mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
Merge branch 'nf-core:master' into maxquant
This commit is contained in:
Veit Schwämmle
GitHub
commit
2e13607a6a
158 changed files with 1327 additions and 450 deletions
|
|
@ -43,7 +43,10 @@ process ARTIC_MINION {
|
|||
summary = ""
|
||||
model = file(medaka_model).exists() ? "--medaka-model ./$medaka_model" : "--medaka-model $medaka_model"
|
||||
}
|
||||
def hd5_plugin_path = task.ext.hd5_plugin_path ? "export HDF5_PLUGIN_PATH=" + task.ext.hd5_plugin_path : "export HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin"
|
||||
"""
|
||||
$hd5_plugin_path
|
||||
|
||||
artic \\
|
||||
minion \\
|
||||
$args \\
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@ process ATAQV_ATAQV {
|
|||
conda (params.enable_conda ? "bioconda::ataqv=1.2.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/ataqv:1.2.1--py39ha23c084_2' :
|
||||
'quay.io/biocontainers/ataqv:1.2.1--py36hfdecbe1_2' }"
|
||||
'quay.io/biocontainers/ataqv:1.2.1--py39ha23c084_2' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam), path(bai), path(peak_file)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process BCFTOOLS_CONCAT {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0' :
|
||||
'quay.io/biocontainers/bcftools:1.11--h7c999a4_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
|
||||
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcfs)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process BCFTOOLS_CONSENSUS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
|
||||
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
|
||||
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(tbi), path(fasta)
|
||||
|
|
@ -18,9 +18,12 @@ process BCFTOOLS_CONSENSUS {
|
|||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
cat $fasta | bcftools consensus $vcf $args > ${prefix}.fa
|
||||
header=\$(head -n 1 ${prefix}.fa | sed 's/>//g')
|
||||
sed -i 's/\${header}/${meta.id}/g' ${prefix}.fa
|
||||
cat $fasta \\
|
||||
| bcftools \\
|
||||
consensus \\
|
||||
$vcf \\
|
||||
$args \\
|
||||
> ${prefix}.fa
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process BCFTOOLS_FILTER {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
|
||||
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
|
||||
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process BCFTOOLS_INDEX {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
|
||||
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
|
||||
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
|
|
@ -13,7 +13,7 @@ process BCFTOOLS_INDEX {
|
|||
output:
|
||||
tuple val(meta), path("*.csi"), optional:true, emit: csi
|
||||
tuple val(meta), path("*.tbi"), optional:true, emit: tbi
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process BCFTOOLS_ISEC {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
|
||||
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
|
||||
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcfs), path(tbis)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process BCFTOOLS_MERGE {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
|
||||
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
|
||||
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcfs), path(tbis)
|
||||
|
|
|
|||
|
|
@ -2,19 +2,21 @@ process BCFTOOLS_MPILEUP {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
|
||||
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
|
||||
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
path fasta
|
||||
path fasta
|
||||
val save_mpileup
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.gz") , emit: vcf
|
||||
tuple val(meta), path("*.tbi") , emit: tbi
|
||||
tuple val(meta), path("*stats.txt"), emit: stats
|
||||
tuple val(meta), path("*.mpileup") , emit: mpileup, optional: true
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
|
|
@ -22,13 +24,16 @@ process BCFTOOLS_MPILEUP {
|
|||
def args2 = task.ext.args2 ?: ''
|
||||
def args3 = task.ext.args3 ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def mpileup = save_mpileup ? "| tee ${prefix}.mpileup" : ""
|
||||
"""
|
||||
echo "${meta.id}" > sample_name.list
|
||||
|
||||
bcftools mpileup \\
|
||||
bcftools \\
|
||||
mpileup \\
|
||||
--fasta-ref $fasta \\
|
||||
$args \\
|
||||
$bam \\
|
||||
$mpileup \\
|
||||
| bcftools call --output-type v $args2 \\
|
||||
| bcftools reheader --samples sample_name.list \\
|
||||
| bcftools view --output-file ${prefix}.vcf.gz --output-type z $args3
|
||||
|
|
|
|||
|
|
@ -26,6 +26,10 @@ input:
|
|||
type: file
|
||||
description: FASTA reference file
|
||||
pattern: "*.{fasta,fa}"
|
||||
- save_mpileup:
|
||||
type: boolean
|
||||
description: Save mpileup file generated by bcftools mpileup
|
||||
patter: "*.mpileup"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process BCFTOOLS_NORM {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bcftools=1.13" : null)
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
|
||||
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
|
||||
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process BCFTOOLS_QUERY {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bcftools=1.13" : null)
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
|
||||
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
|
||||
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(index)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process BCFTOOLS_REHEADER {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bcftools=1.13" : null)
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
|
||||
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
|
||||
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
|
|
|
|||
32
modules/bcftools/sort/main.nf
Normal file
32
modules/bcftools/sort/main.nf
Normal file
|
|
@ -0,0 +1,32 @@
|
|||
process BCFTOOLS_SORT {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bcftools=1.14" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0':
|
||||
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.gz"), emit: vcf
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
bcftools \\
|
||||
sort \\
|
||||
--output ${prefix}.vcf.gz \\
|
||||
$args \\
|
||||
$vcf
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
43
modules/bcftools/sort/meta.yml
Normal file
43
modules/bcftools/sort/meta.yml
Normal file
|
|
@ -0,0 +1,43 @@
|
|||
name: bcftools_sort
|
||||
