mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-21 10:48:18 +00:00
Merge branch 'master' into seqtk/seq-indent-fix
This commit is contained in:
Sateesh Peri
GitHub
commit
14825510cb
109 changed files with 1866 additions and 155 deletions
6
.github/PULL_REQUEST_TEMPLATE.md
vendored
6
.github/PULL_REQUEST_TEMPLATE.md
vendored
|
|
@ -27,6 +27,6 @@ Closes #XXX <!-- If this PR fixes an issue, please link it here! -->
|
|||
- [ ] Add a resource `label`
|
||||
- [ ] Use BioConda and BioContainers if possible to fulfil software requirements.
|
||||
- Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
|
||||
- [ ] `PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd`
|
||||
- [ ] `PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd`
|
||||
- [ ] `PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd`
|
||||
- [ ] `PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware`
|
||||
- [ ] `PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware`
|
||||
- [ ] `PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware`
|
||||
|
|
|
|||
2
.github/workflows/pytest-workflow.yml
vendored
2
.github/workflows/pytest-workflow.yml
vendored
|
|
@ -86,7 +86,7 @@ jobs:
|
|||
# Test the module
|
||||
- name: Run pytest-workflow
|
||||
# only use one thread for pytest-workflow to avoid race condition on conda cache.
|
||||
run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof
|
||||
run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware
|
||||
|
||||
- name: Output log on failure
|
||||
if: failure()
|
||||
|
|
|
|||
|
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@ -11,9 +11,15 @@ process ADAPTERREMOVAL {
|
|||
tuple val(meta), path(reads)
|
||||
|
||||
output:
|
||||
tuple val(meta), path('*.fastq.gz'), emit: reads
|
||||
tuple val(meta), path('*.log') , emit: log
|
||||
path "versions.yml" , emit: versions
|
||||
tuple val(meta), path('*.truncated.gz') , optional: true, emit: singles_truncated
|
||||
tuple val(meta), path('*.discarded.gz') , optional: true, emit: discarded
|
||||
tuple val(meta), path('*.pair1.truncated.gz') , optional: true, emit: pair1_truncated
|
||||
tuple val(meta), path('*.pair2.truncated.gz') , optional: true, emit: pair2_truncated
|
||||
tuple val(meta), path('*.collapsed.gz') , optional: true, emit: collapsed
|
||||
tuple val(meta), path('*.collapsed.truncated') , optional: true, emit: collapsed_truncated
|
||||
tuple val(meta), path('*paired.gz') , optional: true, emit: paired_interleaved
|
||||
tuple val(meta), path('*.log') , emit: log
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
|
@ -28,30 +34,27 @@ process ADAPTERREMOVAL {
|
|||
--file1 $reads \\
|
||||
$args \\
|
||||
--basename $prefix \\
|
||||
--threads $task.cpus \\
|
||||
--threads ${task.cpus} \\
|
||||
--settings ${prefix}.log \\
|
||||
--output1 ${prefix}.trimmed.fastq.gz \\
|
||||
--seed 42 \\
|
||||
--gzip \\
|
||||
--gzip
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
|
||||
END_VERSIONS
|
||||
"""
|
||||
} else if (!meta.single_end && !meta.collapse) {
|
||||
} else if (!meta.single_end ) {
|
||||
"""
|
||||
AdapterRemoval \\
|
||||
--file1 ${reads[0]} \\
|
||||
--file2 ${reads[1]} \\
|
||||
$args \\
|
||||
--basename $prefix \\
|
||||
--threads $task.cpus \\
|
||||
--threads ${task.cpus} \\
|
||||
--settings ${prefix}.log \\
|
||||
--output1 ${prefix}.pair1.trimmed.fastq.gz \\
|
||||
--output2 ${prefix}.pair2.trimmed.fastq.gz \\
|
||||
--seed 42 \\
|
||||
--gzip \\
|
||||
--gzip
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
@ -63,13 +66,12 @@ process ADAPTERREMOVAL {
|
|||
AdapterRemoval \\
|
||||
--file1 ${reads[0]} \\
|
||||
--file2 ${reads[1]} \\
|
||||
--collapse \\
|
||||
$args \\
|
||||
--basename $prefix \\
|
||||
--threads $task.cpus \\
|
||||
--settings ${prefix}.log \\
|
||||
--seed 42 \\
|
||||
--gzip \\
|
||||
--gzip
|
||||
|
||||
cat *.collapsed.gz *.collapsed.truncated.gz > ${prefix}.merged.fastq.gz
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
|
|
|
|||
|
|
@ -17,13 +17,13 @@ input:
|
|||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false, collapse:false ]
|
||||
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.
|
||||
pattern: "*.{fq,fastq,fg.gz,fastq.gz}"
|
||||
pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
|
|
@ -31,12 +31,45 @@ output:
|
|||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- reads:
|
||||
- singles_truncated:
|
||||
type: file
|
||||
description: |
|
||||
List of input adapter trimmed FastQ files of size 1 or 2 for
|
||||
single-end or collapsed data and paired-end data, respectively.
|
||||
pattern: "*.{fastq.gz}"
|
||||
Adapter trimmed FastQ files of either single-end reads, or singleton
|
||||
'orphaned' reads from merging of paired-end data (i.e., one of the pair
|
||||
was lost due to filtering thresholds).
|
||||
pattern: "*.truncated.gz"
|
||||
- discarded:
|
||||
type: file
|
||||
description: |
|
||||
Adapter trimmed FastQ files of reads that did not pass filtering
|
||||
thresholds.
|
||||
pattern: "*.discarded.gz"
|
||||
- pair1_truncated:
|
||||
type: file
|
||||
description: |
|
||||
Adapter trimmed R1 FastQ files of paired-end reads that did not merge
|
||||
with their respective R2 pair due to long templates. The respective pair
|
||||
is stored in 'pair2_truncated'.
|
||||
pattern: "*.pair1.truncated.gz"
|
||||
- pair2_truncated:
|
||||
type: file
|
||||
description: |
|
||||
Adapter trimmed R2 FastQ files of paired-end reads that did not merge
|
||||
with their respective R1 pair due to long templates. The respective pair
|
||||
is stored in 'pair1_truncated'.
|
||||
pattern: "*.pair2.truncated.gz"
|
||||
- collapsed:
|
||||
type: file
|
||||
description: |
|
||||
Collapsed FastQ of paired-end reads that successfully merged with their
|
||||
respective R1 pair but were not trimmed.
|
||||
pattern: "*.collapsed.gz"
|
||||
- collapsed_truncated:
|
||||
type: file
|
||||
description: |
|
||||
Collapsed FastQ of paired-end reads that successfully merged with their
|
||||
respective R1 pair and were trimmed of adapter due to sufficient overlap.
|
||||
pattern: "*.collapsed.truncated.gz"
|
||||
- log:
|
||||
type: file
|
||||
description: AdapterRemoval log file
|
||||
|
|
@ -48,3 +81,4 @@ output:
|
|||
|
||||
authors:
|
||||
- "@maxibor"
|
||||
- "@jfy133"
|
||||
|
|
|
|||
42
modules/bcftools/annotate/main.nf
Normal file
42
modules/bcftools/annotate/main.nf
Normal file
|
|
@ -0,0 +1,42 @@
|
|||
process BCFTOOLS_ANNOTATE {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bcftools=1.15" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/bcftools:1.15--haf5b3da_0':
|
||||
'quay.io/biocontainers/bcftools:1.15--haf5b3da_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*_annotated.vcf.gz"), optional:true , emit: vcf
|
||||
tuple val(meta), path("*_annotated.bcf") , optional:true , emit: bcf
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
|
||||
def matcher = input ==~ /\S+\.*vcf\.\S*/
|
||||
def output_suffix = matcher ? "vcf.gz" : "bcf"
|
||||
def output_type_compressed = matcher ? "z" : "b"
|
||||
"""
|
||||
bcftools \\
|
||||
annotate \\
|
||||
$args \\
|
||||
--output ${prefix}_annotated.${output_suffix} \\
|
||||
--output-type $output_type_compressed \\
|
||||
--threads $task.cpus \\
|
||||
$input
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
bcftools: \$( bcftools --version |& sed '1!d; s/^.*bcftools //' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
45
modules/bcftools/annotate/meta.yml
Normal file
45
modules/bcftools/annotate/meta.yml
Normal file
|
|
@ -0,0 +1,45 @@
|
|||
name: bcftools_annotate
|
||||
description: Add or remove annotations.
|
||||
keywords:
|
||||
- bcftools
|
||||
- annotate
|
||||
- vcf
|
||||
- remove
|
||||
- add
|
||||
tools:
|
||||
- annotate:
|
||||
description: Add or remove annotations.
|
||||
homepage: http://samtools.github.io/bcftools/bcftools.html
|
||||
documentation: https://samtools.github.io/bcftools/bcftools.html#annotate
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ['MIT']
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- input:
|
||||
type: files
|
||||
description: Query VCF or BCF file, can be either uncompressed or compressed
|
||||
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: Compressed annotated VCF file
|
||||
pattern: "*_annotated.vcf.gz"
|
||||
- bcf:
|
||||
type: file
|
||||
description: Compressed annotated BCF file
|
||||
pattern: "*_annotated.bcf"
|
||||
authors:
|
||||
- "@projectoriented"
|
||||
|
|
@ -2,10 +2,10 @@ process BWA_MEM {
|
|||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
|
||||
conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' :
|
||||
'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' }"
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' :
|
||||
'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process BWA_SAMPE {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
|
||||
conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' :
|
||||
'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' }"
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' :
|
||||
'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads), path(sai)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process BWA_SAMSE {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
|
||||
conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' :
|
||||
'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0' }"
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' :
|
||||
'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads), path(sai)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process BWAMEM2_MEM {
|
|||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.12" : null)
|
||||
conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.15" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:cf603b12db30ec91daa04ba45a8ee0f35bbcd1e2-0' :
|
||||
'quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:cf603b12db30ec91daa04ba45a8ee0f35bbcd1e2-0' }"
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:8ee25ae85d7a2bacac3e3139db209aff3d605a18-0' :
|
||||
'quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:8ee25ae85d7a2bacac3e3139db209aff3d605a18-0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
|
|
|
|||
158
modules/controlfreec/main.nf
Normal file
158
modules/controlfreec/main.nf
Normal file
|
|
@ -0,0 +1,158 @@
|
|||
