millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-11-10 20:23:10 +00:00
Code Issues Releases Packages Activity

Merge remote-tracking branch 'nf-core/master'

Browse source
This commit is contained in:
Chris Cheshire 2022-01-28 09:11:14 +00:00
commit b83db65f33
247 changed files with 3284 additions and 816 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

82
.github/check_duplicate_md5s.py vendored Normal file
View file

@ -0,0 +1,82 @@
#!/usr/bin/env python
from rich import print
from rich.table import Table
import click
import glob
import os
import yaml
@click.command()
@click.option(
"--min_dups",
default=5,
show_default=True,
help="Minimum number of duplicates to report",
)
@click.option(
"--search_dir",
default=f"{os.path.dirname(__file__)}/../tests/**/test.yml",
show_default=True,
help="Glob directory pattern used to find test YAML files",
)
def find_duplicate_md5s(min_dups, search_dir):
"""
Find duplicate file MD5 sums in test YAML files.
"""
md5_filenames = {}
md5_output_fn_counts = {}
module_counts = {}
# Loop through all files in tests/ called test.yml
for test_yml in glob.glob(search_dir, recursive=True):
# Open file and parse YAML
with open(test_yml, "r") as fh:
test_config = yaml.safe_load(fh)
# Loop through tests and check for duplicate md5s
for test in test_config:
for test_file in test.get("files", []):
if "md5sum" in test_file:
md5 = test_file["md5sum"]
md5_filenames[md5] = md5_filenames.get(md5, []) + [
os.path.basename(test_file.get("path"))
]
md5_output_fn_counts[md5] = md5_output_fn_counts.get(md5, 0) + 1
# Log the module that this md5 was in
modname = os.path.basename(os.path.dirname(test_yml))
# If tool/subtool show the whole thing
# Ugly code but trying to stat os-agnostic
if os.path.basename(
os.path.dirname(os.path.dirname(test_yml))
) not in ["modules", "config", "subworkflows"]:
modname = "{}/{}".format(
os.path.basename(
os.path.dirname(os.path.dirname(test_yml))
),
os.path.basename(os.path.dirname(test_yml)),
)
module_counts[md5] = module_counts.get(md5, []) + [modname]
# Set up rich table
table = Table(title="Duplicate MD5s", row_styles=["dim", ""])
table.add_column("MD5", style="cyan", no_wrap=True)
table.add_column("Count", style="magenta", justify="right")
table.add_column("Num modules", style="blue", justify="right")
table.add_column("Filenames", style="green")
# Add rows - sort md5_output_fn_counts by value
for md5 in sorted(md5_output_fn_counts, key=md5_output_fn_counts.get):
if md5_output_fn_counts[md5] >= min_dups:
table.add_row(
md5,
str(md5_output_fn_counts[md5]),
str(len(set(module_counts[md5]))),
", ".join(set(md5_filenames[md5])),
)
print(table)
if __name__ == "__main__":
find_duplicate_md5s()

15
.github/workflows/pytest-workflow.yml vendored
View file

@ -48,11 +48,6 @@ jobs:
restore-keys: |
${{ runner.os }}-pip-
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install Python dependencies
run: python -m pip install --upgrade pip pytest-workflow
@ -93,6 +88,16 @@ jobs:
# only use one thread for pytest-workflow to avoid race condition on conda cache.
run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof
- name: Output log on failure
if: failure()
run: |
echo "======> log.out <======="
cat /home/runner/pytest_workflow_*/*/log.out
echo
echo
echo "======> log.err <======="
cat /home/runner/pytest_workflow_*/*/log.err
- name: Upload logs on failure
if: failure()
uses: actions/upload-artifact@v2

10
.gitpod.yml Normal file
View file

@ -0,0 +1,10 @@
# List the start up tasks. Learn more https://www.gitpod.io/docs/config-start-tasks/
tasks:
- name: Install Nextflow
init: |
curl -s https://get.nextflow.io | bash
sudo mv nextflow /usr/local/bin
- name: Install pytest-workflow
init: |
pip install pytest-workflow

3
modules/artic/minion/main.nf
View file

@ -43,7 +43,10 @@ process ARTIC_MINION {
summary = ""
model = file(medaka_model).exists() ? "--medaka-model ./$medaka_model" : "--medaka-model $medaka_model"
}
def hd5_plugin_path = task.ext.hd5_plugin_path ? "export HDF5_PLUGIN_PATH=" + task.ext.hd5_plugin_path : "export HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin"
"""
$hd5_plugin_path
artic \\
minion \\
$args \\

2
modules/ataqv/ataqv/main.nf
View file

@ -5,7 +5,7 @@ process ATAQV_ATAQV {
conda (params.enable_conda ? "bioconda::ataqv=1.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ataqv:1.2.1--py39ha23c084_2' :
'quay.io/biocontainers/ataqv:1.2.1--py36hfdecbe1_2' }"
'quay.io/biocontainers/ataqv:1.2.1--py39ha23c084_2' }"
input:
tuple val(meta), path(bam), path(bai), path(peak_file)

6
modules/bcftools/concat/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_CONCAT {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0' :
'quay.io/biocontainers/bcftools:1.11--h7c999a4_0' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input:
tuple val(meta), path(vcfs)

15
modules/bcftools/consensus/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_CONSENSUS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input:
tuple val(meta), path(vcf), path(tbi), path(fasta)
@ -18,9 +18,12 @@ process BCFTOOLS_CONSENSUS {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
cat $fasta | bcftools consensus $vcf $args > ${prefix}.fa
header=\$(head -n 1 ${prefix}.fa | sed 's/>//g')
sed -i 's/\${header}/${meta.id}/g' ${prefix}.fa
cat $fasta \\
| bcftools \\
consensus \\
$vcf \\
$args \\
> ${prefix}.fa
cat <<-END_VERSIONS > versions.yml
"${task.process}":

6
modules/bcftools/filter/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_FILTER {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input:
tuple val(meta), path(vcf)

8
modules/bcftools/index/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_INDEX {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input:
tuple val(meta), path(vcf)
@ -13,7 +13,7 @@ process BCFTOOLS_INDEX {
output:
tuple val(meta), path("*.csi"), optional:true, emit: csi
tuple val(meta), path("*.tbi"), optional:true, emit: tbi
path "versions.yml" , emit: version
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''

6
modules/bcftools/isec/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_ISEC {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input:
tuple val(meta), path(vcfs), path(tbis)

6
modules/bcftools/merge/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_MERGE {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input:
tuple val(meta), path(vcfs), path(tbis)

15
modules/bcftools/mpileup/main.nf
View file

@ -2,19 +2,21 @@ process BCFTOOLS_MPILEUP {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input:
tuple val(meta), path(bam)
path fasta
path fasta
val save_mpileup
output:
tuple val(meta), path("*.gz") , emit: vcf
tuple val(meta), path("*.tbi") , emit: tbi
tuple val(meta), path("*stats.txt"), emit: stats
tuple val(meta), path("*.mpileup") , emit: mpileup, optional: true
path "versions.yml" , emit: versions
script:
@ -22,13 +24,16 @@ process BCFTOOLS_MPILEUP {
def args2 = task.ext.args2 ?: ''
def args3 = task.ext.args3 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def mpileup = save_mpileup ? "| tee ${prefix}.mpileup" : ""
"""
echo "${meta.id}" > sample_name.list
bcftools mpileup \\
bcftools \\
mpileup \\
--fasta-ref $fasta \\
$args \\
$bam \\
$mpileup \\
| bcftools call --output-type v $args2 \\
| bcftools reheader --samples sample_name.list \\
| bcftools view --output-file ${prefix}.vcf.gz --output-type z $args3