description: Sorts VCF files
|
||||
keywords:
|
||||
- sorting
|
||||
- VCF
|
||||
- variant calling
|
||||
tools:
|
||||
- sort:
|
||||
description: Sort VCF files by coordinates.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: http://www.htslib.org/doc/bcftools.html
|
||||
tool_dev_url: https://github.com/samtools/bcftools
|
||||
doi: "10.1093/bioinformatics/btp352"
|
||||
licence: ['MIT']
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: The VCF/BCF file to be sorted
|
||||
pattern: "*.{vcf.gz,vcf,bcf}"
|
||||
|
||||
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: Sorted VCF file
|
||||
pattern: "*.{vcf.gz}"
|
||||
|
||||
authors:
|
||||
- "@Gwennid"
|
||||
|
|
@ -2,10 +2,10 @@ process BCFTOOLS_STATS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
|
||||
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
|
||||
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process BCFTOOLS_VIEW {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bcftools=1.13" : null)
|
||||
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
|
||||
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
|
||||
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(index)
|
||||
|
|
|
|||
|
|
@ -2,27 +2,28 @@ process BOWTIE2_ALIGN {
|
|||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::bowtie2=2.4.2 bioconda::samtools=1.11 conda-forge::pigz=2.3.4' : null)
|
||||
conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4 bioconda::samtools=1.14 conda-forge::pigz=2.6' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0' :
|
||||
'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0' }"
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' :
|
||||
'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
path index
|
||||
val save_unaligned
|
||||
|
||||
output:
|
||||
tuple val(meta), path('*.bam'), emit: bam
|
||||
tuple val(meta), path('*.log'), emit: log
|
||||
path "versions.yml" , emit: versions
|
||||
tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq
|
||||
tuple val(meta), path('*.bam') , emit: bam
|
||||
tuple val(meta), path('*.log') , emit: log
|
||||
tuple val(meta), path('*fastq.gz'), emit: fastq, optional:true
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def args2 = task.ext.args2 ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
if (meta.single_end) {
|
||||
def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
|
||||
def unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
|
||||
"""
|
||||
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
|
||||
bowtie2 \\
|
||||
|
|
@ -42,7 +43,7 @@ process BOWTIE2_ALIGN {
|
|||
END_VERSIONS
|
||||
"""
|
||||
} else {
|
||||
def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
|
||||
def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
|
||||
"""
|
||||
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
|
||||
bowtie2 \\
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@ process BOWTIE2_BUILD {
|
|||
conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' :
|
||||
'quay.io/biocontainers/bowtie2:2.4.4--py36hd4290be_0' }"
|
||||
'quay.io/biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }"
|
||||
|
||||
input:
|
||||
path fasta
|
||||
|
|
|
|||
|
|
@ -18,30 +18,28 @@ process CAT_CAT {
|
|||
def args = task.ext.args ?: ''
|
||||
def args2 = task.ext.args2 ?: ''
|
||||
def file_list = files_in.collect { it.toString() }
|
||||
if (file_list.size > 1) {
|
||||
|
||||
// | input | output | command1 | command2 |
|
||||
// |-----------|------------|----------|----------|
|
||||
// | gzipped | gzipped | cat | |
|
||||
// | ungzipped | ungzipped | cat | |
|
||||
// | gzipped | ungzipped | zcat | |
|
||||
// | ungzipped | gzipped | cat | pigz |
|
||||
// | input | output | command1 | command2 |
|
||||
// |-----------|------------|----------|----------|
|
||||
// | gzipped | gzipped | cat | |
|
||||
// | ungzipped | ungzipped | cat | |
|
||||
// | gzipped | ungzipped | zcat | |
|
||||
// | ungzipped | gzipped | cat | pigz |
|
||||
|
||||
def in_zip = file_list[0].endsWith('.gz')
|
||||
def out_zip = file_out.endsWith('.gz')
|
||||
def command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
|
||||
def command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
|
||||
"""
|
||||
$command1 \\
|
||||
$args \\
|
||||
${file_list.join(' ')} \\
|
||||
$command2 \\
|
||||
> $file_out
|
||||
def in_zip = file_list[0].endsWith('.gz')
|
||||
def out_zip = file_out.endsWith('.gz')
|
||||
def command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
|
||||
def command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
|
||||
"""
|
||||
$command1 \\
|
||||
$args \\
|
||||
${file_list.join(' ')} \\
|
||||
$command2 \\
|
||||
> $file_out
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,13 +1,12 @@
|
|||
def VERSION = '0.1' // Version information not provided by tool on CLI
|
||||
|
||||
process CHROMAP_INDEX {
|
||||
tag '$fasta'
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::chromap=0.1 bioconda::samtools=1.13" : null)
|
||||
conda (params.enable_conda ? "bioconda::chromap=0.1.5" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0' :
|
||||
'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0' }"
|
||||
'https://depot.galaxyproject.org/singularity/chromap:0.1.5--h9a82719_0' :
|
||||
'quay.io/biocontainers/chromap:0.1.5--h9a82719_0' }"
|
||||
|
||||
|
||||
input:
|
||||
path fasta
|
||||
|
|
@ -29,8 +28,7 @@ process CHROMAP_INDEX {
|
|||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
chromap: $VERSION
|
||||
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
chromap: \$(echo \$(chromap --version 2>&1))
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@ process CUTADAPT {
|
|||
conda (params.enable_conda ? 'bioconda::cutadapt=3.4' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/cutadapt:3.4--py39h38f01e4_1' :
|
||||
'quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1' }"
|
||||
'quay.io/biocontainers/cutadapt:3.4--py39h38f01e4_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
|
|
|
|||
44
modules/deepvariant/main.nf
Normal file
44
modules/deepvariant/main.nf
Normal file
|
|
@ -0,0 +1,44 @@
|
|||
process DEEPVARIANT {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
|
||||
if (params.enable_conda) {
|
||||
exit 1, "Conda environments cannot be used when using the DeepVariant tool. Please use docker or singularity containers."