process CONTROLFREEC {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::control-freec=11.6" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1':
|
||||
'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(mpileup_normal), path(mpileup_tumor), path(cpn_normal), path(cpn_tumor), path(minipileup_normal), path(minipileup_tumor)
|
||||
path fasta
|
||||
path fai
|
||||
path snp_position
|
||||
path known_snps
|
||||
path known_snps_tbi
|
||||
path chr_directory
|
||||
path mappability
|
||||
path target_bed
|
||||
path gccontent_profile
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*_ratio.BedGraph") , emit: bedgraph, optional: true
|
||||
tuple val(meta), path("*_control.cpn") , emit: control_cpn
|
||||
tuple val(meta), path("*_sample.cpn") , emit: sample_cpn
|
||||
tuple val(meta), path("GC_profile.*.cpn") , emit: gcprofile_cpn, optional:true
|
||||
tuple val(meta), path("*_BAF.txt") , emit: BAF
|
||||
tuple val(meta), path("*_CNVs") , emit: CNV
|
||||
tuple val(meta), path("*_info.txt") , emit: info
|
||||
tuple val(meta), path("*_ratio.txt") , emit: ratio
|
||||
tuple val(meta), path("config.txt") , emit: config
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
//"General" configurations
|
||||
def bedgraphoutput = task.ext.args?["general"]?["bedgraphoutput"] ? "BedGraphOutput = ${task.ext.args["general"]["bedgraphoutput"]}" : ""
|
||||
def chr_files = chr_directory ? "chrFiles =\${PWD}/${chr_directory}" : ""
|
||||
def chr_length = fai ? "chrLenFile = \${PWD}/${fai}" : ""
|
||||
def breakpointthreshold = task.ext.args?["general"]?["breakpointthreshold"] ? "breakPointThreshold = ${task.ext.args["general"]["breakpointthreshold"]}" : ""
|
||||
def breakpointtype = task.ext.args?["general"]?["breakpointtype"] ? "breakPointType = ${task.ext.args["general"]["breakpointtype"]}" : ""
|
||||
def coefficientofvariation = task.ext.args?["general"]?["coefficient"] ? "coefficientOfVariation = ${task.ext.args["general"]["coefficientofvariation"]}" : ""
|
||||
def contamination = task.ext.args?["general"]?["contamination"] ? "contamination = ${task.ext.args["general"]["contamination"]}" : ""
|
||||
def contaminationadjustment = task.ext.args?["general"]?["contaminationadjustment"] ? "contaminationAdjustment = ${task.ext.args["general"]["contaminationadjustment"]}" : ""
|
||||
def degree = task.ext.args?["general"]?["degree"] ? "degree = ${task.ext.args["general"]["degree"]}" : ""
|
||||
def forcegccontentnormalization = task.ext.args?["general"]?["forcegccontentnormalization"] ? "forceGCcontentNormalization = ${task.ext.args["general"]["forcegccontentnormalization"]}" : ""
|
||||
def gccontentprofile = gccontent_profile ? "GCcontentProfile = ${gccontent_profile}" : ""
|
||||
def mappability = mappability ? "gemMappabilityFile = \${PWD}/${mappability}" : ""
|
||||
def intercept = task.ext.args?["general"]?["intercept"] ? "intercept = ${task.ext.args["general"]["intercept"]}" : ""
|
||||
def mincnalength = task.ext.args?["general"]?["mincnalength"] ? "minCNAlength = ${task.ext.args["general"]["mincnalength"]}" : ""
|
||||
def minmappabilityperwindow = task.ext.args?["general"]?["minmappabilityperwindow"] ? "minMappabilityPerWindow = ${task.ext.args["general"]["minmappabilityperwindow"]}" : ""
|
||||
def minexpectedgc = task.ext.args?["general"]?["minexpectedgc"] ? "minExpectedGC = ${task.ext.args["general"]["minexpectedgc"]}" : ""
|
||||
def maxexpectedgc = task.ext.args?["general"]?["maxexpectedgc"] ? "maxExpectedGC = ${task.ext.args["general"]["maxexpectedgc"]}" : ""
|
||||
def minimalsubclonepresence = task.ext.args?["general"]?["minimalsubclonepresence"] ? "minimalSubclonePresence = ${task.ext.args["general"]["minimalsubclonepresence"]}" : ""
|
||||
def noisydata = task.ext.args?["general"]?["noisydata"] ? "noisyData = ${task.ext.args["general"]["noisydata"]}" : ""
|
||||
def output = task.ext.prefix ? "outputDir = \${PWD}/${task.ext.prefix}" : ""
|
||||
def ploidy = task.ext.args?["general"]?["ploidy"] ? "ploidy = ${task.ext.args["general"]["ploidy"]}" : ""
|
||||
def printNA = task.ext.args?["general"]?["printNA"] ? "printNA = ${task.ext.args["general"]["printNA"]}" : ""
|
||||
def readcountthreshold = task.ext.args?["general"]?["readcountthreshold"] ? "readCountThreshold = ${task.ext.args["general"]["readcountthreshold"]}" : ""
|
||||
def sex = task.ext.args?["general"]?["sex"] ? "sex = ${task.ext.args["general"]["sex"]}" : ""
|
||||
def step = task.ext.args?["general"]?["step"] ? "step = ${task.ext.args["general"]["step"]}" : ""
|
||||
def telocentromeric = task.ext.args?["general"]?["telocentromeric"] ? "telocentromeric = ${task.ext.args["general"]["telocentromeric"]} " : ""
|
||||
def uniquematch = task.ext.args?["general"]?["uniquematch"] ? "uniqueMatch = ${task.ext.args["general"]["uniquematch"]}" : ""
|
||||
def window = task.ext.args?["general"]?["window"] ? "window = ${task.ext.args["general"]["window"]}" : ""
|
||||
|
||||
//"Control" configurations
|
||||
def matefile_normal = mpileup_normal ? "mateFile = \${PWD}/${mpileup_normal}" : ""
|
||||
def matecopynumberfile_normal = cpn_normal ? "mateCopyNumberFile = \${PWD}/${cpn_normal}" : ""
|
||||
def minipileup_normal = minipileup_normal ? "miniPileup = \${PWD}/${minipileup_normal}" : ""
|
||||
def inputformat_normal = task.ext.args?["control"]?["inputformat"] ? "inputFormat = ${task.ext.args["control"]["inputformat"]}" : ""
|
||||
def mateorientation_normal = task.ext.args?["control"]?["mateorientation"] ? "mateOrientation = ${task.ext.args["control"]["mateorientation"]}" : ""
|
||||
|
||||
//"Sample" configuration
|
||||
def matefile_tumor = mpileup_tumor ? "mateFile = \${PWD}/${mpileup_tumor}" : ""
|
||||
def matecopynumberfile_tumor = cpn_tumor ? "mateCopyNumberFile = \${PWD}/${cpn_tumor}" : ""
|
||||
def minipileup_tumor = minipileup_tumor ? "miniPileup = \${PWD}/${minipileup_tumor}" : ""
|
||||
def inputformat_tumor = task.ext.args?["sample"]?["inputformat"] ? "inputFormat = ${task.ext.args["sample"]["inputformat"]}" : ""
|
||||
def mateorientation_tumor = task.ext.args?["sample"]?["mateorientation"] ? "mateOrientation = ${task.ext.args["sample"]["mateorientation"]}" : ""
|
||||
|
||||
//"BAF" configuration
|
||||
def makepileup = snp_position ? "makePileup = \${PWD}/${snp_position}" : ""
|
||||
def fastafile = fasta ? "fastaFile = \${PWD}/${fasta}" : ""
|
||||
def minimalcoverageperposition = task.ext.args?["BAF"]?["minimalcoverageperposition"] ? "minimalCoveragePerPosition = ${task.ext.args["BAF"]["minimalcoverageperposition"]}" : ""
|
||||
def minimalqualityperposition = task.ext.args?["BAF"]?["minimalqualityperposition"] ? "minimalQualityPerPosition = ${task.ext.args["BAF"]["minimalqualityperposition"]}" : ""
|
||||
def shiftinquality = task.ext.args?["BAF"]?["shiftinquality"] ? "shiftInQuality = ${task.ext.args["BAF"]["shiftinquality"]}" : ""
|
||||
def snpfile = known_snps ? "SNPfile = \$PWD/${known_snps}" : ""
|
||||
|
||||
//"Target" configuration
|
||||
def target_bed = target_bed ? "captureRegions = ${target_bed}" : ""
|
||||
"""
|
||||
touch config.txt
|
||||
|
||||
echo "[general]" >> config.txt
|
||||
echo ${bedgraphoutput} >> config.txt
|
||||
echo ${breakpointthreshold} >> config.txt
|
||||
echo ${breakpointtype} >> config.txt
|
||||
echo ${chr_files} >> config.txt
|
||||
echo ${chr_length} >> config.txt
|
||||
echo ${coefficientofvariation} >> config.txt
|
||||
echo ${contamination} >> config.txt
|
||||
echo ${contaminationadjustment} >> config.txt
|
||||
echo ${degree} >> config.txt
|
||||
echo ${forcegccontentnormalization} >> config.txt
|
||||
echo ${gccontentprofile} >> config.txt
|
||||
echo ${mappability} >> config.txt
|
||||
echo ${intercept} >> config.txt
|
||||
echo ${mincnalength} >> config.txt
|
||||
echo ${minmappabilityperwindow} >> config.txt
|
||||
echo ${minexpectedgc} >> config.txt
|
||||
echo ${maxexpectedgc} >> config.txt
|
||||
echo ${minimalsubclonepresence} >> config.txt
|
||||
echo "maxThreads = ${task.cpus}" >> config.txt
|
||||
echo ${noisydata} >> config.txt
|
||||
echo ${output} >> config.txt
|
||||
echo ${ploidy} >> config.txt
|
||||
echo ${printNA} >> config.txt
|
||||
echo ${readcountthreshold} >> config.txt
|
||||
echo ${sex} >> config.txt
|
||||
echo ${step} >> config.txt
|
||||
echo ${telocentromeric} >> config.txt
|
||||
echo ${uniquematch} >> config.txt
|
||||
echo ${window} >> config.txt
|
||||
|
||||
echo "[control]" >> config.txt
|
||||
echo ${matefile_normal} >> config.txt
|
||||
echo ${matecopynumberfile_normal} >> config.txt
|
||||
echo ${minipileup_normal} >> config.txt
|
||||
echo ${inputformat_normal} >> config.txt
|
||||
echo ${mateorientation_normal} >> config.txt
|
||||
|
||||
echo "[sample]" >> config.txt
|
||||
echo ${matefile_tumor} >> config.txt
|
||||
echo ${matecopynumberfile_tumor} >> config.txt
|
||||
echo ${minipileup_tumor} >> config.txt
|
||||
echo ${inputformat_tumor} >> config.txt
|
||||
echo ${mateorientation_tumor} >> config.txt
|
||||
|
||||
echo "[BAF]" >> config.txt
|
||||
echo ${makepileup} >> config.txt
|
||||
echo ${fastafile} >> config.txt
|
||||
echo ${minimalcoverageperposition} >> config.txt
|
||||
echo ${minimalqualityperposition} >> config.txt
|
||||
echo ${shiftinquality} >> config.txt
|
||||
echo ${snpfile} >> config.txt
|
||||
|
||||
echo "[target]" >> config.txt
|
||||
echo ${target_bed} >> config.txt
|
||||
|
||||
freec -conf config.txt
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
183
modules/controlfreec/meta.yml
Normal file
183
modules/controlfreec/meta.yml
Normal file
|
|
@ -0,0 +1,183 @@
|
|||
name: controlfreec
|
||||
description: Copy number and genotype annotation from whole genome and whole exome sequencing data
|
||||
keywords:
|
||||
- cna
|
||||
- cnv
|
||||
- somatic
|
||||
- single
|
||||
- tumor-only
|
||||
tools:
|
||||
- controlfreec:
|
||||
description: Copy number and genotype annotation from whole genome and whole exome sequencing data.
|
||||
homepage: http://boevalab.inf.ethz.ch/FREEC
|
||||
documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html
|
||||
tool_dev_url: https://github.com/BoevaLab/FREEC/
|
||||
doi: "10.1093/bioinformatics/btq635"
|
||||
licence: ['GPL >=2']
|
||||
|
||||
input:
|
||||
- args:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config.
|
||||
<optional> parameters can be removed from the map, if they are not set. All value must be surrounded by quotes, meta map parameters can be set with, i.e. sex = meta.sex:
|
||||
For default values, please check the documentation above.
