"""
|
||||
motus profile \\
|
||||
$args \\
|
||||
$inputs \\
|
||||
$refdb \\
|
||||
-t $task.cpus \\
|
||||
-n $prefix \\
|
||||
-o ${prefix}.out
|
||||
|
||||
## mOTUs version number is not available from command line.
|
||||
## mOTUs save the version number in index database folder.
|
||||
## mOTUs will check the database version is same version as exec version.
|
||||
if [ "$db" == "" ]; then
|
||||
VERSION=\$(echo \$(motus -h 2>&1) | sed 's/^.*Version: //; s/References.*\$//')
|
||||
else
|
||||
VERSION=\$(grep motus $db/db_mOTU_versions | sed 's/motus\\t//g')
|
||||
fi
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
mOTUs: \$VERSION
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
61
modules/motus/profile/meta.yml
Normal file
61
modules/motus/profile/meta.yml
Normal file
|
@ -0,0 +1,61 @@
|
|||
name: "motus_profile"
|
||||
description: Taxonomic meta-omics profiling using universal marker genes
|
||||
keywords:
|
||||
- classify
|
||||
- metagenomics
|
||||
- fastq
|
||||
- taxonomic profiling
|
||||
tools:
|
||||
- "motus":
|
||||
description: "Marker gene-based OTU (mOTU) profiling"
|
||||
homepage: "https://motu-tool.org/"
|
||||
documentation: "https://github.com/motu-tool/mOTUs/wiki"
|
||||
tool_dev_url: "https://github.com/motu-tool/mOTUs"
|
||||
doi: "10.1038/s41467-019-08844-4"
|
||||
licence: "['GPL v3']"
|
||||
|
||||
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/fasta files of size 1 and 2 for single-end and paired-end data,
|
||||
respectively.
|
||||
Or the intermediate bam file mapped by bwa to the mOTUs database or
|
||||
the output bam file from motus profile.
|
||||
Or the intermediate mgc read counts table.
|
||||
pattern: "*.{fastq,fq,fasta,fa,fastq.gz,fq.gz,fasta.gz,fa.gz,.bam,.mgc}"
|
||||
- db:
|
||||
type: directory
|
||||
description: |
|
||||
mOTUs database downloaded by `motus downloadDB`
|
||||
|
||||
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"
|
||||
- out:
|
||||
type: file
|
||||
description: Results with taxonomic classification of each read
|
||||
pattern: "*.out"
|
||||
- bam:
|
||||
type: file
|
||||
description: Optional intermediate sorted BAM file from BWA
|
||||
pattern: "*.{bam}"
|
||||
- mgc:
|
||||
type: file
|
||||
description: Optional intermediate mgc read count table file saved with `-M`.
|
||||
pattern: "*.{mgc}"
|
||||
|
||||
authors:
|
||||
- "@jianhong"
|
|
@ -2,10 +2,10 @@ process PICARD_ADDORREPLACEREADGROUPS {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_CLEANSAM {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_COLLECTHSMETRICS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
@ -24,7 +24,7 @@ process PICARD_COLLECTHSMETRICS {
|
|||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def reference = fasta ? "-R $fasta" : ""
|
||||
def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
|
||||
|
||||
def avail_mem = 3
|
||||
if (!task.memory) {
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_COLLECTMULTIPLEMETRICS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
@ -22,6 +22,7 @@ process PICARD_COLLECTMULTIPLEMETRICS {
|
|||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
|
||||
def avail_mem = 3
|
||||
if (!task.memory) {
|
||||
log.info '[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
||||
|
@ -35,7 +36,7 @@ process PICARD_COLLECTMULTIPLEMETRICS {
|
|||
$args \\
|
||||
--INPUT $bam \\
|
||||
--OUTPUT ${prefix}.CollectMultipleMetrics \\
|
||||
--REFERENCE_SEQUENCE $fasta
|
||||
$reference
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_COLLECTWGSMETRICS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
@ -34,7 +34,7 @@ process PICARD_COLLECTWGSMETRICS {
|
|||
$args \\
|
||||
--INPUT $bam \\
|
||||
--OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\
|
||||
--REFERENCE_SEQUENCE $fasta
|
||||
--REFERENCE_SEQUENCE ${fasta}
|
||||
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_CREATESEQUENCEDICTIONARY {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fasta)
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_CROSSCHECKFINGERPRINTS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input1)
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_FILTERSAMREADS {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam), path(readlist)
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_FIXMATEINFORMATION {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_LIFTOVERVCF {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input_vcf)
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_MERGESAMFILES {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bams)
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_SORTSAM {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
@ -2,10 +2,10 @@ process PICARD_SORTVCF {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
|
|
55
modules/snippy/run/main.nf
Normal file
55
modules/snippy/run/main.nf
Normal file
|
@ -0,0 +1,55 @@
|
|||
process SNIPPY_RUN {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2' :
|
||||
'quay.io/biocontainers/snippy:4.6.0--hdfd78af_2' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
path reference
|
||||
|
||||
output:
|
||||
tuple val(meta), path("${prefix}/${prefix}.tab") , emit: tab
|
||||
tuple val(meta), path("${prefix}/${prefix}.csv") , emit: csv
|
||||
tuple val(meta), path("${prefix}/${prefix}.html") , emit: html
|
||||
tuple val(meta), path("${prefix}/${prefix}.vcf") , emit: vcf
|
||||
tuple val(meta), path("${prefix}/${prefix}.bed") , emit: bed
|
||||
tuple val(meta), path("${prefix}/${prefix}.gff") , emit: gff
|
||||
tuple val(meta), path("${prefix}/${prefix}.bam") , emit: bam
|
||||
tuple val(meta), path("${prefix}/${prefix}.bam.bai") , emit: bai
|
||||
tuple val(meta), path("${prefix}/${prefix}.log") , emit: log
|
||||
tuple val(meta), path("${prefix}/${prefix}.aligned.fa") , emit: aligned_fa
|
||||
tuple val(meta), path("${prefix}/${prefix}.consensus.fa") , emit: consensus_fa
|
||||
tuple val(meta), path("${prefix}/${prefix}.consensus.subs.fa"), emit: consensus_subs_fa
|
||||
tuple val(meta), path("${prefix}/${prefix}.raw.vcf") , emit: raw_vcf
|
||||
tuple val(meta), path("${prefix}/${prefix}.filt.vcf") , emit: filt_vcf
|
||||
tuple val(meta), path("${prefix}/${prefix}.vcf.gz") , emit: vcf_gz
|
||||
tuple val(meta), path("${prefix}/${prefix}.vcf.gz.csi") , emit: vcf_csi
|
||||
tuple val(meta), path("${prefix}/${prefix}.txt") , emit: txt
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def read_inputs = meta.single_end ? "--se ${reads[0]}" : "--R1 ${reads[0]} --R2 ${reads[1]}"
|
||||
"""
|
||||
snippy \\
|
||||
$args \\
|
||||
--cpus $task.cpus \\
|
||||
--outdir $prefix \\
|
||||
--reference $reference \\
|
||||
--prefix $prefix \\
|
||||
$read_inputs
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
snippy: \$(echo \$(snippy --version 2>&1) | sed 's/snippy //')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
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