|
||||
}
|
||||
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'google/deepvariant:1.3.0' :
|
||||
'google/deepvariant:1.3.0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(index), path(intervals)
|
||||
path(fasta)
|
||||
path(fai)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.vcf.gz") , emit: vcf
|
||||
tuple val(meta), path("*g.vcf.gz"), emit: gvcf
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def regions = intervals ? "--regions ${intervals}" : ""
|
||||
|
||||
"""
|
||||
/opt/deepvariant/bin/run_deepvariant \\
|
||||
--ref=${fasta} \\
|
||||
--reads=${input} \\
|
||||
--output_vcf=${prefix}.vcf.gz \\
|
||||
--output_gvcf=${prefix}.g.vcf.gz \\
|
||||
${args} \\
|
||||
${regions} \\
|
||||
--num_shards=${task.cpus}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
deepvariant: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
62
modules/deepvariant/meta.yml
Normal file
62
modules/deepvariant/meta.yml
Normal file
|
|
@ -0,0 +1,62 @@
|
|||
name: deepvariant
|
||||
description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
|
||||
keywords:
|
||||
- variant calling
|
||||
- machine learning
|
||||
tools:
|
||||
- deepvariant:
|
||||
description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
|
||||
homepage: https://github.com/google/deepvariant
|
||||
documentation: https://github.com/google/deepvariant
|
||||
tool_dev_url: https://github.com/google/deepvariant
|
||||
doi: "https://doi.org/10.1038/nbt.4235"
|
||||
licence: ['BSD-3-clause']
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- input:
|
||||
type: file
|
||||
description: BAM/CRAM file
|
||||
pattern: "*.bam/cram"
|
||||
- index:
|
||||
type: file
|
||||
description: Index of BAM/CRAM file
|
||||
pattern: "*.bai/crai"
|
||||
- interval:
|
||||
type: file
|
||||
description: Interval file for targeted regions
|
||||
pattern: "*.bed"
|
||||
- fasta:
|
||||
type: file
|
||||
description: The reference fasta file
|
||||
pattern: "*.fasta"
|
||||
- fai:
|
||||
type: file
|
||||
description: Index of reference fasta file
|
||||
pattern: "*.fai"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: Compressed VCF file
|
||||
pattern: "*.vcf.gz"
|
||||
- gvcf:
|
||||
type: file
|
||||
description: Compressed GVCF file
|
||||
pattern: "*.g.vcf.gz"
|
||||
- version:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "*.{version.txt}"
|
||||
|
||||
authors:
|
||||
- "@abhi18av"
|
||||
|
|
@ -2,16 +2,16 @@ process DSHBIO_EXPORTSEGMENTS {
|
|||
tag "${meta.id}"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.6" : null)
|
||||
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.6--hdfd78af_0' :
|
||||
'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
|
||||
'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(gfa)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.fa"), emit: fasta
|
||||
tuple val(meta), path("*.fa.gz"), emit: fasta
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
|
|
@ -22,7 +22,7 @@ process DSHBIO_EXPORTSEGMENTS {
|
|||
export-segments \\
|
||||
$args \\
|
||||
-i $gfa \\
|
||||
-o ${prefix}.fa
|
||||
-o ${prefix}.fa.gz
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
|
|||
|
|
@ -21,8 +21,8 @@ input:
|
|||
e.g. [ id:'test', single_end:false ]
|
||||
- gfa:
|
||||
type: file
|
||||
description: Assembly segments in GFA 1.0 format
|
||||
pattern: "*.{gfa}"
|
||||
description: Assembly segments in uncompressed or compressed GFA 1.0 format
|
||||
pattern: "*.{gfa|gfa.bgz|gfa.gz|gfa.zst}"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
|
|
@ -31,8 +31,8 @@ output:
|
|||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: Assembly segment sequences in FASTA format
|
||||
pattern: "*.{fa}"
|
||||
description: Assembly segment sequences in gzipped FASTA format
|
||||
pattern: "*.{fa.gz}"
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process DSHBIO_FILTERBED {
|
|||
tag "${meta.id}"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.6" : null)
|
||||
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.6--hdfd78af_0' :
|
||||
'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
|
||||
'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bed)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process DSHBIO_FILTERGFF3 {
|
|||
tag "${meta.id}"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.6" : null)
|
||||
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.6--hdfd78af_0' :
|
||||
'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
|
||||
'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(gff3)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process DSHBIO_SPLITBED {
|
|||
tag "${meta.id}"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.6" : null)
|
||||
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.6--hdfd78af_0' :
|
||||
'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
|
||||
'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bed)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process DSHBIO_SPLITGFF3 {
|
|||
tag "${meta.id}"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.6" : null)
|
||||
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.6--hdfd78af_0' :
|
||||
'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
|
||||
'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(gff3)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process FASTP {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::fastp=0.20.1' : null)
|
||||
conda (params.enable_conda ? 'bioconda::fastp=0.23.2' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/fastp:0.20.1--h8b12597_0' :
|
||||
'quay.io/biocontainers/fastp:0.20.1--h8b12597_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' :
|
||||
'quay.io/biocontainers/fastp:0.23.2--h79da9fb_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@ process FGBIO_FASTQTOBAM {
|
|||
|
||||
output:
|
||||
tuple val(meta), path("*_umi_converted.bam"), emit: umibam
|
||||
path "versions.yml" , emit: version