4
modules/bcftools/mpileup/meta.yml
View file

@ -26,6 +26,10 @@ input:
type: file
description: FASTA reference file
pattern: "*.{fasta,fa}"
- save_mpileup:
type: boolean
description: Save mpileup file generated by bcftools mpileup
patter: "*.mpileup"
output:
- meta:
type: map

6
modules/bcftools/norm/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_NORM {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::bcftools=1.13" : null)
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input:
tuple val(meta), path(vcf)

6
modules/bcftools/query/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_QUERY {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::bcftools=1.13" : null)
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input:
tuple val(meta), path(vcf), path(index)

6
modules/bcftools/reheader/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_REHEADER {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::bcftools=1.13" : null)
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input:
tuple val(meta), path(vcf)

32
modules/bcftools/sort/main.nf Normal file
View file

@ -0,0 +1,32 @@
process BCFTOOLS_SORT {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::bcftools=1.14" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0':
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input:
tuple val(meta), path(vcf)
output:
tuple val(meta), path("*.gz"), emit: vcf
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
bcftools \\
sort \\
--output ${prefix}.vcf.gz \\
$args \\
$vcf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
}

43
modules/bcftools/sort/meta.yml Normal file
View file

@ -0,0 +1,43 @@
name: bcftools_sort
description: Sorts VCF files
keywords:
- sorting
- VCF
- variant calling
tools:
- sort:
description: Sort VCF files by coordinates.
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
tool_dev_url: https://github.com/samtools/bcftools
doi: "10.1093/bioinformatics/btp352"
licence: ['MIT']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: The VCF/BCF file to be sorted
pattern: "*.{vcf.gz,vcf,bcf}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- vcf:
type: file
description: Sorted VCF file
pattern: "*.{vcf.gz}"
authors:
- "@Gwennid"

6
modules/bcftools/stats/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_STATS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input:
tuple val(meta), path(vcf)

6
modules/bcftools/view/main.nf
View file

@ -2,10 +2,10 @@ process BCFTOOLS_VIEW {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::bcftools=1.13" : null)
conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
input:
tuple val(meta), path(vcf), path(index)

19
modules/bowtie2/align/main.nf
View file

@ -2,27 +2,28 @@ process BOWTIE2_ALIGN {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? 'bioconda::bowtie2=2.4.2 bioconda::samtools=1.11 conda-forge::pigz=2.3.4' : null)
conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4 bioconda::samtools=1.14 conda-forge::pigz=2.6' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0' :
'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' :
'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' }"
input:
tuple val(meta), path(reads)
path index
val save_unaligned
output:
tuple val(meta), path('*.bam'), emit: bam
tuple val(meta), path('*.log'), emit: log
path "versions.yml" , emit: versions
tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq
tuple val(meta), path('*.bam') , emit: bam
tuple val(meta), path('*.log') , emit: log
tuple val(meta), path('*fastq.gz'), emit: fastq, optional:true
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if (meta.single_end) {
def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
def unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
"""
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
bowtie2 \\
@ -42,7 +43,7 @@ process BOWTIE2_ALIGN {
END_VERSIONS
"""
} else {
def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
"""
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
bowtie2 \\

2
modules/bowtie2/build/main.nf
View file

@ -5,7 +5,7 @@ process BOWTIE2_BUILD {
conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' :
'quay.io/biocontainers/bowtie2:2.4.4--py36hd4290be_0' }"
'quay.io/biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }"
input:
path fasta

44
modules/cat/cat/main.nf
View file

@ -18,30 +18,28 @@ process CAT_CAT {
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def file_list = files_in.collect { it.toString() }
if (file_list.size > 1) {
// | input | output | command1 | command2 |
// |-----------|------------|----------|----------|
// | gzipped | gzipped | cat | |
// | ungzipped | ungzipped | cat | |
// | gzipped | ungzipped | zcat | |
// | ungzipped | gzipped | cat | pigz |
// | input | output | command1 | command2 |
// |-----------|------------|----------|----------|
// | gzipped | gzipped | cat | |
// | ungzipped | ungzipped | cat | |
// | gzipped | ungzipped | zcat | |
// | ungzipped | gzipped | cat | pigz |
def in_zip = file_list[0].endsWith('.gz')
def out_zip = file_out.endsWith('.gz')
def command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
def command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
"""
$command1 \\
$args \\
${file_list.join(' ')} \\
$command2 \\
> $file_out
def in_zip = file_list[0].endsWith('.gz')
def out_zip = file_out.endsWith('.gz')
def command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
def command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
"""
$command1 \\
$args \\
${file_list.join(' ')} \\
$command2 \\
> $file_out
cat <<-END_VERSIONS > versions.yml
"${task.process}":
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
"""
}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
"""
}

1
modules/cellranger/.gitignore vendored
View file

@ -1 +1,2 @@
cellranger-*.tar.gz
bcl2fastq2-*.zip

13
modules/cellranger/Dockerfile
View file

@ -1,15 +1,22 @@
# Dockerfile to create container with Cell Ranger v6.1.2
# Push to nfcore/cellranger:<VER>
FROM continuumio/miniconda3:4.8.2
LABEL authors="Gisela Gabernet <gisela.gabernet@gmail.com>" \
description="Docker image containing Cell Ranger"
# Disclaimer: this container is not provided nor supported by 10x Genomics.
# Disclaimer: this container is not provided nor supported by Illumina or 10x Genomics.
# Install procps and clean apt cache
RUN apt-get update --allow-releaseinfo-change \
&& apt-get install -y procps \
&& apt-get install -y \
cpio \
procps \
rpm2cpio \
unzip \
&& apt-get clean -y && rm -rf /var/lib/apt/lists/*
# Copy pre-downloaded cellranger file
ENV CELLRANGER_VER 6.0.2
ENV CELLRANGER_VER=6.1.2
COPY cellranger-$CELLRANGER_VER.tar.gz /opt/cellranger-$CELLRANGER_VER.tar.gz
# Install cellranger

16
modules/cellranger/README.md
View file

@ -1,18 +1,24 @@
# Updating the docker container and making a new module release
Cell Ranger is a commercial tool by 10X Genomics. The container provided for the cellranger nf-core module is not provided nor supported by 10x Genomics. Updating the Cell Ranger version in the container and pushing the update to Dockerhub needs to be done manually.
Cell Ranger is a commercial tool from 10X Genomics. The container provided for the cellranger nf-core module is not provided nor supported by 10x Genomics. Updating the Cell Ranger versions in the container and pushing the update to Dockerhub needs to be done manually.
1. Navigate to the [Cell Ranger download page](https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest) and download the tar ball of the desired Cell Ranger version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
1. Navigate to the appropriate download page.
- [Cell Ranger](https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest): download the tar ball of the desired Cell Ranger version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
2. Edit the Dockerfile: update the Cell Ranger version in this line:
2. Edit the Dockerfile. Update the Cell Ranger versions in this line:
```bash
ENV CELLRANGER_VER <VERSION>
ENV CELLRANGER_VER=<VERSION>
```
3. Create the container:
3. Create and test the container:
```bash
docker build . -t nfcore/cellranger:<VERSION>
```
4. Access rights are needed to push the container to the Dockerhub nfcore organization, please ask a core team member to do so.
```bash
docker push nfcore/cellranger:<VERSION>
```