|
||||
|
||||
```
|
||||
{
|
||||
[
|
||||
"general" :[
|
||||
"bedgraphoutput": <optional>,
|
||||
"breakpointthreshold": <optional>,
|
||||
"breakpointtype": <optional>,
|
||||
"coefficientofvariation": <optional>,
|
||||
"contamination": <optional>,
|
||||
"contaminationadjustment": <optional>,
|
||||
"degree": <optional>,
|
||||
"forcegccontentnormalization": <optional>,
|
||||
"gccontentprofile": <optional>,
|
||||
"intercept": <optional>,
|
||||
"mincnalength": <optional>,
|
||||
"minmappabilityperwindow": <optional>,
|
||||
"minexpectedgc": <optional>,
|
||||
"maxexpectedgc": <optional>,
|
||||
"minimalsubclonepresence": <optional>,
|
||||
"noisydata": <optional>,
|
||||
"ploidy": <optional>,
|
||||
"printNA": <optional>,
|
||||
"readcountthreshold": <optional >,
|
||||
"sex": <optional>,
|
||||
"step": <optional value>,
|
||||
"telocentromeric": <optional>,
|
||||
"uniquematch": <optional>,
|
||||
"window": <optional>
|
||||
],
|
||||
"control":[
|
||||
"inputformat": <required>,
|
||||
"mateorientation": <optional>,
|
||||
],
|
||||
"sample":[
|
||||
"inputformat": <required>,
|
||||
"mateorientation": <optional>,
|
||||
],
|
||||
"BAF":[
|
||||
"minimalcoverageperposition": <optional>,
|
||||
"minimalqualityperposition": <optional>,
|
||||
"shiftinquality": <optional>
|
||||
]
|
||||
]
|
||||
}
|
||||
```
|
||||
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- mateFile_normal:
|
||||
type: file
|
||||
description: File with mapped reads
|
||||
pattern: "*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}"
|
||||
- mateFile_tumor:
|
||||
type: file
|
||||
description: File with mapped reads
|
||||
pattern: "*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}"
|
||||
- cpn_normal:
|
||||
type: file
|
||||
description: Raw copy number profiles (optional)
|
||||
pattern: "*.cpn"
|
||||
- cpn_tumor:
|
||||
type: file
|
||||
description: Raw copy number profiles (optional)
|
||||
pattern: "*.cpn"
|
||||
- minipileup_normal:
|
||||
type: file
|
||||
description: miniPileup file from previous run (optional)
|
||||
pattern: "*.pileup"
|
||||
- minipileup_tumor:
|
||||
type: file
|
||||
description: miniPileup file from previous run (optional)
|
||||
pattern: "*.pileup"
|
||||
- fasta:
|
||||
type: file
|
||||
description: Reference file (optional; required if args 'makePileup' is set)
|
||||
pattern: "*.{fasta,fna,fa}"
|
||||
- fai:
|
||||
type: file
|
||||
description: Fasta index
|
||||
pattern: "*.fai"
|
||||
- snp_position:
|
||||
type: file
|
||||
description:
|
||||
pattern: "*.{}"
|
||||
- known_snps:
|
||||
type: file
|
||||
description: File with known SNPs
|
||||
pattern: "*.{vcf,vcf.gz}"
|
||||
- known_snps_tbi:
|
||||
type: file
|
||||
description: Index of known_snps
|
||||
pattern: "*.tbi"
|
||||
- chr_directory:
|
||||
type: file
|
||||
description: Path to directory with chromosome fasta files (optional, required if gccontentprofile is not provided)
|
||||
pattern: "*/"
|
||||
- mappability:
|
||||
type: file
|
||||
description: Contains information of mappable positions (optional)
|
||||
pattern: "*.gem"
|
||||
- target_bed:
|
||||
type: file
|
||||
description: Sorted bed file containing capture regions (optional)
|
||||
pattern: "*.bed"
|
||||
|
||||
|
||||
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"
|
||||
- bedgraph:
|
||||
type: file
|
||||
description: Bedgraph format for the UCSC genome browser
|
||||
pattern: ".bedgraph"
|
||||
- control_cpn:
|
||||
type: file
|
||||
description: files with raw copy number profiles
|
||||
pattern: "*_control.cpn"
|
||||
- sample_cpn:
|
||||
type: file
|
||||
description: files with raw copy number profiles
|
||||
pattern: "*_sample.cpn"
|
||||
- gcprofile_cpn:
|
||||
type: file
|
||||
description: file with GC-content profile.
|
||||
pattern: "GC_profile.*.cpn"
|
||||
- BAF:
|
||||
type: file
|
||||
description: file B-allele frequencies for each possibly heterozygous SNP position
|
||||
pattern: "*_BAF.txt"
|
||||
- CNV:
|
||||
type: file
|
||||
description: file with coordinates of predicted copy number alterations.
|
||||
pattern: "*_CNVs"
|
||||
- info:
|
||||
type: file
|
||||
description: parsable file with information about FREEC run
|
||||
pattern: "*_info.txt"
|
||||
- ratio:
|
||||
type: file
|
||||
description: file with ratios and predicted copy number alterations for each window
|
||||
pattern: "*_ratio.txt"
|
||||
- config:
|
||||
type: file
|
||||
description: Config file used to run Control-FREEC
|
||||
pattern: "config.txt"
|
||||
|
||||
authors:
|
||||
- "@FriederikeHanssen"
|
||||
|
|
@ -2,10 +2,10 @@ process CUSTOM_GETCHROMSIZES {
|
|||
tag "$fasta"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
|
||||
'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
|
||||
'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
|
||||
|
||||
input:
|
||||
path fasta
|
||||
|
|
|
|||
|
|
@ -17,8 +17,8 @@ process DEEPVARIANT {
|
|||
path(fai)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.vcf.gz") , emit: vcf
|
||||
tuple val(meta), path("*g.vcf.gz"), emit: gvcf
|
||||
tuple val(meta), path("${prefix}.vcf.gz") , emit: vcf
|
||||
tuple val(meta), path("${prefix}.g.vcf.gz"), emit: gvcf
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
|
|
@ -26,7 +26,7 @@ process DEEPVARIANT {
|
|||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def regions = intervals ? "--regions ${intervals}" : ""
|
||||
|
||||
"""
|
||||
|
|
|
|||
|
|
@ -13,6 +13,7 @@ process FAQCS {
|
|||
output:
|
||||
tuple val(meta), path('*.trimmed.fastq.gz') , emit: reads
|
||||
tuple val(meta), path('*.stats.txt') , emit: stats
|
||||
tuple val(meta), path('*.txt') , optional:true, emit: txt
|
||||
tuple val(meta), path('*_qc_report.pdf') , optional:true, emit: statspdf
|
||||
tuple val(meta), path('*.log') , emit: log
|
||||
tuple val(meta), path('*.discard.fastq.gz') , optional:true, emit: reads_fail
|
||||
|
|
|
|||
|
|
@ -54,6 +54,10 @@ output:
|
|||
type: file
|
||||
description: trimming/qc text stats file
|
||||
pattern: "*.stats.txt"
|
||||
- txt:
|
||||
type: file
|
||||
description: trimming/qc text txt files from --debug option
|
||||
pattern: "*.txt"
|
||||
- statspdf:
|
||||
type: file
|
||||
description: trimming/qc pdf report file
|
||||
|
|
|
|||
44
modules/hamronization/deeparg/main.nf
Normal file
44
modules/hamronization/deeparg/main.nf
Normal file
|
|
@ -0,0 +1,44 @@
|
|||
process HAMRONIZATION_DEEPARG {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
|
||||
'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(report)
|
||||
val(format)
|
||||
val(software_version)
|
||||
val(reference_db_version)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.json"), optional: true, emit: json
|
||||
tuple val(meta), path("*.tsv") , optional: true, emit: tsv
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
hamronize \\
|
||||
deeparg \\
|
||||
${report} \\
|
||||
$args \\
|
||||
--format ${format} \\
|
||||
--analysis_software_version ${software_version} \\
|
||||
--reference_database_version ${reference_db_version} \\
|
||||
--input_file_name ${prefix} \\
|
||||
> ${prefix}.${format}
|
||||
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
60
modules/hamronization/deeparg/meta.yml
Normal file
60
modules/hamronization/deeparg/meta.yml
Normal file
|
|
@ -0,0 +1,60 @@
|
|||
name: hamronization_deeparg
|
||||
description: Tool to convert and summarize DeepARG outputs using the hAMRonization specification
|
||||
keywords:
|
||||
- amr
|
||||
- antimicrobial resistance
|
||||
- reporting
|
||||
- deeparg
|
||||
tools:
|
||||
- hamronization:
|
||||
description: Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification
|
||||
homepage: https://github.com/pha4ge/hAMRonization/blob/master/README.md
|
||||
documentation: https://github.com/pha4ge/hAMRonization/blob/master/README.md
|
||||
tool_dev_url: https://github.com/pha4ge/hAMRonization
|
||||
doi: ""
|
||||
licence: ['GNU Lesser General Public v3 (LGPL v3)']
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- report:
|
||||
type: file
|
||||
description: Output .mapping.ARG file from DeepARG
|
||||
pattern: "*.mapping.ARG"
|
||||
- format:
|
||||
type: value
|
||||
description: Type of report file to be produced
|
||||
pattern: "tsv|json"
|
||||
- software_version:
|
||||
type: value
|
||||
description: Version of DeepARG used
|
||||
pattern: "[0-9].[0-9].[0-9]"
|
||||
- reference_db_version:
|
||||
type: value
|
||||
description: Database version of DeepARG used
|
||||
pattern: "[0-9]"
|
||||
|
||||
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"
|
||||
- json:
|
||||
type: file
|
||||
description: hAMRonised report in JSON format
|
||||
pattern: "*.json"
|
||||
- tsv:
|
||||
type: file
|
||||
description: hAMRonised report in TSV format
|
||||
pattern: "*.json"
|
||||
|
||||
authors:
|
||||
- "@jfy133"
|
||||
38
modules/hamronization/summarize/main.nf
Normal file
38
modules/hamronization/summarize/main.nf
Normal file
|
|
@ -0,0 +1,38 @@
|
|||
process HAMRONIZATION_SUMMARIZE {
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
|
||||
'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
|
||||
|
||||
input:
|
||||
path(reports)
|
||||
val(format)
|
||||
|
||||
output:
|
||||
path("hamronization_combined_report.json"), optional: true, emit: json
|
||||
path("hamronization_combined_report.tsv") , optional: true, emit: tsv
|
||||
path("hamronization_combined_report.html"), optional: true, emit: html
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def outformat = format == 'interactive' ? 'html' : format
|
||||
"""
|
||||
hamronize \\
|
||||
summarize \\
|
||||
${reports.join(' ')} \\
|
||||
-t ${format} \\
|
||||
$args \\
|
||||
-o hamronization_combined_report.${outformat}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
45
modules/hamronization/summarize/meta.yml
Normal file
45
modules/hamronization/summarize/meta.yml
Normal file
|
|
@ -0,0 +1,45 @@
|
|||
name: hamronization_summarize
|
||||
description: Tool to summarize and combine all hAMRonization reports into a single file
|
||||
keywords:
|
||||
- amr
|
||||
- antimicrobial resistance
|
||||
- reporting
|
||||
tools:
|
||||
- hamronization:
|
||||
description: Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification
|
||||
homepage: https://github.com/pha4ge/hAMRonization/blob/master/README.md
|
||||
documentation: https://github.com/pha4ge/hAMRonization/blob/master/README.md
|
||||
tool_dev_url: https://github.com/pha4ge/hAMRonization
|
||||
doi: ""
|
||||
licence: ['GNU Lesser General Public v3 (LGPL v3)']
|
||||
|
||||
input:
|
||||
- reports:
|
||||
type: file
|
||||
description: List of multiple hAMRonization reports in either JSON or TSV format
|
||||
pattern: "*.{json,tsv}"
|
||||
- format:
|
||||
type: value