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_APPLYBQSR {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_APPLYVQSR {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(tbi), path(recal), path(recalidx), path(tranches)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index), path(intervals)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_BEDTOINTERVALLIST {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bed)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_CALCULATECONTAMINATION {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(pileup), path(matched)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_CREATESEQUENCEDICTIONARY {
|
|||
tag "$fasta"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
path fasta
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_CREATESOMATICPANELOFNORMALS {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(genomicsdb)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(cram)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_FASTQTOSAM {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_FILTERMUTECTCALLS {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(tbi), path(stats), path(orientationbias), path(segmentation), path(contaminationfile), val(contaminationest)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_GATHERBQSRREPORTS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(recal_table)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_GENOMICSDBIMPORT {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(tbi), path(intervalfile), val(intervalval), path(wspace)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_GENOTYPEGVCFS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(gvcf), path(gvcf_index), path(intervals)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_GETPILEUPSUMMARIES {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam), path(bai)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_HAPLOTYPECALLER {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index), path(intervals)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_INDEXFEATUREFILE {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(feature_file)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOOLS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(interval_list)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_LEARNREADORIENTATIONMODEL {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(f1r2)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_MARKDUPLICATES {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bams)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_MERGEBAMALIGNMENT {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(aligned)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_MERGEVCFS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcfs)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_MUTECT2 {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta) , path(input) , path(input_index) , val(which_norm)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_REVERTSAM {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_SAMTOFASTQ {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_SPLITNCIGARREADS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_VARIANTFILTRATION {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(vcf_tbi)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process GATK4_VARIANTRECALIBRATOR {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
|
||||
container "${ 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' }"
|
||||
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf) , path(tbi)
|
||||
|
|
|
|||
|
|
@ -2,6 +2,7 @@ def VERSION = '1.5.0' // Version information not provided by tool on CLI
|
|||
|
||||
process GTDBTK_CLASSIFYWF {
|
||||
tag "${meta.assembler}-${meta.id}"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::gtdbtk=1.5.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@ process IDR {
|
|||
conda (params.enable_conda ? "bioconda::idr=2.0.4.2" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/idr:2.0.4.2--py39hcbe4a3b_5' :
|
||||
'quay.io/biocontainers/idr:2.0.4.2--py38h9af456f_5' }"
|
||||
'quay.io/biocontainers/idr:2.0.4.2--py39hcbe4a3b_5' }"
|
||||
|
||||
input:
|
||||
path peaks
|
||||
|
|
|
|||
|
|
@ -9,7 +9,8 @@ process IVAR_CONSENSUS {
|
|||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
path fasta
|
||||
path fasta
|
||||
val save_mpileup
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.fa") , emit: fasta
|
||||
|
|
@ -21,14 +22,16 @@ process IVAR_CONSENSUS {
|
|||
def args = task.ext.args ?: ''
|
||||
def args2 = task.ext.args2 ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : ""
|
||||
def mpileup = save_mpileup ? "| tee ${prefix}.mpileup" : ""
|
||||
"""
|
||||
samtools mpileup \\
|
||||
samtools \\
|
||||
mpileup \\
|
||||
--reference $fasta \\
|
||||
$args2 \\
|
||||
$bam | \\
|
||||
$save_mpileup \\
|
||||
ivar consensus \\
|
||||
$bam \\
|
||||
$mpileup \\
|
||||
| ivar \\
|
||||
consensus \\
|
||||
$args \\
|
||||
-p $prefix
|
||||
|
||||
|
|
|
|||
|
|
@ -25,6 +25,10 @@ input:
|
|||
type: file
|
||||
description: The reference sequence used for mapping and generating the BAM file
|
||||
pattern: "*.fa"
|
||||
- save_mpileup:
|
||||
type: boolean
|
||||
description: Save mpileup file generated by ivar consensus
|
||||
patter: "*.mpileup"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
|
|
|
|||
|
|
@ -11,6 +11,7 @@ process IVAR_VARIANTS {
|
|||
tuple val(meta), path(bam)
|
||||
path fasta
|
||||
path gff
|
||||
val save_mpileup
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.tsv") , emit: tsv
|
||||
|
|
@ -21,15 +22,17 @@ process IVAR_VARIANTS {
|
|||
def args = task.ext.args ?: ''
|
||||
def args2 = task.ext.args2 ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : ""
|
||||
def features = params.gff ? "-g $gff" : ""
|
||||
def features = gff ? "-g $gff" : ""
|
||||
def mpileup = save_mpileup ? "| tee ${prefix}.mpileup" : ""
|
||||
"""
|
||||
samtools mpileup \\
|
||||
samtools \\
|
||||
mpileup \\
|
||||
$args2 \\
|
||||
--reference $fasta \\
|
||||
$bam | \\
|
||||
$save_mpileup \\
|
||||
ivar variants \\
|
||||
$bam \\
|
||||
$mpileup \\
|
||||
| ivar \\
|
||||
variants \\
|
||||
$args \\
|
||||
$features \\
|
||||
-r $fasta \\
|
||||
|
|
|
|||
|
|
@ -29,6 +29,10 @@ input:
|
|||
type: file
|
||||
description: A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done.