2
modules/cellranger/count/main.nf
View file

@ -5,7 +5,7 @@ process CELLRANGER_COUNT {
if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
}
container "nfcore/cellranger:6.0.2"
container "nfcore/cellranger:6.1.2"
input:
tuple val(meta), path(reads)

40
modules/cellranger/mkfastq/Dockerfile Normal file
View file

@ -0,0 +1,40 @@
# Dockerfile to create container with Cell Ranger v6.1.2 and bcl2fastq v2.20.0
# Push to nfcore/cellrangermkfastq:<VER>
FROM continuumio/miniconda3:4.8.2
LABEL authors="Regina Reynolds, Gisela Gabernet <gisela.gabernet@gmail.com>" \
description="Docker image containing bcl2fastq2 and Cell Ranger"
# Disclaimer: this container is not provided nor supported by Illumina or 10x Genomics.
# Install procps and clean apt cache
RUN apt-get update --allow-releaseinfo-change \
&& apt-get install -y \
cpio \
procps \
rpm2cpio \
unzip \
&& apt-get clean -y && rm -rf /var/lib/apt/lists/*
# Copy pre-downloaded bcl2fastq2 and cellranger file
ENV BCL2FASTQ2_VER=v2-20-0-linux-x86-64 \
CELLRANGER_VER=6.1.2
COPY bcl2fastq2-$BCL2FASTQ2_VER.zip /tmp/bcl2fastq2-$BCL2FASTQ2_VER.zip
COPY cellranger-$CELLRANGER_VER.tar.gz /opt/cellranger-$CELLRANGER_VER.tar.gz
# Install bcl2fastq2
RUN \
cd /tmp && \
unzip bcl2fastq2-$BCL2FASTQ2_VER.zip && \
mv *.rpm bcl2fastq2-$BCL2FASTQ2_VER.rpm && \
rpm2cpio ./bcl2fastq2-$BCL2FASTQ2_VER.rpm | cpio -idmv && \
export PATH=/tmp/usr/local/bin/:$PATH && \
ln -s /tmp/usr/local/bin/bcl2fastq /usr/bin/bcl2fastq && \
rm -rf bcl2fastq2-$BCL2FASTQ2_VER.*
# Install cellranger
RUN \
cd /opt && \
tar -xzvf cellranger-$CELLRANGER_VER.tar.gz && \
export PATH=/opt/cellranger-$CELLRANGER_VER:$PATH && \
ln -s /opt/cellranger-$CELLRANGER_VER/cellranger /usr/bin/cellranger && \
rm -rf /opt/cellranger-$CELLRANGER_VER.tar.gz

26
modules/cellranger/mkfastq/README.md Normal file
View file

@ -0,0 +1,26 @@
# Updating the docker container and making a new module release
Bcl2fastq2 and Cell Ranger are commercial tools from Illumina and 10X Genomics, respectively. The container provided for the cellranger nf-core module is not provided nor supported by either Illumina or 10x Genomics. Updating the bcl2fastq2 or Cell Ranger versions in the container and pushing the update to Dockerhub needs to be done manually.
1. Navigate to the appropriate download pages.
- [bcl2fastq2](https://emea.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html): download the linux rpm installer of the desired bcl2fastq2 version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
- [Cell Ranger](https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest): download the tar ball of the desired Cell Ranger version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
2. Edit the Dockerfile. Update the bcl2fastq2 and Cell Ranger versions in this line:
```bash
ENV BCL2FASTQ2_VER=<VERSION> \
CELLRANGER_VER=<VERSION>
```
3. Create and test the container:
```bash
docker build . -t nfcore/cellrangermkfastq:<CELLRANGER_VERSION>
```
4. Access rights are needed to push the container to the Dockerhub nfcore organization, please ask a core team member to do so.
```bash
docker push nfcore/cellrangermkfastq:<CELLRANGER_VERSION>
```

17
modules/cellranger/mkfastq/main.nf
View file

@ -5,7 +5,7 @@ process CELLRANGER_MKFASTQ {
if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
}
container "litd/docker-cellranger:v6.1.1" // FIXME Add bcl2fastq to nf-core docker image
container "nfcore/cellrangermkfastq:6.1.2"
input:
path bcl
@ -13,14 +13,14 @@ process CELLRANGER_MKFASTQ {
output:
path "versions.yml", emit: versions
path "*.fastq.gz" , emit: fastq
path "${bcl.getSimpleName()}/outs/fastq_path/*.fastq.gz" , emit: fastq
script:
def args = task.ext.args ?: ''
"""
cellranger mkfastq --id=${bcl.getSimpleName()} \
--run=$bcl \
--csv=$csv
--csv=$csv \
$args
cat <<-END_VERSIONS > versions.yml
@ -28,4 +28,15 @@ process CELLRANGER_MKFASTQ {
cellranger: \$(echo \$( cellranger --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' )
END_VERSIONS
"""
stub:
"""
mkdir -p "${bcl.getSimpleName()}/outs/fastq_path/"
touch ${bcl.getSimpleName()}/outs/fastq_path/fake_file.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cellranger: \$(echo \$( cellranger --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' )
END_VERSIONS
"""
}

2
modules/cellranger/mkgtf/main.nf
View file

@ -5,7 +5,7 @@ process CELLRANGER_MKGTF {
if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
}
container "nfcore/cellranger:6.0.2"
container "nfcore/cellranger:6.1.2"
input:
path gtf

2
modules/cellranger/mkref/main.nf
View file

@ -5,7 +5,7 @@ process CELLRANGER_MKREF {
if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
}
container "nfcore/cellranger:6.0.2"
container "nfcore/cellranger:6.1.2"
input:
path fasta

16
modules/chromap/chromap/main.nf
View file

@ -1,13 +1,11 @@
def VERSION = '0.1' // Version information not provided by tool on CLI
process CHROMAP_CHROMAP {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::chromap=0.1 bioconda::samtools=1.13" : null)
conda (params.enable_conda ? "bioconda::chromap=0.1.5 bioconda::samtools=1.14" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0' :
'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:724a1037d59f6a19c9d4e7bdba77b52b37de0dc3-0' :
'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:724a1037d59f6a19c9d4e7bdba77b52b37de0dc3-0' }"
input:
tuple val(meta), path(reads)
@ -45,7 +43,7 @@ process CHROMAP_CHROMAP {
args_list << "--pairs-natural-chr-order $pairs_chr_order"
}
def final_args = args_list.join(' ')
def compression_cmds = "gzip ${prefix}.${file_extension}"
def compression_cmds = "gzip -n ${prefix}.${file_extension}"
if (args.contains("--SAM")) {
compression_cmds = """
samtools view $args2 -@ $task.cpus -bh \\
@ -67,7 +65,8 @@ process CHROMAP_CHROMAP {
cat <<-END_VERSIONS > versions.yml
"${task.process}":
chromap: $VERSION
chromap: \$(echo \$(chromap --version 2>&1))
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
} else {
@ -85,7 +84,8 @@ process CHROMAP_CHROMAP {
cat <<-END_VERSIONS > versions.yml
"${task.process}":
chromap: $VERSION
chromap: \$(echo \$(chromap --version 2>&1))
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}