|
||||
description: Type of final combined report file to be produced
|
||||
pattern: "tsv|json|interactive"
|
||||
|
||||
output:
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- json:
|
||||
type: file
|
||||
description: hAMRonised summary in JSON format
|
||||
pattern: "*.json"
|
||||
- tsv:
|
||||
type: file
|
||||
description: hAMRonised summary in TSV format
|
||||
pattern: "*.json"
|
||||
- html:
|
||||
type: file
|
||||
description: hAMRonised summary in HTML format
|
||||
pattern: "*.html"
|
||||
|
||||
authors:
|
||||
- "@jfy133"
|
||||
44
modules/hpsuissero/main.nf
Normal file
44
modules/hpsuissero/main.nf
Normal file
|
|
@ -0,0 +1,44 @@
|
|||
def VERSION = '1.0.1' // Version information not provided by tool on CLI
|
||||
|
||||
process HPSUISSERO {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::hpsuissero=1.0.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/hpsuissero%3A1.0.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/hpsuissero:1.0.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fasta)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.tsv"), emit: tsv
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def is_compressed = fasta.getName().endsWith(".gz") ? true : false
|
||||
def fasta_name = fasta.getName().replace(".gz", "")
|
||||
"""
|
||||
if [ "$is_compressed" == "true" ]; then
|
||||
gzip -c -d $fasta > $fasta_name
|
||||
fi
|
||||
|
||||
HpsuisSero.sh \\
|
||||
-i $fasta_name \\
|
||||
-o ./ \\
|
||||
-s $prefix \\
|
||||
-x fasta \\
|
||||
-t $task.cpus
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
hpsuissero: $VERSION
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
43
modules/hpsuissero/meta.yml
Normal file
43
modules/hpsuissero/meta.yml
Normal file
|
|
@ -0,0 +1,43 @@
|
|||
name: hpsuissero
|
||||
description: Serotype prediction of Haemophilus parasuis assemblies
|
||||
keywords:
|
||||
- bacteria
|
||||
- fasta
|
||||
- haemophilus
|
||||
tools:
|
||||
- hpsuissero:
|
||||
description: Rapid Haemophilus parasuis serotyping pipeline for Nanpore data
|
||||
homepage: https://github.com/jimmyliu1326/HpsuisSero
|
||||
documentation: https://github.com/jimmyliu1326/HpsuisSero
|
||||
tool_dev_url: https://github.com/jimmyliu1326/HpsuisSero
|
||||
doi: ""
|
||||
licence: ['MIT']
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: Assembly in FASTA format
|
||||
pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- tsv:
|
||||
type: file
|
||||
description: Tab-delimited serotype prediction
|
||||
pattern: "*.{tsv}"
|
||||
|
||||
authors:
|
||||
- "@rpetit3"
|
||||
|
|
@ -61,11 +61,11 @@ output:
|
|||
pattern: "*.r1.fail.fq.gz"
|
||||
- unmerged_r2_fq_pass:
|
||||
type: file
|
||||
description: Passed unmerged R1 FASTQs
|
||||
description: Passed unmerged R2 FASTQs
|
||||
pattern: "*.r2.fq.gz"
|
||||
- unmerged_r2_fq_pass:
|
||||
type: file
|
||||
description: Failed unmerged R1 FASTQs
|
||||
description: Failed unmerged R2 FASTQs
|
||||
pattern: "*.r2.fail.fq.gz"
|
||||
- log:
|
||||
type: file
|
||||
|
|
|
|||
35
modules/mafft/main.nf
Normal file
35
modules/mafft/main.nf
Normal file
|
|
@ -0,0 +1,35 @@
|
|||
process MAFFT {
|
||||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::mafft=7.490" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/mafft:7.490--h779adbc_0':
|
||||
'quay.io/biocontainers/mafft:7.490--h779adbc_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fasta)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.fas"), emit: fas
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
mafft \\
|
||||
--thread ${task.cpus} \\
|
||||
${args} \\
|
||||
${fasta} \\
|
||||
> ${prefix}.fas
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
mafft: \$(mafft --version 2>&1 | sed 's/^v//' | sed 's/ (.*)//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
42
modules/mafft/meta.yml
Normal file
42
modules/mafft/meta.yml
Normal file
|
|
@ -0,0 +1,42 @@
|
|||
name: mafft
|
||||
description: Multiple sequence alignment using MAFFT
|
||||
keywords:
|
||||
- msa
|
||||
- multiple sequence alignment
|
||||
tools:
|
||||
- mafft:
|
||||
description: Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
|
||||
homepage: https://mafft.cbrc.jp/alignment/software/
|
||||
documentation: https://mafft.cbrc.jp/alignment/software/manual/manual.html
|
||||
tool_dev_url: https://mafft.cbrc.jp/alignment/software/source.html
|
||||
doi: "10.1093/nar/gkf436"
|
||||
licence: ['BSD']
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: FASTA file containing the sequences to align
|
||||
pattern: "*.{fa,fasta}"
|
||||
|
||||
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"
|
||||
- fas:
|
||||
type: file
|
||||
description: Aligned sequences in FASTA format
|
||||
pattern: "*.{fas}"
|
||||
|
||||
authors:
|
||||
- "@MillironX"
|
||||
|
|
@ -1,4 +1,5 @@
|
|||
process MALT_RUN {
|
||||
tag "$meta.id"
|
||||
label 'process_high'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::malt=0.53" : null)
|
||||
|
|
@ -7,21 +8,22 @@ process MALT_RUN {
|
|||
'quay.io/biocontainers/malt:0.53--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
path fastqs
|
||||
tuple val(meta), path(fastqs)
|
||||
val mode
|
||||
path index
|
||||
|
||||
output:
|
||||
path "*.rma6" , emit: rma6
|
||||
path "*.{tab,text,sam}", optional:true, emit: alignments
|
||||
path "*.log" , emit: log
|
||||
path "versions.yml" , emit: versions
|
||||
tuple val(meta), path("*.rma6") , emit: rma6
|
||||
tuple val(meta), path("*.{tab,text,sam}"), optional:true, emit: alignments
|
||||
tuple val(meta), path("*.log") , emit: log
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def avail_mem = 6
|
||||
if (!task.memory) {
|
||||
log.info '[MALT_RUN] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
|
||||
|
|
@ -38,7 +40,7 @@ process MALT_RUN {
|
|||
$args \\
|
||||
--inFile ${fastqs.join(' ')} \\
|
||||
-m $mode \\
|
||||
--index $index/ |&tee malt-run.log
|
||||
--index $index/ |&tee ${prefix}-malt-run.log
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
|
|||
|
|
@ -19,6 +19,11 @@ tools:
|
|||
licence: ["GPL v3"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fastqs:
|
||||
type: file
|
||||
description: Input FASTQ files
|
||||
|
|
@ -47,7 +52,7 @@ output:
|
|||
- log:
|
||||
type: file
|
||||
description: Log of verbose MALT stdout
|
||||
pattern: "malt-run.log"
|
||||
pattern: "*-malt-run.log"
|
||||
|
||||
authors:
|
||||
- "@jfy133"
|
||||
|
|
|
|||
|
|
@ -29,8 +29,9 @@ process MAXBIN2 {
|
|||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def associate_files = reads ? "-reads $reads" : "-abund $abund"
|
||||
"""
|
||||
mkdir input/ && mv $contigs input/
|
||||
run_MaxBin.pl \\
|
||||
-contig $contigs \\
|
||||
-contig input/$contigs \\
|
||||
$associate_files \\
|
||||
-thread $task.cpus \\
|
||||
$args \\
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
process PICARD_CLEANSAM {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
|
|
@ -8,10 +8,10 @@ process PICARD_CLEANSAM {
|
|||
'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(sam)
|
||||
tuple val(meta), path(bam)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.sam"), emit: sam
|
||||
tuple val(meta), path("*.bam"), emit: bam
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
|
|
@ -20,7 +20,6 @@ process PICARD_CLEANSAM {
|
|||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def STRINGENCY = task.ext.stringency ?: "STRICT"
|
||||
def avail_mem = 3
|
||||
if (!task.memory) {
|
||||
log.info '[Picard CleanSam] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
||||
|
|
@ -32,9 +31,8 @@ process PICARD_CLEANSAM {
|
|||
-Xmx${avail_mem}g \\
|
||||
CleanSam \\
|
||||
${args} \\
|
||||
-I ${sam} \\
|
||||
-O ${prefix}.sam \\
|
||||
--VALIDATION_STRINGENCY ${STRINGENCY}
|
||||
-I ${bam} \\
|
||||
-O ${prefix}.bam
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
|
|||
|
|
@ -1,8 +1,7 @@
|
|||
name: picard_cleansam
|
||||
description: Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads
|
||||
description: Cleans the provided BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads
|
||||
keywords:
|
||||
- clean
|
||||
- sam
|
||||
- bam
|
||||
tools:
|
||||
- picard:
|
||||
|
|
@ -22,8 +21,8 @@ input:
|
|||
e.g. [ id:'test', single_end:false ]
|
||||
- sam:
|
||||
type: file
|
||||
description: SAM file
|
||||
pattern: "*.{sam}"
|
||||
description: BAM file
|
||||
pattern: "*.{bam}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
|
|
@ -37,8 +36,8 @@ output:
|
|||
pattern: "versions.yml"
|
||||
- sam:
|
||||
type: file
|
||||
description: Cleaned SAM file
|
||||
pattern: "*.{sam}"
|
||||
description: Cleaned BAM file
|
||||
pattern: "*.{bam}"
|
||||
|
||||
authors:
|
||||
- "@sateeshperi"
|
||||
|
|
|
|||
49
modules/picard/sortvcf/main.nf
Normal file
49
modules/picard/sortvcf/main.nf
Normal file
|
|
@ -0,0 +1,49 @@
|
|||
process PICARD_SORTVCF {
|
||||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
|
||||
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
path reference
|
||||
path sequence_dict
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*_sorted.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 seq_dict = sequence_dict ? "-SEQUENCE_DICTIONARY $sequence_dict" : ""
|
||||
def reference = reference ? "-REFERENCE_SEQUENCE $reference" : ""
|
||||
def avail_mem = 3
|
||||
if (!task.memory) {
|
||||
log.info '[Picard SortVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
|
||||
} else {
|
||||
avail_mem = task.memory.giga
|
||||
}
|
||||
|
||||
"""
|
||||
picard \\
|
||||
SortVcf \\
|
||||
-Xmx${avail_mem}g \\
|
||||
--INPUT $vcf \\
|
||||
$args \\
|
||||
$seq_dict \\
|
||||
$reference \\
|
||||
--OUTPUT ${prefix}_sorted.vcf.gz
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
picard: \$(picard SortVcf --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
40
modules/picard/sortvcf/meta.yml
Normal file
40
modules/picard/sortvcf/meta.yml
Normal file
|
|
@ -0,0 +1,40 @@
|
|||
name: picard_sortvcf
|
||||
description: Sorts vcf files
|
||||
keywords:
|
||||
- sort
|
||||
- vcf
|
||||
tools:
|
||||
- picard:
|
||||
description: Java tools for working with NGS data in the BAM/CRAM/SAM and VCF format
|
||||
homepage: https://broadinstitute.github.io/picard/
|
||||
documentation: https://broadinstitute.github.io/picard/command-line-overview.html#SortVcf
|
||||
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}"
|
||||
|
||||
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}"
|
||||
|
||||
authors:
|
||||
- "@ramprasadn"
|
||||
|
|
@ -23,11 +23,13 @@ process PLINK2_EXTRACT {
|
|||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
if( "$pgen" == "${prefix}.pgen" ) error "Input and output names are the same, use \"task.ext.prefix\" in modules.config to disambiguate!"