|
||||
patter: "*.gff"
|
||||
- save_mpileup:
|
||||
type: boolean
|
||||
description: Save mpileup file generated by ivar variants
|
||||
patter: "*.mpileup"
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
|
|
|
|||
|
|
@ -9,7 +9,7 @@ process JUPYTERNOTEBOOK {
|
|||
//ipykernel, jupytext, papermill and nbconvert Python packages.
|
||||
conda (params.enable_conda ? "ipykernel=6.0.3 jupytext=1.11.4 nbconvert=6.1.0 papermill=2.3.3 matplotlib=3.4.2" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963%3A879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' :
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' :
|
||||
'quay.io/biocontainers/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' }"
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process KRAKEN2_KRAKEN2 {
|
|||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::kraken2=2.1.1 conda-forge::pigz=2.6' : null)
|
||||
conda (params.enable_conda ? 'bioconda::kraken2=2.1.2 conda-forge::pigz=2.6' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:941789bd7fe00db16531c26de8bf3c5c985242a5-0' :
|
||||
'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:941789bd7fe00db16531c26de8bf3c5c985242a5-0' }"
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' :
|
||||
'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
|
|
|
|||
|
|
@ -8,8 +8,6 @@ process KRONA_KRONADB {
|
|||
'https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5' :
|
||||
'quay.io/biocontainers/krona:2.7.1--pl526_5' }"
|
||||
|
||||
input:
|
||||
|
||||
output:
|
||||
path 'taxonomy/taxonomy.tab', emit: db
|
||||
path "versions.yml" , emit: versions
|
||||
|
|
|
|||
|
|
@ -1,6 +1,5 @@
|
|||
process MALT_RUN {
|
||||
|
||||
label 'process_high_memory'
|
||||
label 'process_high'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::malt=0.53" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
|
|
|
|||
34
modules/mash/dist/main.nf
vendored
Normal file
34
modules/mash/dist/main.nf
vendored
Normal file
|
|
@ -0,0 +1,34 @@
|
|||
process MASH_DIST {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::mash=2.3" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1' :
|
||||
'quay.io/biocontainers/mash:2.3--he348c14_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(query)
|
||||
path reference
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.txt"), emit: dist
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
mash \\
|
||||
dist \\
|
||||
-p $task.cpus \\
|
||||
$args \\
|
||||
$reference \\
|
||||
$query > ${prefix}.txt
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
mash: \$(mash --version 2>&1)
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
45
modules/mash/dist/meta.yml
vendored
Normal file
45
modules/mash/dist/meta.yml
vendored
Normal file
|
|
@ -0,0 +1,45 @@
|
|||
name: mash_dist
|
||||
description: Calculate Mash distances between reference and query seqeunces
|
||||
keywords:
|
||||
- mash/dist
|
||||
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 ]
|
||||
- reference:
|
||||
type: file
|
||||
description: FASTA, FASTQ or Mash sketch
|
||||
pattern: "*.{fasta,fasta.gz,fastq,fastq.gz,msh}"
|
||||
- query:
|
||||
type: file
|
||||
description: FASTA, FASTQ or Mash sketch
|
||||
pattern: "*.{fasta,fasta.gz,fastq,fastq.gz,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"
|
||||
- dist:
|
||||
type: file
|
||||
description: The results from mash dist
|
||||
pattern: "*.txt"
|
||||
|
||||
authors:
|
||||
- "@rpetit3"
|
||||
|
|
@ -2,10 +2,10 @@ process MINIA {
|
|||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::minia=3.2.4" : null)
|
||||
conda (params.enable_conda ? "bioconda::minia=3.2.6" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/minia:3.2.4--he513fc3_0' :
|
||||
'quay.io/biocontainers/minia:3.2.4--he513fc3_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/minia:3.2.6--h9a82719_0' :
|
||||
'quay.io/biocontainers/minia:3.2.6--h9a82719_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process NANOPLOT {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::nanoplot=1.38.0' : null)
|
||||
conda (params.enable_conda ? 'bioconda::nanoplot=1.39.0' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/nanoplot:1.38.0--pyhdfd78af_0' :
|
||||
'quay.io/biocontainers/nanoplot:1.38.0--pyhdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/nanoplot:1.39.0--pyhdfd78af_0' :
|
||||
'quay.io/biocontainers/nanoplot:1.39.0--pyhdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(ontfile)
|
||||
|
|
|
|||
39
modules/nextclade/datasetget/main.nf
Normal file
39
modules/nextclade/datasetget/main.nf
Normal file
|
|
@ -0,0 +1,39 @@