12
modules/chromap/index/main.nf
View file

@ -1,13 +1,12 @@
def VERSION = '0.1' // Version information not provided by tool on CLI
process CHROMAP_INDEX {
tag '$fasta'
label 'process_medium'
conda (params.enable_conda ? "bioconda::chromap=0.1 bioconda::samtools=1.13" : null)
conda (params.enable_conda ? "bioconda::chromap=0.1.5" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0' :
'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0' }"
'https://depot.galaxyproject.org/singularity/chromap:0.1.5--h9a82719_0' :
'quay.io/biocontainers/chromap:0.1.5--h9a82719_0' }"
input:
path fasta
@ -29,8 +28,7 @@ process CHROMAP_INDEX {
cat <<-END_VERSIONS > versions.yml
"${task.process}":
chromap: $VERSION
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
chromap: \$(echo \$(chromap --version 2>&1))
END_VERSIONS
"""
}

2
modules/cutadapt/main.nf
View file

@ -5,7 +5,7 @@ process CUTADAPT {
conda (params.enable_conda ? 'bioconda::cutadapt=3.4' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cutadapt:3.4--py39h38f01e4_1' :
'quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1' }"
'quay.io/biocontainers/cutadapt:3.4--py39h38f01e4_1' }"
input:
tuple val(meta), path(reads)

30
modules/deeparg/downloaddata/main.nf Normal file
View file

@ -0,0 +1,30 @@
def VERSION='1.0.2'
process DEEPARG_DOWNLOADDATA {
label 'process_low'
conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/deeparg:1.0.2--pyhdfd78af_1' :
'quay.io/biocontainers/deeparg:1.0.2--pyhdfd78af_1' }"
input:
output:
path "db/" , emit: db
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
"""
deeparg \\
download_data \\
$args \\
-o db/
cat <<-END_VERSIONS > versions.yml
"${task.process}":
deeparg: $VERSION
END_VERSIONS
"""
}

33
modules/deeparg/downloaddata/meta.yml Normal file
View file

@ -0,0 +1,33 @@
name: deeparg_downloaddata
description: A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes
keywords:
- download
- database
- deeparg
- antimicrobial resistance genes
- deep learning
- prediction
tools:
- deeparg:
description: A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes
homepage: https://bench.cs.vt.edu/deeparg
documentation: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/
tool_dev_url: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/
doi: "10.1186/s40168-018-0401-z"
licence: ['MIT']
input:
- none: There is no input. This module downloads a pre-built database for use with deepARG.
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- db:
type: directory
description: Directory containing database required for deepARG.
pattern: "db/"
authors:
- "@jfy133"

40
modules/deeparg/predict/main.nf Normal file
View file

@ -0,0 +1,40 @@
def VERSION="1.0.2"
process DEEPARG_PREDICT {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity//deeparg:1.0.2--pyhdfd78af_1' :
'quay.io/biocontainers/deeparg:1.0.2--pyhdfd78af_1' }"
input:
tuple val(meta), path(fasta), val(model)
path(db)
output:
tuple val(meta), path("*.align.daa") , emit: daa
tuple val(meta), path("*.align.daa.tsv") , emit: daa_tsv
tuple val(meta), path("*.mapping.ARG") , emit: arg
tuple val(meta), path("*.mapping.potential.ARG"), emit: potential_arg
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
deeparg \\
predict \\
$args \\
-i $fasta \\
-o ${prefix} \\
-d $db \\
--model $model
cat <<-END_VERSIONS > versions.yml
"${task.process}":
deeparg: $VERSION
END_VERSIONS
"""
}

68
modules/deeparg/predict/meta.yml Normal file
View file

@ -0,0 +1,68 @@
name: deeparg_predict
description: A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes
keywords:
- deeparg
- antimicrobial resistance
- antimicrobial resistance genes
- arg
- deep learning
- prediction
- contigs
- metagenomes
tools:
- deeparg:
description: A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes
homepage: https://bench.cs.vt.edu/deeparg
documentation: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/
tool_dev_url: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/
doi: "10.1186/s40168-018-0401-z"
licence: ['MIT']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test' ]
- fasta:
type: file
description: FASTA file containing gene-like sequences
pattern: "*.{fasta,fa,fna}"
- model:
type: string
description: Which model to use, depending on input data. Either 'LS' or 'SS' for long or short sequences respectively
pattern: "LS|LS"
- db:
type: directory
description: Path to a directory containing the deepARG pre-built models
pattern: "*/"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- daa:
type: file
description: Sequences of ARG-like sequences from DIAMOND alignment
pattern: "*.align.daa"
- daa_tsv:
type: file
description: Alignments scores against ARG-like sequences from DIAMOND alignment
pattern: "*.align.daa.tsv"
- arg:
type: file
description: Table containing sequences with an ARG-like probability of more than specified thresholds
pattern: "*.mapping.ARG"
- potential_arg:
type: file
description: Table containing sequences with an ARG-like probability of less than specified thresholds, and requires manual inspection
pattern: "*.mapping.potential.ARG"
authors:
- "@jfy133"

44
modules/deepvariant/main.nf Normal file
View file

@ -0,0 +1,44 @@
process DEEPVARIANT {
tag "$meta.id"
label 'process_medium'
if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the DeepVariant tool. Please use docker or singularity containers."
}
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'google/deepvariant:1.3.0' :
'google/deepvariant:1.3.0' }"
input:
tuple val(meta), path(input), path(index), path(intervals)
path(fasta)
path(fai)
output:
tuple val(meta), path("*.vcf.gz") , emit: vcf
tuple val(meta), path("*g.vcf.gz"), emit: gvcf
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def regions = intervals ? "--regions ${intervals}" : ""
"""
/opt/deepvariant/bin/run_deepvariant \\
--ref=${fasta} \\
--reads=${input} \\
--output_vcf=${prefix}.vcf.gz \\
--output_gvcf=${prefix}.g.vcf.gz \\
${args} \\
${regions} \\
--num_shards=${task.cpus}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
deepvariant: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' )
END_VERSIONS
"""
}

62
modules/deepvariant/meta.yml Normal file
View file

@ -0,0 +1,62 @@
name: deepvariant
description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
keywords:
- variant calling
- machine learning
tools:
- deepvariant:
description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
homepage: https://github.com/google/deepvariant
documentation: https://github.com/google/deepvariant
tool_dev_url: https://github.com/google/deepvariant
doi: "https://doi.org/10.1038/nbt.4235"
licence: ['BSD-3-clause']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input:
type: file
description: BAM/CRAM file
pattern: "*.bam/cram"
- index:
type: file
description: Index of BAM/CRAM file
pattern: "*.bai/crai"
- interval:
type: file
description: Interval file for targeted regions
pattern: "*.bed"
- fasta:
type: file
description: The reference fasta file
pattern: "*.fasta"
- fai:
type: file
description: Index of reference fasta file
pattern: "*.fai"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: Compressed VCF file
pattern: "*.vcf.gz"
- gvcf:
type: file
description: Compressed GVCF file
pattern: "*.g.vcf.gz"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@abhi18av"

10
modules/dshbio/exportsegments/main.nf
View file

@ -2,16 +2,16 @@ process DSHBIO_EXPORTSEGMENTS {
tag "${meta.id}"
label 'process_medium'
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.6" : null)
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.6--hdfd78af_0' :
'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
input:
tuple val(meta), path(gfa)
output:
tuple val(meta), path("*.fa"), emit: fasta
tuple val(meta), path("*.fa.gz"), emit: fasta
path "versions.yml" , emit: versions
script:
@ -22,7 +22,7 @@ process DSHBIO_EXPORTSEGMENTS {
export-segments \\
$args \\
-i $gfa \\
-o ${prefix}.fa
-o ${prefix}.fa.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":