|
||||
def mem_mb = task.memory.toMega()
|
||||
"""
|
||||
plink2 \\
|
||||
--threads $task.cpus \\
|
||||
--memory $mem_mb \\
|
||||
--pfile ${pgen.baseName} \\
|
||||
$args \\
|
||||
--threads $task.cpus \\
|
||||
--extract $variants \\
|
||||
--make-pgen vzs \\
|
||||
--out ${prefix}
|
||||
|
|
|
|||
39
modules/plink2/score/main.nf
Normal file
39
modules/plink2/score/main.nf
Normal file
|
|
@ -0,0 +1,39 @@
|
|||
process PLINK2_SCORE {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' :
|
||||
'quay.io/biocontainers/plink2:2.00a2.3--h712d239_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(pgen), path(psam), path(pvar)
|
||||
path(scorefile)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.sscore"), emit: score
|
||||
path("versions.yml") , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def mem_mb = task.memory.toMega() // plink is greedy
|
||||
"""
|
||||
plink2 \\
|
||||
--threads $task.cpus \\
|
||||
--memory $mem_mb \\
|
||||
--pfile ${pgen.baseName} vzs \\
|
||||
--score ${scorefile} \\
|
||||
$args \\
|
||||
--out ${prefix}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
plink2: \$(plink2 --version 2>&1 | sed 's/^PLINK v//; s/ 64.*\$//' )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
56
modules/plink2/score/meta.yml
Normal file
56
modules/plink2/score/meta.yml
Normal file
|
|
@ -0,0 +1,56 @@
|
|||
name: plink2_score
|
||||
description: Apply a scoring system to each sample in a plink 2 fileset
|
||||
keywords:
|
||||
- plink2
|
||||
- score
|
||||
tools:
|
||||
- plink2:
|
||||
description: |
|
||||
Whole genome association analysis toolset, designed to perform a range
|
||||
of basic, large-scale analyses in a computationally efficient manner
|
||||
homepage: http://www.cog-genomics.org/plink/2.0/
|
||||
documentation: http://www.cog-genomics.org/plink/2.0/general_usage
|
||||
tool_dev_url: None
|
||||
doi: "10.1186/s13742-015-0047-8"
|
||||
licence: ['GPL v3']
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- pgen:
|
||||
type: file
|
||||
description: PLINK 2 binary genotype table
|
||||
pattern: "*.{pgen}"
|
||||
- psam:
|
||||
type: file
|
||||
description: PLINK 2 sample information file
|
||||
pattern: "*.{psam}"
|
||||
- pvar:
|
||||
type: file
|
||||
description: PLINK 2 variant information file
|
||||
pattern: "*.{pvar}"
|
||||
- scorefile:
|
||||
type: file
|
||||
description: A text file containing variant identifiers and weights
|
||||
pattern: "*.{scores,txt,scorefile}"
|
||||
|
||||
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"
|
||||
- score:
|
||||
type: file
|
||||
description: A text file containing sample scores, in plink 2 .sscore format
|
||||
pattern: "*.{sscore}"
|
||||
|
||||
authors:
|
||||
- "@nebfield"
|
||||
|
|
@ -11,10 +11,10 @@ process PLINK2_VCF {
|
|||
tuple val(meta), path(vcf)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.pgen"), emit: pgen
|
||||
tuple val(meta), path("*.psam"), emit: psam
|
||||
tuple val(meta), path("*.pvar"), emit: pvar
|
||||
path "versions.yml" , emit: versions
|
||||
tuple val(meta), path("*.pgen") , emit: pgen
|
||||
tuple val(meta), path("*.psam") , emit: psam
|
||||
tuple val(meta), path("*.pvar.zst"), emit: pvar
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
|
@ -22,10 +22,14 @@ process PLINK2_VCF {
|
|||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def mem_mb = task.memory.toMega()
|
||||
"""
|
||||
plink2 \\
|
||||
--threads $task.cpus \\
|
||||
--memory $mem_mb \\
|
||||
$args \\
|
||||
--vcf $vcf \\
|
||||
--make-pgen vzs \\
|
||||
--out ${prefix}
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
|
|
|
|||
|
|
@ -46,7 +46,7 @@ output:
|
|||
- pvar:
|
||||
type: file
|
||||
description: PLINK 2 variant information file
|
||||
pattern: "*.{psam}"
|
||||
pattern: "*.{pvar.zst}"
|
||||
|
||||
authors:
|
||||
- "@nebfield"
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process QUALIMAP_BAMQCCRAM {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.12" : null)
|
||||
conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.15" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:4bf11d12f2c3eccf1eb585097c0b6fd31c18c418-0' :
|
||||
'quay.io/biocontainers/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:4bf11d12f2c3eccf1eb585097c0b6fd31c18c418-0' }"
|
||||
'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:9838874d42d4477d5042782ee019cec9854da7d5-0' :
|
||||
'quay.io/biocontainers/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:9838874d42d4477d5042782ee019cec9854da7d5-0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(cram), path(crai)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process SAMTOOLS_AMPLICONCLIP {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
|
||||
'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
|
||||
'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process SAMTOOLS_BAM2FQ {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
|
||||
'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
|
||||
'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(inputbam)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process SAMTOOLS_DEPTH {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
|
||||
'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
|
||||
'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process SAMTOOLS_FAIDX {
|
|||
tag "$fasta"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
|
||||
'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
|
||||
'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fasta)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process SAMTOOLS_FASTQ {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
|
||||
'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
|
||||
'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process SAMTOOLS_FIXMATE {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
|
||||
'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
|
||||
'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process SAMTOOLS_FLAGSTAT {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
|
||||
'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
|
||||
'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam), path(bai)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process SAMTOOLS_IDXSTATS {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
|
||||
'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
|
||||
'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam), path(bai)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process SAMTOOLS_INDEX {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
|
||||
'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
|
||||
'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process SAMTOOLS_MERGE {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
|
||||
'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
|
||||
'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input_files)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process SAMTOOLS_MPILEUP {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
|
||||
'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
|
||||
'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process SAMTOOLS_SORT {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
|
||||
'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
|
||||
'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process SAMTOOLS_STATS {
|
|||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
|
||||
'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
|
||||
'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index)
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@ process SAMTOOLS_VIEW {
|
|||
tag "$meta.id"
|
||||
label 'process_medium'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
|
||||
conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
|
||||
'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
|
||||
'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input)
|
||||
|
|
|
|||
44
modules/ssuissero/main.nf
Normal file
44
modules/ssuissero/main.nf
Normal file
|
|
@ -0,0 +1,44 @@
|
|||
def VERSION = '1.0.1' // Version information not provided by tool on CLI
|
||||
|
||||
process SSUISSERO {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::ssuissero=1.0.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/ssuissero%3A1.0.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/ssuissero:1.0.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(fasta)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.tsv"), emit: tsv
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
def is_compressed = fasta.getName().endsWith(".gz") ? true : false
|
||||
def fasta_name = fasta.getName().replace(".gz", "")
|
||||
"""
|
||||
if [ "$is_compressed" == "true" ]; then
|
||||
gzip -c -d $fasta > $fasta_name
|
||||
fi
|
||||
|
||||
SsuisSero.sh \\
|
||||
-i $fasta_name \\
|
||||
-o ./ \\
|
||||
-s $prefix \\
|
||||
-x fasta \\
|
||||
-t $task.cpus
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
ssuissero: $VERSION
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
43
modules/ssuissero/meta.yml
Normal file
43
modules/ssuissero/meta.yml
Normal file
|
|
@ -0,0 +1,43 @@
|
|||
name: ssuissero
|
||||
description: Serotype prediction of Streptococcus suis assemblies
|
||||
keywords:
|
||||
- bacteria
|
||||
- fasta
|
||||
- streptococcus
|
||||
tools:
|
||||
- ssuissero:
|
||||
description: Rapid Streptococcus suis serotyping pipeline for Nanopore Data
|
||||
homepage: https://github.com/jimmyliu1326/SsuisSero
|
||||
documentation: https://github.com/jimmyliu1326/SsuisSero
|
||||
tool_dev_url: https://github.com/jimmyliu1326/SsuisSero
|
||||
doi: ""
|
||||
licence: ['MIT']
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- fasta:
|
||||
type: file
|
||||
description: Assembly in FASTA format
|
||||
pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- tsv:
|
||||
type: file
|
||||
description: Tab-delimited serotype prediction
|
||||
pattern: "*.{tsv}"
|
||||
|
||||
authors:
|
||||
- "@rpetit3"
|
||||
33
modules/stranger/main.nf
Normal file
33
modules/stranger/main.nf
Normal file
|
|
@ -0,0 +1,33 @@
|
|||
process STRANGER {
|
||||
tag "$meta.id"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "bioconda::stranger=0.8.1" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/stranger:0.8.1--pyh5e36f6f_0':
|
||||
'quay.io/biocontainers/stranger:0.8.1--pyh5e36f6f_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
|
||||
output:
|
||||
tuple val(meta), path("*.gz"), emit: vcf
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
task.ext.when == null || task.ext.when
|
||||
|
||||
script:
|
||||
def args = task.ext.args ?: ''
|
||||
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||
"""
|
||||
stranger \\
|
||||
$args \\
|
||||
$vcf | gzip --no-name > ${prefix}.vcf.gz
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
stranger: \$( stranger --version )
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
44
modules/stranger/meta.yml
Normal file
44
modules/stranger/meta.yml
Normal file
|
|
@ -0,0 +1,44 @@
|
|||
name: stranger
|
||||
description: Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes.
|
||||
keywords:
|
||||
- STR
|
||||
- repeat_expansions
|
||||
- annotate
|
||||
- vcf
|
||||
tools:
|
||||
- stranger:
|
||||
description: Annotate VCF files with str variants
|
||||
homepage: https://github.com/moonso/stranger
|
||||
documentation: https://github.com/moonso/stranger
|
||||
tool_dev_url: https://github.com/moonso/stranger