|
|||
process NEXTCLADE_DATASETGET {
|
||||
tag "$dataset"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::nextclade=1.9.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/nextclade:1.9.0--h9ee0642_0' :
|
||||
'quay.io/biocontainers/nextclade:1.9.0--h9ee0642_0' }"
|
||||
|
||||
input:
|
||||
val dataset
|
||||
val reference
|
||||
val tag
|
||||
|
||||
output:
|
||||
path "$prefix" , emit: dataset
|
||||
path "versions.yml", emit: versions
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
prefix = task.ext.prefix ?: "${dataset}"
|
||||
def fasta = reference ? "--reference ${reference}" : ''
|
||||
def version = tag ? "--tag ${tag}" : ''
|
||||
"""
|
||||
nextclade \\
|
||||
dataset \\
|
||||
get \\
|
||||
$args \\
|
||||
--name $dataset \\
|
||||
$fasta \\
|
||||
$version \\
|
||||
--output-dir $prefix
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
nextclade: \$(nextclade --version 2>&1)
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
42
modules/nextclade/datasetget/meta.yml
Normal file
42
modules/nextclade/datasetget/meta.yml
Normal file
|
|
@ -0,0 +1,42 @@
|
|||
name: nextclade_datasetget
|
||||
description: Get dataset for SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation)
|
||||
keywords:
|
||||
- nextclade
|
||||
- variant
|
||||
- consensus
|
||||
tools:
|
||||
- nextclade:
|
||||
description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks
|
||||
homepage: https://github.com/nextstrain/nextclade
|
||||
documentation: https://github.com/nextstrain/nextclade
|
||||
tool_dev_url: https://github.com/nextstrain/nextclade
|
||||
doi: ""
|
||||
licence: ['MIT']
|
||||
|
||||
input:
|
||||
- dataset:
|
||||
type: string
|
||||
description: Name of dataset to retrieve. A list of available datasets can be obtained using the nextclade dataset list command.
|
||||
pattern: ".+"
|
||||
- reference:
|
||||
type: string
|
||||
description: Accession id to download dataset based on a particular reference sequence. A list of available datasets can be obtained using the nextclade dataset list command.
|
||||
pattern: ".+"
|
||||
- tag:
|
||||
type: string
|
||||
description: Version tag of the dataset to download. A list of available datasets can be obtained using the nextclade dataset list command.
|
||||
pattern: ".+"
|
||||
|
||||
output:
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- prefix:
|
||||
type: path
|
||||
description: A directory containing the dataset files needed for nextclade run
|
||||
pattern: "prefix"
|
||||
|
||||
authors:
|
||||
- "@antunderwood"
|
||||
- "@drpatelh"
|
||||
|
|
@ -1,40 +0,0 @@
|
|||
process NEXTCLADE {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::nextclade_js=0.14.4" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/nextclade_js:0.14.4--h9ee0642_0' :
|
||||
'quay.io/biocontainers/nextclade_js:0.14.4--h9ee0642_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fasta)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("${prefix}.csv") , emit: csv
|
||||
tuple val(meta), path("${prefix}.json") , emit: json
|
||||
tuple val(meta), path("${prefix}.tree.json") , emit: json_tree
|
||||
tuple val(meta), path("${prefix}.tsv") , emit: tsv
|
||||
tuple val(meta), path("${prefix}.clades.tsv"), optional:true, emit: tsv_clades
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
nextclade \\
|
||||
$args \\
|
||||
--jobs $task.cpus \\
|
||||
--input-fasta $fasta \\
|
||||
--output-json ${prefix}.json \\
|
||||
--output-csv ${prefix}.csv \\
|
||||
--output-tsv ${prefix}.tsv \\
|
||||
--output-tsv-clades-only ${prefix}.clades.tsv \\
|
||||
--output-tree ${prefix}.tree.json
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
nextclade: \$(nextclade --version 2>&1)
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
42
modules/nextclade/run/main.nf
Normal file
42
modules/nextclade/run/main.nf
Normal file
|
|
@ -0,0 +1,42 @@
|
|||
process NEXTCLADE_RUN {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::nextclade=1.9.0" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/nextclade:1.9.0--h9ee0642_0' :
|
||||
'quay.io/biocontainers/nextclade:1.9.0--h9ee0642_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fasta)
|
||||
path dataset
|
||||
|
||||
output:
|
||||
tuple val(meta), path("${prefix}.csv") , emit: csv
|
||||
tuple val(meta), path("${prefix}.tsv") , emit: tsv
|
||||
tuple val(meta), path("${prefix}.json") , emit: json
|
||||
tuple val(meta), path("${prefix}.tree.json"), emit: json_tree
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
nextclade \\
|
||||
run \\
|
||||
$args \\
|
||||
--jobs $task.cpus \\
|
||||