8
modules/dshbio/exportsegments/meta.yml
View file

@ -21,8 +21,8 @@ input:
e.g. [ id:'test', single_end:false ]
- gfa:
type: file
description: Assembly segments in GFA 1.0 format
pattern: "*.{gfa}"
description: Assembly segments in uncompressed or compressed GFA 1.0 format
pattern: "*.{gfa|gfa.bgz|gfa.gz|gfa.zst}"
output:
- meta:
type: map
@ -31,8 +31,8 @@ output:
e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: Assembly segment sequences in FASTA format
pattern: "*.{fa}"
description: Assembly segment sequences in gzipped FASTA format
pattern: "*.{fa.gz}"
- versions:
type: file
description: File containing software versions

6
modules/dshbio/filterbed/main.nf
View file

@ -2,10 +2,10 @@ process DSHBIO_FILTERBED {
tag "${meta.id}"
label 'process_medium'
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.6" : null)
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.6--hdfd78af_0' :
'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
input:
tuple val(meta), path(bed)

6
modules/dshbio/filtergff3/main.nf
View file

@ -2,10 +2,10 @@ process DSHBIO_FILTERGFF3 {
tag "${meta.id}"
label 'process_medium'
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.6" : null)
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.6--hdfd78af_0' :
'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
input:
tuple val(meta), path(gff3)

6
modules/dshbio/splitbed/main.nf
View file

@ -2,10 +2,10 @@ process DSHBIO_SPLITBED {
tag "${meta.id}"
label 'process_medium'
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.6" : null)
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.6--hdfd78af_0' :
'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
input:
tuple val(meta), path(bed)

6
modules/dshbio/splitgff3/main.nf
View file

@ -2,10 +2,10 @@ process DSHBIO_SPLITGFF3 {
tag "${meta.id}"
label 'process_medium'
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.6" : null)
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.6--hdfd78af_0' :
'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
input:
tuple val(meta), path(gff3)

6
modules/fastp/main.nf
View file

@ -2,10 +2,10 @@ process FASTP {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? 'bioconda::fastp=0.20.1' : null)
conda (params.enable_conda ? 'bioconda::fastp=0.23.2' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/fastp:0.20.1--h8b12597_0' :
'quay.io/biocontainers/fastp:0.20.1--h8b12597_0' }"
'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' :
'quay.io/biocontainers/fastp:0.23.2--h79da9fb_0' }"
input:
tuple val(meta), path(reads)

2
modules/fgbio/fastqtobam/main.nf
View file

@ -13,7 +13,7 @@ process FGBIO_FASTQTOBAM {
output:
tuple val(meta), path("*_umi_converted.bam"), emit: umibam
path "versions.yml" , emit: version
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''

18
modules/gatk4/applybqsr/main.nf
View file

@ -2,26 +2,28 @@ process GATK4_APPLYBQSR {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(input), path(input_index), path(bqsr_table)
tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
path fasta
path fai
path dict
path intervals
output:
tuple val(meta), path("*.bam"), emit: bam
path "versions.yml" , emit: versions
tuple val(meta), path("*.bam"), emit: bam, optional: true
tuple val(meta), path("*.cram"), emit: cram, optional: true
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def interval = intervals ? "-L ${intervals}" : ""
def file_type = input.getExtension()
def avail_mem = 3
if (!task.memory) {
log.info '[GATK ApplyBQSR] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@ -35,7 +37,7 @@ process GATK4_APPLYBQSR {
--bqsr-recal-file $bqsr_table \\
$interval \\
--tmp-dir . \\
-O ${prefix}.bam \\
-O ${prefix}.${file_type} \\
$args
cat <<-END_VERSIONS > versions.yml

7
modules/gatk4/applybqsr/meta.yml
View file

@ -31,6 +31,9 @@ input:
- bqsr_table:
type: file
description: Recalibration table from gatk4_baserecalibrator
- intervals:
type: file
description: Bed file with the genomic regions included in the library (optional)
- fasta:
type: file
description: The reference fasta file
@ -43,9 +46,7 @@ input:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
- intervalsBed:
type: file
description: Bed file with the genomic regions included in the library (optional)
output:
- meta:

55
modules/gatk4/applyvqsr/main.nf Normal file
View file

@ -0,0 +1,55 @@
process GATK4_APPLYVQSR {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(vcf), path(tbi), path(recal), path(recalidx), path(tranches)
path fasta
path fai
path dict
val allelespecific
val truthsensitivity
val mode
output:
tuple val(meta), path("*.vcf.gz") , emit: vcf
tuple val(meta), path("*.tbi") , emit: tbi
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
refCommand = fasta ? "-R ${fasta} " : ''
alleleSpecificCommand = allelespecific ? '-AS' : ''
truthSensitivityCommand = truthsensitivity ? "--truth-sensitivity-filter-level ${truthsensitivity}" : ''
modeCommand = mode ? "--mode ${mode} " : 'SNP'
def avail_mem = 3
if (!task.memory) {
log.info '[GATK ApplyVQSR] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk --java-options "-Xmx${avail_mem}g" ApplyVQSR \\
${refCommand} \\
-V ${vcf} \\
-O ${prefix}.vcf.gz \\
${alleleSpecificCommand} \\
${truthSensitivityCommand} \\
--tranches-file $tranches \\
--recal-file $recal \\
${modeCommand} \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}

88
modules/gatk4/applyvqsr/meta.yml Normal file
View file

@ -0,0 +1,88 @@
name: gatk4_applyvqsr
description: |
Apply a score cutoff to filter variants based on a recalibration table.
AplyVQSR performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR).
Specifically, it applies filtering to the input variants based on the recalibration table produced
in the first step by VariantRecalibrator and a target sensitivity value.
keywords:
- gatk4
- applyvqsr
- VQSR
tools:
- gatk4:
description: |
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
with a primary focus on variant discovery and genotyping. Its powerful processing engine
and high-performance computing features make it capable of taking on projects of any size.
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
licence: ['Apache-2.0']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test']
- vcf:
type: file
description: VCF file to be recalibrated, this should be the same file as used for the first stage VariantRecalibrator.
pattern: "*.vcf"
- tbi:
type: file
description: Tbi index for the input vcf file.
pattern: "*.vcf.tbi"
- recal:
type: file
description: Recalibration file produced when the input vcf was run through VariantRecalibrator in stage 1.
pattern: "*.recal"
- recalidx:
type: file
description: Index file for the recalibration file.
pattern: ".recal.idx"
- tranches:
type: boolean
description: Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1.
pattern: ".tranches"
- fasta:
type: file
description: The reference fasta file
pattern: "*.fasta"
- fai:
type: file
description: Index of reference fasta file
pattern: "*.fasta.fai"
- dict:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
- allelespecific:
type: boolean
description: Whether or not to run ApplyVQSR in allele specific mode, this should be kept the same as the stage 1 VariantRecalibrator run.
pattern: "{true,false}"
- truthsensitivity:
type: double
description: Value to be used as the truth sensitivity cutoff score.
pattern: "99.0"
- mode:
type: String
description: Specifies which recalibration mode to employ, should be the same as the stage 1 VariantRecalibrator run. (SNP is default, BOTH is intended for testing only)
pattern: "{SNP,INDEL,BOTH}"
output:
- vcf:
type: file
description: compressed vcf file containing the recalibrated variants.
pattern: "*.vcf.gz"
- tbi:
type: file
description: Index of recalibrated vcf file.
pattern: "*vcf.gz.tbi"
- versions:
type: file
description: File containing software versions.
pattern: "versions.yml"
authors:
- "@GCJMackenzie"