|
||||
doi: "10.5281/zenodo.4548873"
|
||||
licence: ['MIT']
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- vcf:
|
||||
type: file
|
||||
description: VCF with repeat expansions
|
||||
pattern: "*.{vcf.gz,vcf}"
|
||||
|
||||
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 with keys STR_STATUS, NormalMax and PathologicMin
|
||||
pattern: "*.{vcf.gz}"
|
||||
|
||||
authors:
|
||||
- "@ljmesi"
|
||||
|
|
@ -2,7 +2,7 @@ process UNTAR {
|
|||
tag "$archive"
|
||||
label 'process_low'
|
||||
|
||||
conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
|
||||
conda (params.enable_conda ? "conda-forge::tar=1.32" : null)
|
||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
|
||||
'biocontainers/biocontainers:v1.2.0_cv1' }"
|
||||
|
|
|
|||
|
|
@ -13,6 +13,7 @@ process YARA_MAPPER {
|
|||
|
||||
output:
|
||||
tuple val(meta), path("*.mapped.bam"), emit: bam
|
||||
tuple val(meta), path("*.mapped.bam.bai"), emit: bai
|
||||
path "versions.yml" , emit: versions
|
||||
|
||||
when:
|
||||
|
|
@ -28,7 +29,9 @@ process YARA_MAPPER {
|
|||
-t $task.cpus \\
|
||||
-f bam \\
|
||||
${index}/yara \\
|
||||
$reads | samtools view -@ $task.cpus -hb -F4 > ${prefix}.mapped.bam
|
||||
$reads | samtools view -@ $task.cpus -hb -F4 | samtools sort -@ $task.cpus > ${prefix}.mapped.bam
|
||||
|
||||
samtools index -@ $task.cpus ${prefix}.mapped.bam
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
@ -46,8 +49,11 @@ process YARA_MAPPER {
|
|||
${reads[0]} \\
|
||||
${reads[1]} > output.bam
|
||||
|
||||
samtools view -@ $task.cpus -hF 4 -f 0x40 -b output.bam > ${prefix}_1.mapped.bam
|
||||
samtools view -@ $task.cpus -hF 4 -f 0x80 -b output.bam > ${prefix}_2.mapped.bam
|
||||
samtools view -@ $task.cpus -hF 4 -f 0x40 -b output.bam | samtools sort -@ $task.cpus > ${prefix}_1.mapped.bam
|
||||
samtools view -@ $task.cpus -hF 4 -f 0x80 -b output.bam | samtools sort -@ $task.cpus > ${prefix}_2.mapped.bam
|
||||
|
||||
samtools index -@ $task.cpus ${prefix}_1.mapped.bam
|
||||
samtools index -@ $task.cpus ${prefix}_2.mapped.bam
|
||||
|
||||
cat <<-END_VERSIONS > versions.yml
|
||||
"${task.process}":
|
||||
|
|
|
|||
|
|
@ -45,6 +45,10 @@ output:
|
|||
type: file
|
||||
description: Sorted BAM file
|
||||
pattern: "*.{bam}"
|
||||
- bai:
|
||||
type: file
|
||||
description: Sorted BAM file index
|
||||
pattern: "*.{bai}"
|
||||
|
||||
authors:
|
||||
- "@apeltzer"
|
||||
|
|
|
|||
|
|
@ -98,6 +98,10 @@ bbmap/index:
|
|||
- modules/bbmap/index/**
|
||||
- tests/modules/bbmap/index/**
|
||||
|
||||
bcftools/annotate:
|
||||
- modules/bcftools/annotate/**
|
||||
- tests/modules/bcftools/annotate/**
|
||||
|
||||
bcftools/concat:
|
||||
- modules/bcftools/concat/**
|
||||
- tests/modules/bcftools/concat/**
|
||||
|
|
@ -352,6 +356,10 @@ cnvkit/batch:
|
|||
- modules/cnvkit/batch/**
|
||||
- tests/modules/cnvkit/batch/**
|
||||
|
||||
controlfreec:
|
||||
- modules/controlfreec/**
|
||||
- tests/modules/controlfreec/**
|
||||
|
||||
cooler/cload:
|
||||
- modules/cooler/cload/**
|
||||
- tests/modules/cooler/cload/**
|
||||
|
|
@ -744,6 +752,14 @@ gunzip:
|
|||
- modules/gunzip/**
|
||||
- tests/modules/gunzip/**
|
||||
|
||||
hamronization/deeparg:
|
||||
- modules/hamronization/deeparg/**
|
||||
- tests/modules/hamronization/deeparg/**
|
||||
|
||||
hamronization/summarize:
|
||||
- modules/hamronization/summarize/**
|
||||
- tests/modules/hamronization/summarize/**
|
||||
|
||||
hicap:
|
||||
- modules/hicap/**
|
||||
- tests/modules/hicap/**
|
||||
|
|
@ -807,6 +823,10 @@ homer/makeucscfile:
|
|||
- modules/homer/makeucscfile/**
|
||||
- tests/modules/homer/makeucscfile/**
|
||||
|
||||
hpsuissero:
|
||||
- modules/hpsuissero/**
|
||||
- tests/modules/hpsuissero/**
|
||||
|
||||
ichorcna/createpon:
|
||||
- modules/ichorcna/createpon/**
|
||||
- tests/modules/ichorcna/createpon/**
|
||||
|
|
@ -960,6 +980,10 @@ macs2/callpeak:
|
|||
- modules/macs2/callpeak/**
|
||||
- tests/modules/macs2/callpeak/**
|
||||
|
||||
mafft:
|
||||
- modules/mafft/**
|
||||
- tests/modules/mafft/**
|
||||
|
||||
malt/build:
|
||||
- modules/malt/build/**
|
||||
- tests/modules/malt/build_test/**
|
||||
|
|
@ -1225,6 +1249,10 @@ picard/sortsam:
|
|||
- modules/picard/sortsam/**
|
||||
- tests/modules/picard/sortsam/**
|
||||
|
||||
picard/sortvcf:
|
||||
- modules/picard/sortvcf/**
|
||||
- tests/modules/picard/sortvcf/**
|
||||
|
||||
pirate:
|
||||
- modules/pirate/**
|
||||
- tests/modules/pirate/**
|
||||
|
|
@ -1245,6 +1273,10 @@ plink2/extract:
|
|||
- modules/plink2/extract/**
|
||||
- tests/modules/plink2/extract/**
|
||||
|
||||
plink2/score:
|
||||
- modules/plink2/score/**
|
||||
- tests/modules/plink2/score/**
|
||||
|
||||
plink2/vcf:
|
||||
- modules/plink2/vcf/**
|
||||
- tests/modules/plink2/vcf/**
|
||||
|
|
@ -1533,6 +1565,10 @@ sratools/prefetch:
|
|||
- modules/sratools/prefetch/**
|
||||
- tests/modules/sratools/prefetch/**
|
||||
|
||||
ssuissero:
|
||||
- modules/ssuissero/**
|
||||
- tests/modules/ssuissero/**
|
||||
|
||||
staphopiasccmec:
|
||||
- modules/staphopiasccmec/**
|
||||
- tests/modules/staphopiasccmec/**
|
||||
|
|
@ -1545,6 +1581,10 @@ star/genomegenerate:
|
|||
- modules/star/genomegenerate/**
|
||||
- tests/modules/star/genomegenerate/**
|
||||
|
||||
stranger:
|
||||
- modules/stranger/**
|
||||
- tests/modules/stranger/**
|
||||
|
||||
strelka/germline:
|
||||
- modules/strelka/germline/**
|
||||
- tests/modules/strelka/germline/**
|
||||
|
|
|
|||
|
|
@ -67,6 +67,8 @@ params {
|
|||
|
||||
test_computematrix_mat_gz = "${test_data_dir}/genomics/sarscov2/illumina/deeptools/test.computeMatrix.mat.gz"
|
||||
|
||||
test_bcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.bcf"
|
||||
|
||||
test_vcf = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf"
|
||||
test_vcf_gz = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz"
|
||||
test_vcf_gz_tbi = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi"
|
||||
|
|
@ -117,14 +119,16 @@ params {
|
|||
genome_bed_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed.gz.tbi"
|
||||
transcriptome_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/transcriptome.fasta"
|
||||
genome2_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/genome2.fasta"
|
||||
genome_chain_gz = "${test_data_dir}/genomics/homo_sapiens/genome/genome.chain.gz"
|
||||
genome_chain_gz = "${test_data_dir}/genomics/homo_sapiens/genome/genome.chain.gz"
|
||||
genome_21_fasta = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta"
|
||||
genome_21_fasta_fai = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai"
|
||||
genome_21_dict = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.dict"
|
||||
genome_21_sizes = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.sizes"
|
||||
genome_21_interval_list = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list"
|
||||
genome_21_multi_interval_bed = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed"
|
||||
genome_21_multi_interval_bed_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz"
|
||||
genome_21_multi_interval_bed_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi"
|
||||
genome_21_chromosomes_dir = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz"
|
||||
|
||||
dbsnp_146_hg38_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
|
||||
dbsnp_146_hg38_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi"
|
||||
|
|
@ -134,6 +138,7 @@ params {
|
|||
mills_and_1000g_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi"
|
||||
syntheticvcf_short_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz"
|
||||
syntheticvcf_short_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi"
|
||||
syntheticvcf_short_score = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.score"
|
||||
gnomad_r2_1_1_sv_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1-sv.vcf.gz"
|
||||
|
||||
hapmap_3_3_hg38_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz"
|
||||
|
|
@ -154,7 +159,7 @@ params {
|
|||
justhusky_ped = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky.ped"
|
||||
justhusky_minimal_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz"
|
||||
justhusky_minimal_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz.tbi"
|
||||
|
||||
|
||||
vcfanno_tar_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno_grch38_module_test.tar.gz"
|
||||
vcfanno_toml = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml"
|
||||
}
|
||||
|
|
@ -270,6 +275,9 @@ params {
|
|||
test_genome21_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz"
|
||||
test_genome21_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi"
|
||||
|
||||
test_mpileup = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz"
|
||||
test2_mpileup = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz"
|
||||
|
||||
test_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak"
|
||||
test2_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak"
|
||||
|
||||
|
|
@ -314,6 +322,8 @@ params {
|
|||
'genome' {
|
||||
genome_fna_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz"
|
||||
genome_paf = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf"
|
||||
genome_mapping_potential_arg = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.mapping.potential.ARG"
|
||||
|
||||
}
|
||||
'illumina' {
|
||||
test1_contigs_fa_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz"
|
||||
|
|
|
|||
|
|
@ -1,31 +1,44 @@
|
|||
- name: adapterremoval test_adapterremoval_single_end
|
||||
command: nextflow run ./tests/modules/adapterremoval -entry test_adapterremoval_single_end -c ./tests/config/nextflow.config -c ./tests/modules/adapterremoval/nextflow.config
|
||||
command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- adapterremoval
|
||||
files:
|
||||
- path: output/adapterremoval/test.discarded.gz
|
||||
- path: output/adapterremoval/test.log
|
||||
md5sum: 2fd3d5d703b63ba33a83021fccf25f77
|
||||
- path: output/adapterremoval/test.trimmed.fastq.gz
|
||||
- path: output/adapterremoval/test.truncated.gz
|
||||
md5sum: 62139afee94defad5b83bdd0b8475a1f
|
||||
- path: output/adapterremoval/versions.yml
|
||||
md5sum: ac5b46719719b7ee62739530b80869fc
|
||||
|
||||
- name: adapterremoval test_adapterremoval_paired_end
|
||||
command: nextflow run ./tests/modules/adapterremoval -entry test_adapterremoval_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/adapterremoval/nextflow.config
|
||||
command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- adapterremoval
|
||||
files:
|
||||
- path: output/adapterremoval/test.discarded.gz
|
||||
- path: output/adapterremoval/test.log
|
||||
md5sum: b8a451d3981b327f3fdb44f40ba2d6d1
|
||||
- path: output/adapterremoval/test.pair1.trimmed.fastq.gz
|
||||
- path: output/adapterremoval/test.pair1.truncated.gz
|
||||
md5sum: 294a6277f0139bd597e57c6fa31f39c7
|
||||
- path: output/adapterremoval/test.pair2.trimmed.fastq.gz
|
||||
- path: output/adapterremoval/test.pair2.truncated.gz
|
||||
md5sum: de7b38e2c881bced8671acb1ab452d78
|
||||
- path: output/adapterremoval/test.singleton.truncated.gz
|
||||
- path: output/adapterremoval/versions.yml
|
||||
md5sum: fa621c887897da5a379c719399c17db7
|
||||
|
||||
- name: adapterremoval test_adapterremoval_paired_end_collapse
|
||||
command: nextflow run ./tests/modules/adapterremoval -entry test_adapterremoval_paired_end_collapse -c ./tests/config/nextflow.config -c ./tests/modules/adapterremoval/nextflow.config
|
||||
command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end_collapse -c tests/config/nextflow.config
|
||||
tags:
|
||||