--input-fasta $fasta \\
|
||||
--input-dataset $dataset \\
|
||||
--output-csv ${prefix}.csv \\
|
||||
--output-tsv ${prefix}.tsv \\
|
||||
--output-json ${prefix}.json \\
|
||||
--output-tree ${prefix}.tree.json \\
|
||||
--output-basename ${prefix}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
nextclade: \$(nextclade --version 2>&1)
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
21
modules/nextclade/meta.yml → modules/nextclade/run/meta.yml
Executable file → Normal file
21
modules/nextclade/meta.yml → modules/nextclade/run/meta.yml
Executable file → Normal file
|
|
@ -1,17 +1,17 @@
|
|||
name: nextclade
|
||||
description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (Javascript implementation)
|
||||
name: nextclade_run
|
||||
description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation)
|
||||
keywords:
|
||||
- nextclade
|
||||
- variant
|
||||
- consensus
|
||||
tools:
|
||||
- nextclade:
|
||||
description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (Javascript implementation)
|
||||
homepage: https://clades.nextstrain.org
|
||||
documentation: None
|
||||
description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks
|
||||
homepage: https://github.com/nextstrain/nextclade
|
||||
documentation: https://github.com/nextstrain/nextclade
|
||||
tool_dev_url: https://github.com/nextstrain/nextclade
|
||||
doi: ""
|
||||
licence: ["MIT"]
|
||||
licence: ['MIT']
|
||||
|
||||
input:
|
||||
- meta:
|
||||
|
|
@ -19,6 +19,10 @@ input:
|
|||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- dataset:
|
||||
type: path
|
||||
description: Path containing the dataset files obtained by running nextclade dataset get
|
||||
pattern: "*"
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA file containing one or more consensus sequences
|
||||
|
|
@ -50,10 +54,7 @@ output:
|
|||
type: file
|
||||
description: TSV file containing nextclade results
|
||||
pattern: "*.{tsv}"
|
||||
- tsv_clades:
|
||||
type: file
|
||||
description: TSV file containing nextclade results for clades only
|
||||
pattern: "*.{clades.tsv}"
|
||||
|
||||
authors:
|
||||
- "@antunderwood"
|
||||
- "@drpatelh"
|
||||
|
|
@ -2,10 +2,10 @@ process PANGOLIN {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? 'bioconda::pangolin=3.1.11' : null)
|
||||
conda (params.enable_conda ? 'bioconda::pangolin=3.1.17' : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/pangolin:3.1.11--pyhdfd78af_1' :
|
||||
'quay.io/biocontainers/pangolin:3.1.11--pyhdfd78af_1' }"
|
||||
'https://depot.galaxyproject.org/singularity/pangolin:3.1.17--pyhdfd78af_0' :
|
||||
'quay.io/biocontainers/pangolin:3.1.17--pyhdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fasta)
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@ process PARACLU {
|
|||
|
||||
conda (params.enable_conda ? "bioconda::paraclu=10" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/paraclu%3A10--h9a82719_1' :
|
||||
'https://depot.galaxyproject.org/singularity/paraclu:10--h9a82719_1' :
|
||||
'quay.io/biocontainers/paraclu:10--h9a82719_1' }"
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process PICARD_COLLECTHSMETRICS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process PICARD_COLLECTMULTIPLEMETRICS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process PICARD_COLLECTWGSMETRICS {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam), path(bai)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process PICARD_FILTERSAMREADS {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam), path(readlist)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process PICARD_MERGESAMFILES {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bams)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process PICARD_SORTSAM {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
|||
|
|
@ -4,7 +4,7 @@ process PIRATE {
|
|||
|
||||
conda (params.enable_conda ? "bioconda::pirate=1.0.4" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/pirate%3A1.0.4--hdfd78af_1' :
|
||||
'https://depot.galaxyproject.org/singularity/pirate:1.0.4--hdfd78af_1' :
|
||||
'quay.io/biocontainers/pirate:1.0.4--hdfd78af_1' }"
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@ process PORECHOP {
|
|||
conda (params.enable_conda ? "bioconda::porechop=0.2.4" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2' :
|
||||
'quay.io/biocontainers/porechop:0.2.4--py38h8c62d01_2' }"
|
||||
'quay.io/biocontainers/porechop:0.2.4--py39h7cff6ad_2' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
|
|
|
|||
|
|
@ -9,7 +9,7 @@ process RMARKDOWNNOTEBOOK {
|
|||
//yaml and rmarkdown R packages.