13
modules/gatk4/baserecalibrator/main.nf
View file

@ -2,17 +2,16 @@ process GATK4_BASERECALIBRATOR {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(input), path(input_index)
tuple val(meta), path(input), path(input_index), path(intervals)
path fasta
path fai
path dict
path intervalsBed
path knownSites
path knownSites_tbi
@ -23,14 +22,16 @@ process GATK4_BASERECALIBRATOR {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def intervalsCommand = intervalsBed ? "-L ${intervalsBed}" : ""
def intervalsCommand = intervals ? "-L ${intervals}" : ""
def sitesCommand = knownSites.collect{"--known-sites ${it}"}.join(' ')
def avail_mem = 3
if (!task.memory) {
log.info '[GATK BaseRecalibrator] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk --java-options "-Xmx${avail_mem}g" BaseRecalibrator \
-R $fasta \

6
modules/gatk4/baserecalibrator/meta.yml
View file

@ -28,6 +28,9 @@ input:
type: file
description: BAI/CRAI file from alignment
pattern: "*.{bai,crai}"
- intervals:
type: file
description: Bed file with the genomic regions included in the library (optional)
- fasta:
type: file
description: The reference fasta file
@ -40,9 +43,6 @@ input:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
- intervalsBed:
type: file
description: Bed file with the genomic regions included in the library (optional)
- knownSites:
type: file
description: Bed file with the genomic regions included in the library (optional)

6
modules/gatk4/bedtointervallist/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_BEDTOINTERVALLIST {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(bed)

12
modules/gatk4/calculatecontamination/main.nf
View file

@ -2,19 +2,19 @@ process GATK4_CALCULATECONTAMINATION {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(pileup), path(matched)
val segmentout
output:
tuple val(meta), path('*.contamination.table') , emit: contamination
tuple val(meta), path('*.segmentation.table') , optional:true, emit: segmentation
path "versions.yml" , emit: versions
tuple val(meta), path('*.contamination.table'), emit: contamination
tuple val(meta), path('*.segmentation.table') , emit: segmentation, optional:true
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''

6
modules/gatk4/createsequencedictionary/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_CREATESEQUENCEDICTIONARY {
tag "$fasta"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
path fasta

6
modules/gatk4/createsomaticpanelofnormals/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_CREATESOMATICPANELOFNORMALS {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(genomicsdb)

6
modules/gatk4/estimatelibrarycomplexity/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(cram)

6
modules/gatk4/fastqtosam/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_FASTQTOSAM {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(reads)

6
modules/gatk4/filtermutectcalls/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_FILTERMUTECTCALLS {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(vcf), path(tbi), path(stats), path(orientationbias), path(segmentation), path(contaminationfile), val(contaminationest)

6
modules/gatk4/gatherbqsrreports/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_GATHERBQSRREPORTS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_1':
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_1' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(recal_table)

6
modules/gatk4/genomicsdbimport/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_GENOMICSDBIMPORT {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(vcf), path(tbi), path(intervalfile), val(intervalval), path(wspace)

12
modules/gatk4/genotypegvcfs/main.nf
View file

@ -2,29 +2,29 @@ process GATK4_GENOTYPEGVCFS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0' :
'quay.io/biocontainers/gatk4:4.2.0.0--0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(gvcf), path(gvcf_index)
tuple val(meta), path(gvcf), path(gvcf_index), path(intervals)
path fasta
path fasta_index
path fasta_dict
path dbsnp
path dbsnp_index
path intervals_bed
output:
tuple val(meta), path("*.vcf.gz"), emit: vcf
tuple val(meta), path("*.tbi") , emit: tbi
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def dbsnp_options = dbsnp ? "-D ${dbsnp}" : ""
def interval_options = intervals_bed ? "-L ${intervals_bed}" : ""
def interval_options = intervals ? "-L ${intervals}" : ""
def gvcf_options = gvcf.name.endsWith(".vcf") || gvcf.name.endsWith(".vcf.gz") ? "$gvcf" : "gendb://$gvcf"
def avail_mem = 3
if (!task.memory) {

11
modules/gatk4/genotypegvcfs/meta.yml
View file

@ -25,6 +25,9 @@ input:
description: |
Tuple of gVCF(.gz) file (first) and its index (second) or the path to a GenomicsDB (and empty)
pattern: ["*.{vcf,vcf.gz}", "*.{idx,tbi}"]
- intervals:
type: file
description: Bed file with the genomic regions included in the library (optional)
- fasta:
type: file
description: Reference fasta file
@ -45,10 +48,6 @@ input:
type: tuple of files
description: dbSNP VCF index file
pattern: "*.tbi"
- intervals_bed:
type: file
description: An intevals BED file
pattern: "*.bed"
output:
- meta:
@ -60,6 +59,10 @@ output:
type: file
description: Genotyped VCF file
pattern: "*.vcf.gz"
- tbi:
type: file
description: Tbi index for VCF file
pattern: "*.vcf.gz"
- versions:
type: file
description: File containing software versions

6
modules/gatk4/getpileupsummaries/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_GETPILEUPSUMMARIES {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam), path(bai)

11
modules/gatk4/haplotypecaller/main.nf
View file

@ -2,19 +2,18 @@ process GATK4_HAPLOTYPECALLER {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(input), path(input_index)
tuple val(meta), path(input), path(input_index), path(intervals)
path fasta
path fai
path dict
path dbsnp
path dbsnp_tbi
path interval
output:
tuple val(meta), path("*.vcf.gz"), emit: vcf
@ -24,7 +23,7 @@ process GATK4_HAPLOTYPECALLER {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def interval_option = interval ? "-L ${interval}" : ""
def interval_option = intervals ? "-L ${intervals}" : ""
def dbsnp_option = dbsnp ? "-D ${dbsnp}" : ""
def avail_mem = 3
if (!task.memory) {

6
modules/gatk4/haplotypecaller/meta.yml
View file

@ -29,6 +29,9 @@ input:
type: file
description: BAI/CRAI file from alignment
pattern: "*.{bai,crai}"
- intervals:
type: file
description: Bed file with the genomic regions included in the library (optional)
- fasta:
type: file
description: The reference fasta file
@ -47,9 +50,6 @@ input:
- dbsnp_tbi:
type: file
description: VCF index of dbsnp (optional)
- interval:
type: file
description: Bed file with the genomic regions included in the library (optional)
output:
- meta:

6
modules/gatk4/indexfeaturefile/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_INDEXFEATUREFILE {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0' :
'quay.io/biocontainers/gatk4:4.2.0.0--0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(feature_file)

6
modules/gatk4/intervallisttools/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOOLS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(interval_list)

6
modules/gatk4/learnreadorientationmodel/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_LEARNREADORIENTATIONMODEL {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(f1r2)

6
modules/gatk4/markduplicates/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_MARKDUPLICATES {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(bams)

17
modules/gatk4/mergebamalignment/main.nf
View file

@ -2,14 +2,13 @@ process GATK4_MERGEBAMALIGNMENT {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(aligned)
path unmapped
tuple val(meta), path(aligned), path(unmapped)
path fasta
path dict
@ -28,10 +27,10 @@ process GATK4_MERGEBAMALIGNMENT {
}
"""
gatk --java-options "-Xmx${avail_mem}g" MergeBamAlignment \\
ALIGNED=$aligned \\
UNMAPPED=$unmapped \\
R=$fasta \\
O=${prefix}.bam \\
-ALIGNED $aligned \\
-UNMAPPED $unmapped \\
-R $fasta \\
-O ${prefix}.bam \\
$args
cat <<-END_VERSIONS > versions.yml

6
modules/gatk4/mergevcfs/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_MERGEVCFS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(vcfs)