- adapterremoval
|
||||
files:
|
||||
- path: output/adapterremoval/test.discarded.gz
|
||||
- path: output/adapterremoval/test.log
|
||||
md5sum: 7f0b2328152226e46101a535cce718b3
|
||||
- path: output/adapterremoval/test.merged.fastq.gz
|
||||
md5sum: 07a8f725bfd3ecbeabdc41b32d898dee
|
||||
md5sum: b8a451d3981b327f3fdb44f40ba2d6d1
|
||||
- path: output/adapterremoval/test.pair1.truncated.gz
|
||||
md5sum: 294a6277f0139bd597e57c6fa31f39c7
|
||||
- path: output/adapterremoval/test.pair2.truncated.gz
|
||||
md5sum: de7b38e2c881bced8671acb1ab452d78
|
||||
- path: output/adapterremoval/test.singleton.truncated.gz
|
||||
- path: output/adapterremoval/versions.yml
|
||||
md5sum: fd428f92a8446e0b34c5ae1c447215b8
|
||||
|
|
|
|||
23
tests/modules/bcftools/annotate/main.nf
Normal file
23
tests/modules/bcftools/annotate/main.nf
Normal file
|
|
@ -0,0 +1,23 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { BCFTOOLS_ANNOTATE } from '../../../../modules/bcftools/annotate/main.nf'
|
||||
|
||||
workflow test_bcftools_annotate_out_vcf {
|
||||
|
||||
input = [
|
||||
[ id:'test_compressed_vcf', single_end:false ], // meta map
|
||||
file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
|
||||
|
||||
BCFTOOLS_ANNOTATE ( input )
|
||||
}
|
||||
|
||||
workflow test_bcftools_annotate_out_bcf {
|
||||
|
||||
input = [
|
||||
[ id:'test_compressed_bcf', single_end:false ], // meta map
|
||||
file(params.test_data['sarscov2']['illumina']['test_bcf'], checkIfExists: true) ]
|
||||
|
||||
BCFTOOLS_ANNOTATE ( input )
|
||||
}
|
||||
5
tests/modules/bcftools/annotate/nextflow.config
Normal file
5
tests/modules/bcftools/annotate/nextflow.config
Normal file
|
|
@ -0,0 +1,5 @@
|
|||
process {
|
||||
ext.args = "-x ID,INFO/DP,FORMAT/DP"
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
||||
19
tests/modules/bcftools/annotate/test.yml
Normal file
19
tests/modules/bcftools/annotate/test.yml
Normal file
|
|
@ -0,0 +1,19 @@
|
|||
- name: bcftools annotate test_bcftools_annotate_out_vcf
|
||||
command: nextflow run tests/modules/bcftools/annotate -entry test_bcftools_annotate_out_vcf -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bcftools/annotate
|
||||
- bcftools
|
||||
files:
|
||||
- path: output/bcftools/test_compressed_vcf_annotated.vcf.gz
|
||||
- path: output/bcftools/versions.yml
|
||||
md5sum: de86d4d411baef1aaee0e72f519dbe1f
|
||||
|
||||
- name: bcftools annotate test_bcftools_annotate_out_bcf
|
||||
command: nextflow run tests/modules/bcftools/annotate -entry test_bcftools_annotate_out_bcf -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bcftools/annotate
|
||||
- bcftools
|
||||
files:
|
||||
- path: output/bcftools/test_compressed_bcf_annotated.bcf
|
||||
- path: output/bcftools/versions.yml
|
||||
md5sum: a57e62a5a189fe85aabd52c010d88ca6
|
||||
|
|
@ -5,4 +5,4 @@
|
|||
- bwa/sampe
|
||||
files:
|
||||
- path: output/bwa/test.bam
|
||||
md5sum: f6ad85d66d44c5d26e692109d2e34100
|
||||
md5sum: 01d1d71c88b6de07ed51d1d06e9e970b
|
||||
|
|
|
|||
|
|
@ -5,4 +5,4 @@
|
|||
- bwa/samse
|
||||
files:
|
||||
- path: output/bwa/test.bam
|
||||
md5sum: 27eb91146e45dee65664c18596be4262
|
||||
md5sum: ddfa4a8f6b65d44704a2d9528abc7e79
|
||||
|
|
|
|||
37
tests/modules/controlfreec/main.nf
Normal file
37
tests/modules/controlfreec/main.nf
Normal file
|
|
@ -0,0 +1,37 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { CONTROLFREEC } from '../../../modules/controlfreec/main.nf'
|
||||
include { UNTAR } from '../../../modules/untar/main.nf'
|
||||
workflow test_controlfreec {
|
||||
|
||||
input = [
|
||||
[ id:'test', single_end:false, sex:'XX' ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
|
||||
[],[],[],[]
|
||||
]
|
||||
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||||
|
||||
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
|
||||
dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
|
||||
|
||||
chrfiles = file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true)
|
||||
target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
|
||||
|
||||
UNTAR(chrfiles)
|
||||
CONTROLFREEC ( input,
|
||||
fasta,
|
||||
fai,
|
||||
[],
|
||||
dbsnp,
|
||||
dbsnp_tbi,
|
||||
UNTAR.out.untar,
|
||||
[],
|
||||
target_bed,
|
||||
[]
|
||||
)
|
||||
}
|
||||
26
tests/modules/controlfreec/nextflow.config
Normal file
26
tests/modules/controlfreec/nextflow.config
Normal file
|
|
@ -0,0 +1,26 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
withName:CONTROLFREEC{
|
||||
ext.args = { [
|
||||
"sample":[
|
||||
inputformat: 'pileup',
|
||||
mateorientation: 'FR'
|
||||
],
|
||||
"general" :[
|
||||
bedgraphoutput: "TRUE",
|
||||
noisydata: "TRUE",
|
||||
minexpectedgc: "0",
|
||||
readcountthreshold: "1",
|
||||
sex: meta.sex,
|
||||
window: "10",
|
||||
],
|
||||
"control":[
|
||||
inputformat: "pileup",
|
||||
mateorientation: "FR"
|
||||
]
|
||||
]
|
||||
}
|
||||
}
|
||||
}
|
||||
22
tests/modules/controlfreec/test.yml
Normal file
22
tests/modules/controlfreec/test.yml
Normal file
|
|
@ -0,0 +1,22 @@
|
|||
- name: controlfreec test_controlfreec
|
||||
command: nextflow run tests/modules/controlfreec -entry test_controlfreec -c tests/config/nextflow.config
|
||||
tags:
|
||||
- controlfreec
|
||||
files:
|
||||
- path: output/controlfreec/config.txt
|
||||
- path: output/controlfreec/test.mpileup.gz_control.cpn
|
||||
md5sum: 1768b571677c418560e5a8fe203bdc79
|
||||
- path: output/controlfreec/test2.mpileup.gz_BAF.txt
|
||||
md5sum: 3bb7437001cf061a77eaf87b8558c48d
|
||||
- path: output/controlfreec/test2.mpileup.gz_CNVs
|
||||
md5sum: 1f4f5834dbd1490afdb22f6d3091c4c9
|
||||
- path: output/controlfreec/test2.mpileup.gz_info.txt
|
||||
md5sum: 1a3055d35028525ccc9e693cc9f335e0
|
||||
- path: output/controlfreec/test2.mpileup.gz_ratio.BedGraph
|
||||
md5sum: 8ba455b232be20cdcc5bf1e4035e8032
|
||||
- path: output/controlfreec/test2.mpileup.gz_ratio.txt
|
||||
md5sum: b76b2434de710325069e37fb1e132760
|
||||
- path: output/controlfreec/test2.mpileup.gz_sample.cpn
|
||||
md5sum: c80dad58a77b1d7ba6d273999f4b4b4b
|
||||
- path: output/controlfreec/versions.yml
|
||||
md5sum: ff93f6466d4686aab708425782c6c848
|
||||
|
|
@ -1,5 +1,6 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
ext.args = {"--debug" }
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -3,8 +3,20 @@
|
|||
tags:
|
||||
- faqcs
|
||||
files:
|
||||
- path: output/faqcs/qa.test.base_content.txt
|
||||
md5sum: f992603f01ca430c03c8aae02eba2f5d
|
||||
- path: output/faqcs/qa.test.for_qual_histogram.txt
|
||||
md5sum: a3d462ab84151e982f99f85f52c21de3
|
||||
- path: output/faqcs/qa.test.length_count.txt
|
||||
md5sum: 80915f09fbaf5884c32e95acab2d031c
|
||||
- path: output/faqcs/test.base_content.txt
|
||||
md5sum: f992603f01ca430c03c8aae02eba2f5d
|
||||
- path: output/faqcs/test.fastp.log
|
||||
md5sum: be79dc893f87de1f82faf749cdfb848c
|
||||
- path: output/faqcs/test.for_qual_histogram.txt
|
||||
md5sum: a3d462ab84151e982f99f85f52c21de3
|
||||
- path: output/faqcs/test.length_count.txt
|
||||
md5sum: 80915f09fbaf5884c32e95acab2d031c
|
||||
- path: output/faqcs/test.stats.txt
|
||||
md5sum: ea20e93706b2e4c676004253baa3cec6
|
||||
- path: output/faqcs/test.trimmed.fastq.gz
|
||||
|
|
@ -18,8 +30,20 @@
|
|||
tags:
|
||||
- faqcs
|
||||
files:
|
||||
- path: output/faqcs/qa.test.base_content.txt
|
||||
md5sum: 99aa9a775ccd8d6503f0cf80f775203c
|
||||
- path: output/faqcs/qa.test.for_qual_histogram.txt
|
||||
md5sum: 4f4b131be5425bdfa4b3237e44fa7d48
|
||||
- path: output/faqcs/qa.test.length_count.txt
|
||||
md5sum: 420298983c762754d5b0ef32c9d5dad4
|
||||
- path: output/faqcs/test.base_content.txt
|
||||
md5sum: 99aa9a775ccd8d6503f0cf80f775203c
|
||||
- path: output/faqcs/test.fastp.log
|
||||
md5sum: be79dc893f87de1f82faf749cdfb848c
|
||||
- path: output/faqcs/test.for_qual_histogram.txt
|
||||
md5sum: 4f4b131be5425bdfa4b3237e44fa7d48
|
||||
- path: output/faqcs/test.length_count.txt
|
||||
md5sum: 420298983c762754d5b0ef32c9d5dad4
|
||||
- path: output/faqcs/test.stats.txt
|
||||
md5sum: 9a693f8af94ab8c485519d9a523aa622
|
||||
- path: output/faqcs/test_1.trimmed.fastq.gz
|
||||
|
|
|
|||
15
tests/modules/hamronization/deeparg/main.nf
Normal file
15
tests/modules/hamronization/deeparg/main.nf
Normal file
|
|
@ -0,0 +1,15 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { HAMRONIZATION_DEEPARG } from '../../../../modules/hamronization/deeparg/main.nf'
|
||||
|
||||
workflow test_hamronization_deeparg {
|
||||
|
||||
input = [
|
||||
[ id:'test', single_end:false ], // meta map
|
||||
file(params.test_data['bacteroides_fragilis']['genome']['genome_mapping_potential_arg'], checkIfExists: true),
|
||||
]
|
||||
|
||||
HAMRONIZATION_DEEPARG ( input, 'tsv', '1.0.2', '2' )
|
||||
}
|
||||
5
tests/modules/hamronization/deeparg/nextflow.config
Normal file
5
tests/modules/hamronization/deeparg/nextflow.config
Normal file
|
|
@ -0,0 +1,5 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
||||
8
tests/modules/hamronization/deeparg/test.yml
Normal file
8
tests/modules/hamronization/deeparg/test.yml
Normal file
|
|
@ -0,0 +1,8 @@
|
|||
- name: hamronization deeparg test_hamronization_deeparg
|
||||
command: nextflow run tests/modules/hamronization/deeparg -entry test_hamronization_deeparg -c tests/config/nextflow.config
|
||||
tags:
|
||||
- hamronization
|
||||
- hamronization/deeparg
|
||||
files:
|
||||
- path: output/hamronization/test.tsv
|
||||
md5sum: 3c315605aca0c5964796bb5fd4cdd522
|
||||
36
tests/modules/hamronization/summarize/main.nf
Normal file
36
tests/modules/hamronization/summarize/main.nf
Normal file
|
|
@ -0,0 +1,36 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { HAMRONIZATION_DEEPARG } from '../../../../modules/hamronization/deeparg/main.nf'
|
||||
include { HAMRONIZATION_DEEPARG as HAMRONIZATION_DEEPARG_SECOND } from '../../../../modules/hamronization/deeparg/main.nf'
|
||||
include { HAMRONIZATION_SUMMARIZE } from '../../../../modules/hamronization/summarize/main.nf'
|
||||
|
||||
workflow test_hamronization_summarize {
|
||||
|
||||
input = [
|
||||
[ id:'test', single_end:false ], // meta map
|
||||
file(params.test_data['bacteroides_fragilis']['genome']['genome_mapping_potential_arg'], checkIfExists: true),
|
||||
]
|
||||
|
||||
input2 = [
|
||||
[ id:'test2', single_end:false ], // meta map
|
||||
file(params.test_data['bacteroides_fragilis']['genome']['genome_mapping_potential_arg'], checkIfExists: true),
|
||||
]
|
||||
|
||||
HAMRONIZATION_DEEPARG ( input, 'tsv', '1.0.2', '2' )
|
||||
HAMRONIZATION_DEEPARG_SECOND ( input2, 'tsv', '1.0.2', '2' )
|
||||
|
||||
ch_deeparg_run_one = HAMRONIZATION_DEEPARG.out.tsv
|
||||
ch_deeparg_run_two = HAMRONIZATION_DEEPARG_SECOND.out.tsv
|
||||
|
||||
ch_deeparg_run_one
|
||||
.mix( ch_deeparg_run_two )
|
||||
.map{
|
||||
[ it[1] ]
|
||||
}
|
||||
.collect()
|
||||
.set { ch_input_for_summarize }
|
||||
|
||||
HAMRONIZATION_SUMMARIZE ( ch_input_for_summarize , 'json' )
|
||||
}
|
||||
5
tests/modules/hamronization/summarize/nextflow.config
Normal file
5
tests/modules/hamronization/summarize/nextflow.config
Normal file
|
|
@ -0,0 +1,5 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
||||
14
tests/modules/hamronization/summarize/test.yml
Normal file
14
tests/modules/hamronization/summarize/test.yml
Normal file
|
|
@ -0,0 +1,14 @@
|
|||
- name: hamronization summarize test_hamronization_summarize
|
||||
command: nextflow run tests/modules/hamronization/summarize -entry test_hamronization_summarize -c tests/config/nextflow.config
|
||||
tags:
|
||||
- hamronization
|
||||
- hamronization/summarize