|
||||
conda (params.enable_conda ? "r-base=4.1.0 r-rmarkdown=2.9 r-yaml=2.2.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5%3A0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' :
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' :
|
||||
'quay.io/biocontainers/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' }"
|
||||
|
||||
input:
|
||||
|
|
|
|||
|
|
@ -22,8 +22,9 @@ process SAMTOOLS_AMPLICONCLIP {
|
|||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def rejects = save_cliprejects ? "--rejects-file ${prefix}.cliprejects.bam" : ""
|
||||
def stats = save_clipstats ? "-f ${prefix}.clipstats.txt" : ""
|
||||
def rejects = save_cliprejects ? "--rejects-file ${prefix}.cliprejects.bam" : ""
|
||||
def stats = save_clipstats ? "-f ${prefix}.clipstats.txt" : ""
|
||||
if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
|
||||
"""
|
||||
samtools \\
|
||||
ampliconclip \\
|
||||
|
|
|
|||
|
|
@ -9,11 +9,11 @@ process SAMTOOLS_BAM2FQ {
|
|||
|
||||
input:
|
||||
tuple val(meta), path(inputbam)
|
||||
val(split)
|
||||
val split
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.fq.gz"), emit: reads
|
||||
path "versions.yml" , emit: versions
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
|
|
@ -50,5 +50,4 @@ process SAMTOOLS_BAM2FQ {
|
|||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -12,12 +12,11 @@ process SAMTOOLS_DEPTH {
|
|||
|
||||
output:
|
||||
tuple val(meta), path("*.tsv"), emit: tsv
|
||||
path "versions.yml" , emit: versions
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
||||
"""
|
||||
samtools \\
|
||||
depth \\
|
||||
|
|
|
|||
|
|
@ -11,13 +11,16 @@ process SAMTOOLS_FAIDX {
|
|||
tuple val(meta), path(fasta)
|
||||
|
||||
output:
|
||||
tuple val(meta), path ("*.fai") , emit: fai
|
||||
path "versions.yml" , emit: versions
|
||||
tuple val(meta), path ("*.fai"), emit: fai
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
"""
|
||||
samtools faidx $fasta
|
||||
samtools \\
|
||||
faidx \\
|
||||
$fasta
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
|
|
|
|||
|
|
@ -18,13 +18,14 @@ process SAMTOOLS_FASTQ {
|
|||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def endedness = meta.single_end ? "-0 ${prefix}.fastq.gz" : "-1 ${prefix}_1.fastq.gz -2 ${prefix}_2.fastq.gz"
|
||||
|
||||
"""
|
||||
samtools fastq \\
|
||||
samtools \\
|
||||
fastq \\
|
||||
$args \\
|
||||
--threads ${task.cpus-1} \\
|
||||
$endedness \\
|
||||
$bam
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
|
|
|
|||
|
|
@ -18,7 +18,6 @@ process SAMTOOLS_FIXMATE {
|
|||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
|
||||
|
||||
"""
|
||||
samtools \\
|
||||
fixmate \\
|
||||
|
|
|
|||
|
|
@ -17,7 +17,12 @@ process SAMTOOLS_FLAGSTAT {
|
|||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
"""
|
||||
samtools flagstat --threads ${task.cpus-1} $bam > ${bam}.flagstat
|
||||
samtools \\
|
||||
flagstat \\
|
||||
--threads ${task.cpus-1} \\
|
||||
$bam \\
|
||||
> ${bam}.flagstat
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
|
|
|
|||
|
|
@ -17,7 +17,11 @@ process SAMTOOLS_IDXSTATS {
|
|||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
"""
|
||||
samtools idxstats $bam > ${bam}.idxstats
|
||||
samtools \\
|
||||
idxstats \\
|
||||
$bam \\
|
||||
> ${bam}.idxstats
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
|
|
|
|||
|
|
@ -19,7 +19,11 @@ process SAMTOOLS_INDEX {
|
|||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
"""
|
||||
samtools index -@ ${task.cpus-1} $args $input
|
||||
samtools \\
|
||||
index \\
|
||||
-@ ${task.cpus-1} \\
|
||||
$args \\
|
||||
$input
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
|
|||
|
|
@ -12,7 +12,7 @@ process SAMTOOLS_MERGE {
|
|||
path fasta
|
||||
|
||||
output:
|
||||
tuple val(meta), path("${prefix}.bam"), optional:true, emit: bam
|
||||
tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam
|
||||
tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
|
|
@ -22,7 +22,13 @@ process SAMTOOLS_MERGE {
|
|||
def file_type = input_files[0].getExtension()
|
||||
def reference = fasta ? "--reference ${fasta}" : ""
|
||||
"""
|
||||
samtools merge --threads ${task.cpus-1} $args ${reference} ${prefix}.${file_type} $input_files
|
||||
samtools \\
|
||||
merge \\
|
||||
--threads ${task.cpus-1} \\
|
||||
$args \\
|
||||
${reference} \\
|
||||
${prefix}.${file_type} \\
|
||||
$input_files
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
|
|||
Some files were not shown because too many files have changed in this diff Show more
Loading…
Reference in a new issue