6
modules/gatk4/mutect2/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_MUTECT2 {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta) , path(input) , path(input_index) , val(which_norm)

6
modules/gatk4/revertsam/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_REVERTSAM {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam)

6
modules/gatk4/samtofastq/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_SAMTOFASTQ {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam)

6
modules/gatk4/splitncigarreads/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_SPLITNCIGARREADS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam)

6
modules/gatk4/variantfiltration/main.nf
View file

@ -2,10 +2,10 @@ process GATK4_VARIANTFILTRATION {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(vcf), path(vcf_tbi)

62
modules/gatk4/variantrecalibrator/main.nf Normal file
View file

@ -0,0 +1,62 @@
process GATK4_VARIANTRECALIBRATOR {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
input:
tuple val(meta), path(vcf) , path(tbi)
path fasta
path fai
path dict
val allelespecific
tuple path(resvcfs), path(restbis), val(reslabels)
val annotation
val mode
val create_rscript
output:
tuple val(meta), path("*.recal") , emit: recal
tuple val(meta), path("*.idx") , emit: idx
tuple val(meta), path("*.tranches"), emit: tranches
tuple val(meta), path("*plots.R") , emit: plots, optional:true
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
refCommand = fasta ? "-R ${fasta} " : ''
alleleSpecificCommand = allelespecific ? '-AS' : ''
resourceCommand = '--resource:' + reslabels.join( ' --resource:')
annotationCommand = '-an ' + annotation.join( ' -an ')
modeCommand = mode ? "--mode ${mode} " : 'SNP'
rscriptCommand = create_rscript ? "--rscript-file ${prefix}.plots.R" : ''
def avail_mem = 3
if (!task.memory) {
log.info '[GATK VariantRecalibrator] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
gatk --java-options "-Xmx${avail_mem}g" VariantRecalibrator \\
${refCommand} \\
-V ${vcf} \\
${alleleSpecificCommand} \\
${resourceCommand} \\
${annotationCommand} \\
${modeCommand} \\
-O ${prefix}.recal \\
--tranches-file ${prefix}.tranches \\
${rscriptCommand}\\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}

98
modules/gatk4/variantrecalibrator/meta.yml Normal file
View file

@ -0,0 +1,98 @@
name: gatk4_variantrecalibrator
description: |
Build a recalibration model to score variant quality for filtering purposes.
It is highly recommended to follow GATK best practices when using this module,
the gaussian mixture model requires a large number of samples to be used for the
tool to produce optimal results. For example, 30 samples for exome data. For more details see
https://gatk.broadinstitute.org/hc/en-us/articles/4402736812443-Which-training-sets-arguments-should-I-use-for-running-VQSR-
keywords:
- VariantRecalibrator
- gatk4
- recalibration_model
tools:
- gatk4:
description: |
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
with a primary focus on variant discovery and genotyping. Its powerful processing engine
and high-performance computing features make it capable of taking on projects of any size.
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test' ]
- vcf:
type: file
description: input vcf file containing the variants to be recalibrated
pattern: "*.vcf.gz"
- tbi:
type: file
description: tbi file matching with -vcf
pattern: "*.vcf.gz.tbi"
- fasta:
type: file
description: The reference fasta file
pattern: "*.fasta"
- fai:
type: file
description: Index of reference fasta file
pattern: "fasta.fai"
- dict:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
- allelespecific:
type: boolean
description: specify whether to use allele specific annotations
pattern: "{true,false}"
- resvcfs:
type: list
description: resource files to be used as truth, training and known sites resources, this imports the files into the module, file names are specified again in the resource_labels to be called via the command.
pattern: '*/hapmap_3.3.hg38_chr21.vcf.gz'
- restbis:
type: list
description: tbis for the corresponding vcfs files to be used as truth, training and known resources.
pattern: '*/hapmap_3.3.hg38_chr21.vcf.gz.tbi'
- reslabels:
type: list
description: labels for the resource files to be used as truth, training and known sites resources, label should include an identifier,which kind of resource(s) it is, prior value and name of the file.
pattern: "hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38_chr21.vcf.gz"
- annotation:
type: list
description: specify which annotations should be used for calculations.
pattern: "['QD', 'MQ', 'FS', 'SOR']"
- mode:
type: string
description: specifies which recalibration mode to employ (SNP is default, BOTH is intended for testing only)
pattern: "{SNP,INDEL,BOTH}"
- rscript:
type: boolean
description: specify whether to generate rscript.plot output file
pattern: "{true,false}"
output:
- recal:
type: file
description: Output recal file used by ApplyVQSR
pattern: "*.recal"
- idx:
type: file
description: Index file for the recal output file
pattern: "*.idx"
- tranches:
type: file
description: Output tranches file used by ApplyVQSR
pattern: "*.tranches"
- plots:
type: file
description: Optional output rscript file to aid in visualization of the input data and learned model.
pattern: "*plots.R"
- version:
type: file
description: File containing software versions
pattern: "*.versions.yml"
authors:
- "@GCJMackenzie"

1
modules/gtdbtk/classifywf/main.nf
View file

@ -2,6 +2,7 @@ def VERSION = '1.5.0' // Version information not provided by tool on CLI
process GTDBTK_CLASSIFYWF {
tag "${meta.assembler}-${meta.id}"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gtdbtk=1.5.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

4
modules/hmmcopy/gccounter/main.nf
View file

@ -5,8 +5,8 @@ process HMMCOPY_GCCOUNTER {
conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_5' :
'quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_5' }"
'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7' :
'quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_7' }"
input:
path fasta

38
modules/hmmcopy/generatemap/main.nf Normal file
View file

@ -0,0 +1,38 @@
def VERSION = '0.1.1'
process HMMCOPY_GENERATEMAP {
tag '$bam'
label 'process_long'
conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7':
'quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_7' }"
input:
path fasta
output:
path "*.map.bw" , emit: bigwig
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
"""
# build required indexes
generateMap.pl -b \\
$args \\
$fasta
# run
generateMap.pl \\
$args \\
$fasta
cat <<-END_VERSIONS > versions.yml
"${task.process}":
hmmcopy: \$(echo $VERSION)
END_VERSIONS
"""
}

32
modules/hmmcopy/generatemap/meta.yml Normal file
View file

@ -0,0 +1,32 @@
name: hmmcopy_generatemap
description: Perl script (generateMap.pl) generates the mappability of a genome given a certain size of reads, for input to hmmcopy mapcounter. Takes a very long time on large genomes, is not parallelised at all.
keywords:
- hmmcopy
- mapcounter
- mappability
tools:
- hmmcopy:
description: C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy
homepage: https://github.com/shahcompbio/hmmcopy_utils
documentation: https://github.com/shahcompbio/hmmcopy_utils
tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils
doi: ""
licence: ['GPL v3']
input:
- fasta:
type: file
description: Input genome fasta file
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- bigwig:
type: file
description: bigwig file containing the mappability of the genome
pattern: "*.{map.bw}"
authors:
- "@sppearce"

31
modules/hmmcopy/mapcounter/main.nf Normal file
View file

@ -0,0 +1,31 @@
def VERSION = '0.1.1' // Version information not provided by tool on CLI
process HMMCOPY_MAPCOUNTER {
label 'process_medium'
conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7':
'quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_7' }"
input:
path bigwig
output:
path "*.map.wig" , emit: wig
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
"""
mapCounter \\
$args \\
$bigwig > ${bigwig.baseName}.map.wig
cat <<-END_VERSIONS > versions.yml
"${task.process}":
hmmcopy: \$(echo $VERSION)
END_VERSIONS
"""
}