|
||||
files:
|
||||
- path: output/hamronization/hamronization_combined_report.json
|
||||
md5sum: 1623b6cc3b213208a425e023edd94691
|
||||
- path: output/hamronization/test.tsv
|
||||
md5sum: 3c315605aca0c5964796bb5fd4cdd522
|
||||
- path: output/hamronization/test2.tsv
|
||||
md5sum: 453f38502e35261a50a0849dca34f05b
|
||||
- path: output/hamronization/versions.yml
|
||||
md5sum: 99b5046fac643e16ca3362d1baf3284b
|
||||
15
tests/modules/hpsuissero/main.nf
Normal file
15
tests/modules/hpsuissero/main.nf
Normal file
|
|
@ -0,0 +1,15 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { HPSUISSERO } from '../../../modules/hpsuissero/main.nf'
|
||||
|
||||
workflow test_hpsuissero {
|
||||
|
||||
input = [
|
||||
[ id:'test', single_end:false ], // meta map
|
||||
file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true)
|
||||
]
|
||||
|
||||
HPSUISSERO ( input )
|
||||
}
|
||||
5
tests/modules/hpsuissero/nextflow.config
Normal file
5
tests/modules/hpsuissero/nextflow.config
Normal file
|
|
@ -0,0 +1,5 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
||||
9
tests/modules/hpsuissero/test.yml
Normal file
9
tests/modules/hpsuissero/test.yml
Normal file
|
|
@ -0,0 +1,9 @@
|
|||
- name: hpsuissero test_hpsuissero
|
||||
command: nextflow run tests/modules/hpsuissero -entry test_hpsuissero -c tests/config/nextflow.config
|
||||
tags:
|
||||
- hpsuissero
|
||||
files:
|
||||
- path: output/hpsuissero/test_serotyping_res.tsv
|
||||
md5sum: 559dd2ca386eeb58f3975e3204ce9d43
|
||||
- path: output/hpsuissero/versions.yml
|
||||
md5sum: f65438e63a74ac6ee365bfdbbd3f996a
|
||||
15
tests/modules/mafft/main.nf
Normal file
15
tests/modules/mafft/main.nf
Normal file
|
|
@ -0,0 +1,15 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { MAFFT } from '../../../modules/mafft/main.nf'
|
||||
|
||||
workflow test_mafft {
|
||||
|
||||
input = [
|
||||
[ id:'test', single_end:false ], // meta map
|
||||
file(params.test_data['sarscov2']['illumina']['scaffolds_fasta'], checkIfExists: true)
|
||||
]
|
||||
|
||||
MAFFT ( input )
|
||||
}
|
||||
6
tests/modules/mafft/nextflow.config
Normal file
6
tests/modules/mafft/nextflow.config
Normal file
|
|
@ -0,0 +1,6 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
ext.args = "--auto"
|
||||
|
||||
}
|
||||
9
tests/modules/mafft/test.yml
Normal file
9
tests/modules/mafft/test.yml
Normal file
|
|
@ -0,0 +1,9 @@
|
|||
- name: mafft test_mafft
|
||||
command: nextflow run tests/modules/mafft -entry test_mafft -c tests/config/nextflow.config
|
||||
tags:
|
||||
- mafft
|
||||
files:
|
||||
- path: output/mafft/test.fas
|
||||
md5sum: 23426611f4a0df532b6708f072bd445b
|
||||
- path: output/mafft/versions.yml
|
||||
md5sum: b1b5ab3728ae17401808335f1c8f8215
|
||||
|
|
@ -12,10 +12,14 @@ workflow test_malt_run {
|
|||
gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
|
||||
seq_type = "DNA"
|
||||
map_db = file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true)
|
||||
input = file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
|
||||
input = [
|
||||
[ id:'test', single_end:false ], // meta map
|
||||
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
|
||||
]
|
||||
mode = "BlastN"
|
||||
|
||||
UNZIP ( map_db )
|
||||
MALT_BUILD ( fastas, seq_type, gff, UNZIP.out.unzipped_archive )
|
||||
MALT_RUN ( input, mode, MALT_BUILD.out.index )
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -5,4 +5,4 @@
|
|||
- malt/run
|
||||
files:
|
||||
- path: output/malt/test_1.rma6
|
||||
- path: output/malt/malt-run.log
|
||||
- path: output/malt/test-malt-run.log
|
||||
|
|
|
|||
|
|
@ -4,7 +4,7 @@
|
|||
- picard/cleansam
|
||||
- picard
|
||||
files:
|
||||
- path: output/picard/test.sam
|
||||
md5sum: e314171a6060eb79947c13ad126ddf00
|
||||
- path: output/picard/test.bam
|
||||
md5sum: a48f8e77a1480445efc57570c3a38a68
|
||||
- path: output/picard/versions.yml
|
||||
md5sum: e6457d7c6de51bf6f4b577eda65e57ac
|
||||
|
|
|
|||
18
tests/modules/picard/sortvcf/main.nf
Normal file
18
tests/modules/picard/sortvcf/main.nf
Normal file
|
|
@ -0,0 +1,18 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { PICARD_SORTVCF } from '../../../../modules/picard/sortvcf/main.nf'
|
||||
|
||||
workflow test_picard_sortvcf {
|
||||
|
||||
input = [ [ id:'test' ], // meta map
|
||||
file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
|
||||
]
|
||||
|
||||
fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
|
||||
|
||||
dict = [ file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ]
|
||||
|
||||
PICARD_SORTVCF ( input, fasta, dict )
|
||||
}
|
||||
5
tests/modules/picard/sortvcf/nextflow.config
Normal file
5
tests/modules/picard/sortvcf/nextflow.config
Normal file
|
|
@ -0,0 +1,5 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
||||
7
tests/modules/picard/sortvcf/test.yml
Normal file
7
tests/modules/picard/sortvcf/test.yml
Normal file
|
|
@ -0,0 +1,7 @@
|
|||
- name: picard sortvcf
|
||||
command: nextflow run ./tests/modules/picard/sortvcf -entry test_picard_sortvcf -c ./tests/config/nextflow.config -c ./tests/modules/picard/sortvcf/nextflow.config
|
||||
tags:
|
||||
- picard
|
||||
- picard/sortvcf
|
||||
files:
|
||||
- path: output/picard/test_sorted.vcf.gz
|
||||
24
tests/modules/plink2/score/main.nf
Normal file
24
tests/modules/plink2/score/main.nf
Normal file
|
|
@ -0,0 +1,24 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { PLINK2_VCF } from '../../../../modules/plink2/vcf/main.nf'
|
||||
include { PLINK2_SCORE } from '../../../../modules/plink2/score/main.nf'
|
||||
|
||||
workflow test_plink2_score {
|
||||
input = [
|
||||
[ id:'test', single_end:false ], // meta map
|
||||
file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_vcf_gz'], checkIfExists: true)
|
||||
]
|
||||
PLINK2_VCF ( input )
|
||||
|
||||
scorefile = file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_score'], checkIfExists: true)
|
||||
|
||||
PLINK2_VCF.out.pgen
|
||||
.concat(PLINK2_VCF.out.psam, PLINK2_VCF.out.pvar)
|
||||
.groupTuple()
|
||||
.map { it.flatten() }
|
||||
.set { ch_target_genome }
|
||||
|
||||
PLINK2_SCORE ( ch_target_genome, scorefile )
|
||||
}
|
||||
15
tests/modules/plink2/score/nextflow.config
Normal file
15
tests/modules/plink2/score/nextflow.config
Normal file
|
|
@ -0,0 +1,15 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
// relabel input variants to a common scheme chr:pos:alt:ref
|
||||
withName: PLINK2_VCF {
|
||||
ext.args = '--set-missing-var-ids @:#:\\$1:\\$2'
|
||||
}
|
||||
|
||||
// scoring really needs an adjustment for small test dataset (n > 50
|
||||
// normally)
|
||||
withName: PLINK2_SCORE {
|
||||
ext.args = 'no-mean-imputation'
|
||||
}
|
||||
}
|
||||
16
tests/modules/plink2/score/test.yml
Normal file
16
tests/modules/plink2/score/test.yml
Normal file
|
|
@ -0,0 +1,16 @@
|
|||
- name: plink2 score test_plink2_score
|
||||
command: nextflow run tests/modules/plink2/score -entry test_plink2_score -c tests/config/nextflow.config
|
||||
tags:
|
||||
- plink2
|
||||
- plink2/score
|
||||
files:
|
||||
- path: output/plink2/test.pgen
|
||||
md5sum: fac12ca9041d6950f6b7d60ac2120721
|
||||
- path: output/plink2/test.psam
|
||||
md5sum: e6c714488754cb8448c3dfda08c4c0ea
|
||||
- path: output/plink2/test.pvar.zst
|
||||
md5sum: 98d59e9779a8b62d5032cd98b642a63b
|
||||
- path: output/plink2/test.sscore
|
||||
md5sum: 97bde840f69febd65f2c00e9243126e9
|
||||
- path: output/plink2/versions.yml
|
||||
md5sum: 71499ab14e1583c88ced3a7a4f05bfa7
|
||||
|
|
@ -1,12 +1,14 @@
|
|||
- name: plink2 vcf test_plink2_vcf
|
||||
command: nextflow run ./tests/modules/plink2/vcf -entry test_plink2_vcf -c ./tests/config/nextflow.config -c ./tests/modules/plink2/vcf/nextflow.config
|
||||
command: nextflow run tests/modules/plink2/vcf -entry test_plink2_vcf -c tests/config/nextflow.config
|
||||
tags:
|
||||
- plink2/vcf
|
||||
- plink2
|
||||
- plink2/vcf
|
||||
files:
|
||||
- path: output/plink2/test.pgen
|
||||
md5sum: d66d3cd4a6c9cca1a4073d7f4b277041
|
||||
- path: output/plink2/test.psam
|
||||
md5sum: dc3b77d7753a7bed41734323e3549b10
|
||||
- path: output/plink2/test.pvar
|
||||
md5sum: d61e53f847a6335138b584216b4e45d0
|
||||
- path: output/plink2/test.pvar.zst
|
||||
md5sum: b53cccb83e024a39789af5eab8de1c28
|
||||
- path: output/plink2/versions.yml
|
||||
md5sum: 82ada74bc81473b7cba377f696acf54c
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
- samtools/ampliconclip
|
||||
files:
|
||||
- path: output/samtools/test.bam
|
||||
md5sum: 678f9ab04fbe3206f0f96e170fd833e9
|
||||
md5sum: 5d0e8bc9e6059ef3a63ee6328a3935c7
|
||||
|
||||
- name: samtools ampliconclip no stats with rejects
|
||||
command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_no_stats_with_rejects -c ./tests/config/nextflow.config -c ./tests/modules/samtools/ampliconclip/nextflow.config
|
||||
|
|
@ -14,9 +14,9 @@
|
|||
- samtools/ampliconclip
|
||||
files:
|
||||
- path: output/samtools/test.bam
|
||||
md5sum: bbf65ea626539d96c8271e17d1fc988b
|
||||
md5sum: 2c998295d624c59620b7ffdb0cc080e2
|
||||
- path: output/samtools/test.cliprejects.bam
|
||||
md5sum: a0bee15aead020d16d0c81bd9667df46
|
||||
md5sum: f3ebba8d91ad29cc4d2d00943e6f6bab
|
||||
|
||||
- name: samtools ampliconclip with stats with rejects
|
||||
command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_with_stats_with_rejects -c ./tests/config/nextflow.config -c ./tests/modules/samtools/ampliconclip/nextflow.config
|
||||
|
|
@ -25,8 +25,8 @@
|
|||
- samtools/ampliconclip
|
||||
files:
|
||||
- path: output/samtools/test.bam
|
||||
md5sum: f5a3611ecad34ba2dde77096e1c7dd93
|
||||
md5sum: 87882973b425ab27aad6ef18faf11f25
|
||||
- path: output/samtools/test.cliprejects.bam
|
||||
md5sum: 90ee7ce908b4bdb89ab41e4410de9012
|
||||
md5sum: eb5e186e1a69864dc2e99a290f02ff78
|
||||
- path: output/samtools/test.clipstats.txt
|
||||
md5sum: fc23355e1743d47f2541f2cb1a7a0cda
|
||||
|
|
|
|||
|
|
@ -14,9 +14,9 @@
|
|||
- samtools
|
||||
files:
|
||||
- path: output/samtools/test_1.fq.gz
|
||||
md5sum: 4522edbe158ec4804765794569f67493
|
||||
md5sum: 1c84aadcdca10e97be2b5b6ce773f5ed
|
||||
- path: output/samtools/test_2.fq.gz
|
||||
md5sum: 7e00ef40d5cfe272b67461381019dcc1
|
||||
md5sum: e679ec035d3208785e704458d6b68c8c
|
||||
- path: output/samtools/test_other.fq.gz
|
||||
md5sum: 709872fc2910431b1e8b7074bfe38c67
|
||||
- path: output/samtools/test_singleton.fq.gz
|
||||
|
|
|
|||
|
|
@ -7,4 +7,4 @@
|
|||
- path: output/samtools/genome.fasta.fai
|
||||
md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5
|
||||
- path: output/samtools/versions.yml
|
||||
md5sum: d56671a7c8f8058944d3d536c3058f7f
|
||||
md5sum: 6a16b2148a0ab43e6d0506056e6a0409
|
||||
|
|
|
|||
|
|
@ -5,6 +5,6 @@
|
|||
- samtools/fastq
|
||||
files:
|
||||
- path: output/samtools/test_2.fastq.gz
|
||||
md5sum: 3b1c92f33a44a78d82f8360ab4fdfd61
|
||||
md5sum: 51e7a469b554de694799bec982fd722e
|
||||
- path: output/samtools/test_1.fastq.gz
|
||||
md5sum: 5a3f9c69a032c4ffd9071ea31a14e6f9
|
||||
md5sum: 6c2d5b467eb94e058300271a542e34e6
|
||||
|
|
|
|||
|
|
@ -5,4 +5,4 @@
|
|||
- samtools/fixmate
|
||||
files:
|
||||
- path: output/samtools/test.bam
|
||||
md5sum: a4092657a4b17170c7702a76cbf192a1
|
||||
md5sum: c7f574bb0c469e0ccfecb6b7210e03c5
|
||||
|
|
|
|||
|
|
@ -23,4 +23,4 @@
|
|||
- samtools/index
|
||||
files:
|
||||
- path: output/samtools/test.paired_end.sorted.bam.csi
|
||||
md5sum: 3dd9e3ed959fca075b88bb8dc3cf7dbd
|
||||
md5sum: 8d63373007553e74d823fc2b9cbcf84d
|
||||
|
|
|
|||
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Reference in a new issue