34
modules/hmmcopy/mapcounter/meta.yml Normal file
View file

@ -0,0 +1,34 @@
name: hmmcopy_mapcounter
description: mapCounter function from HMMcopy utilities, used to generate mappability in non-overlapping windows from a bigwig file
keywords:
- hmmcopy
- mapcounter
- cnv
tools:
- hmmcopy:
description: C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy
homepage: https://github.com/shahcompbio/hmmcopy_utils
documentation: https://github.com/shahcompbio/hmmcopy_utils
tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils
doi: ""
licence: ['GPL v3']
input:
- bigwig:
type: file
description: BigWig file with the mappability score of the genome, for instance made with generateMap function.
pattern: "*.wig"
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- wig:
type: file
description: wig file containing mappability of each window of the genome
pattern: "*.map.wig"
authors:
- "@sppearce"

4
modules/hmmcopy/readcounter/main.nf
View file

@ -6,8 +6,8 @@ process HMMCOPY_READCOUNTER {
conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_5' :
'quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_5' }"
'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7' :
'quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_7' }"
input:
tuple val(meta), path(bam), path(bai)

2
modules/idr/main.nf
View file

@ -5,7 +5,7 @@ process IDR {
conda (params.enable_conda ? "bioconda::idr=2.0.4.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/idr:2.0.4.2--py39hcbe4a3b_5' :
'quay.io/biocontainers/idr:2.0.4.2--py38h9af456f_5' }"
'quay.io/biocontainers/idr:2.0.4.2--py39hcbe4a3b_5' }"
input:
path peaks

15
modules/ivar/consensus/main.nf
View file

@ -9,7 +9,8 @@ process IVAR_CONSENSUS {
input:
tuple val(meta), path(bam)
path fasta
path fasta
val save_mpileup
output:
tuple val(meta), path("*.fa") , emit: fasta
@ -21,14 +22,16 @@ process IVAR_CONSENSUS {
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : ""
def mpileup = save_mpileup ? "| tee ${prefix}.mpileup" : ""
"""
samtools mpileup \\
samtools \\
mpileup \\
--reference $fasta \\
$args2 \\
$bam | \\
$save_mpileup \\
ivar consensus \\
$bam \\
$mpileup \\
| ivar \\
consensus \\
$args \\
-p $prefix

4
modules/ivar/consensus/meta.yml
View file

@ -25,6 +25,10 @@ input:
type: file
description: The reference sequence used for mapping and generating the BAM file
pattern: "*.fa"
- save_mpileup:
type: boolean
description: Save mpileup file generated by ivar consensus
patter: "*.mpileup"
output:
- meta:
type: map

15
modules/ivar/variants/main.nf
View file

@ -11,6 +11,7 @@ process IVAR_VARIANTS {
tuple val(meta), path(bam)
path fasta
path gff
val save_mpileup
output:
tuple val(meta), path("*.tsv") , emit: tsv
@ -21,15 +22,17 @@ process IVAR_VARIANTS {
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : ""
def features = params.gff ? "-g $gff" : ""
def features = gff ? "-g $gff" : ""
def mpileup = save_mpileup ? "| tee ${prefix}.mpileup" : ""
"""
samtools mpileup \\
samtools \\
mpileup \\
$args2 \\
--reference $fasta \\
$bam | \\
$save_mpileup \\
ivar variants \\
$bam \\
$mpileup \\
| ivar \\
variants \\
$args \\
$features \\
-r $fasta \\

4
modules/ivar/variants/meta.yml
View file

@ -29,6 +29,10 @@ input:
type: file
description: A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done.
patter: "*.gff"
- save_mpileup:
type: boolean
description: Save mpileup file generated by ivar variants
patter: "*.mpileup"
output:
- meta:
type: map

2
modules/jupyternotebook/main.nf
View file

@ -9,7 +9,7 @@ process JUPYTERNOTEBOOK {
//ipykernel, jupytext, papermill and nbconvert Python packages.
conda (params.enable_conda ? "ipykernel=6.0.3 jupytext=1.11.4 nbconvert=6.1.0 papermill=2.3.3 matplotlib=3.4.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963%3A879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' :
'https://depot.galaxyproject.org/singularity/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' :
'quay.io/biocontainers/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' }"
input:

2
modules/kleborate/main.nf
View file

@ -21,7 +21,7 @@ process KLEBORATE {
kleborate \\
$args \\
--outfile ${prefix}.results.txt \\
--assemblies *.fasta
--assemblies $fastas
cat <<-END_VERSIONS > versions.yml
"${task.process}":

6
modules/kraken2/kraken2/main.nf
View file

@ -2,10 +2,10 @@ process KRAKEN2_KRAKEN2 {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? 'bioconda::kraken2=2.1.1 conda-forge::pigz=2.6' : null)
conda (params.enable_conda ? 'bioconda::kraken2=2.1.2 conda-forge::pigz=2.6' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:941789bd7fe00db16531c26de8bf3c5c985242a5-0' :
'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:941789bd7fe00db16531c26de8bf3c5c985242a5-0' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' :
'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' }"
input:
tuple val(meta), path(reads)

2
modules/krona/kronadb/main.nf
View file

@ -8,8 +8,6 @@ process KRONA_KRONADB {
'https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5' :
'quay.io/biocontainers/krona:2.7.1--pl526_5' }"
input:
output:
path 'taxonomy/taxonomy.tab', emit: db
path "versions.yml" , emit: versions

2
modules/last/postmask/main.nf
View file

@ -17,7 +17,7 @@ process LAST_POSTMASK {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if( "$maf" == "${prefix}.maf.gz" ) error "Input and output names are the same, use the suffix option to disambiguate"
if( "$maf" == "${prefix}.maf.gz" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
"""
last-postmask $args $maf | gzip --no-name > ${prefix}.maf.gz

11
modules/lima/main.nf
View file

@ -12,9 +12,7 @@ process LIMA {
path primers
output:
tuple val(meta), path("*.clips") , emit: clips
tuple val(meta), path("*.counts") , emit: counts
tuple val(meta), path("*.guess") , emit: guess
tuple val(meta), path("*.report") , emit: report
tuple val(meta), path("*.summary"), emit: summary
path "versions.yml" , emit: versions
@ -27,10 +25,18 @@ process LIMA {
tuple val(meta), path("*.fastq.gz") , optional: true, emit: fastqgz
tuple val(meta), path("*.xml") , optional: true, emit: xml
tuple val(meta), path("*.json") , optional: true, emit: json
tuple val(meta), path("*.clips") , optional: true, emit: clips
tuple val(meta), path("*.guess") , optional: true, emit: guess
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if( "$ccs" == "${prefix}.bam" ) error "Input and output names are the same, set prefix in module configuration"
if( "$ccs" == "${prefix}.fasta" ) error "Input and output names are the same, set prefix in module configuration"
if( "$ccs" == "${prefix}.fasta.gz" ) error "Input and output names are the same, set prefix in module configuration"
if( "$ccs" == "${prefix}.fastq" ) error "Input and output names are the same, set prefix in module configuration"
if( "$ccs" == "${prefix}.fastq.gz" ) error "Input and output names are the same, set prefix in module configuration"
"""
OUT_EXT=""
@ -46,7 +52,6 @@ process LIMA {
OUT_EXT="fastq.gz"
fi
echo \$OUT_EXT
lima \\
$ccs \\
$primers \\

Some files were not shown because too many files have changed in this diff Show more