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Merge branch 'master' into r-ampir

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Jasmin F 2022-06-10 14:57:24 +02:00 committed by GitHub
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18 changed files with 204 additions and 24 deletions
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2
modules/cellranger/Dockerfile
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@ -1,4 +1,4 @@
# Dockerfile to create container with Cell Ranger v6.1.2
# Dockerfile to create container with Cell Ranger v7.0.0
# Push to nfcore/cellranger:<VER>
FROM continuumio/miniconda3:4.8.2

2
modules/cellranger/count/main.nf
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@ -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:6.1.2"
container "nfcore/cellranger:7.0.0"
input:
tuple val(meta), path(reads)

4
modules/cellranger/mkfastq/Dockerfile
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@ -1,4 +1,4 @@
# Dockerfile to create container with Cell Ranger v6.1.2 and bcl2fastq v2.20.0
# Dockerfile to create container with Cell Ranger v7.0.0 and bcl2fastq v2.20.0
# Push to nfcore/cellrangermkfastq:<VER>
FROM continuumio/miniconda3:4.8.2
@ -17,7 +17,7 @@ RUN apt-get update --allow-releaseinfo-change \
# Copy pre-downloaded bcl2fastq2 and cellranger file
ENV BCL2FASTQ2_VER=v2-20-0-linux-x86-64 \
CELLRANGER_VER=6.1.2
CELLRANGER_VER=7.0.0
COPY bcl2fastq2-$BCL2FASTQ2_VER.zip /tmp/bcl2fastq2-$BCL2FASTQ2_VER.zip
COPY cellranger-$CELLRANGER_VER.tar.gz /opt/cellranger-$CELLRANGER_VER.tar.gz

2
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 "nfcore/cellrangermkfastq:6.1.2"
container "nfcore/cellrangermkfastq:7.0.0"
input:
path bcl

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:6.1.2"
container "nfcore/cellranger:7.0.0"
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:6.1.2"
container "nfcore/cellranger:7.0.0"
input:
path fasta

40
modules/sexdeterrmine/main.nf Normal file
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@ -0,0 +1,40 @@
process SEXDETERRMINE {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::sexdeterrmine=1.1.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/sexdeterrmine:1.1.2--hdfd78af_1':
'quay.io/biocontainers/sexdeterrmine:1.1.2--hdfd78af_1' }"
input:
tuple val(meta), path(depth)
path sample_list_file
output:
tuple val(meta), path("*.json"), emit: json
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 sample_list = sample_list_file ? '-f ${sample_list_file}' : ''
if ("$depth" == "${prefix}.tsv") error "Input depth and output TSV names are the same, set prefix in module configuration to disambiguate!"
"""
sexdeterrmine \\
-I $depth \\
$sample_list \\
$args \\
> ${prefix}.tsv
cat <<-END_VERSIONS > versions.yml
"${task.process}":
sexdeterrmine: \$(echo \$(sexdeterrmine --version 2>&1))
END_VERSIONS
"""
}

48
modules/sexdeterrmine/meta.yml Normal file
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@ -0,0 +1,48 @@
name: "sexdeterrmine"
description: Calculate the relative coverage on the Gonosomes vs Autosomes from the output of samtools depth, with error bars.
keywords:
- sex determination
- genetic sex
- relative coverage
- ancient dna
tools:
- "sexdeterrmine":
description: "A python script carry out calculate the relative coverage of X and Y chromosomes, and their associated error bars, out of capture data."
homepage: "https://github.com/TCLamnidis/Sex.DetERRmine"
documentation: "https://github.com/TCLamnidis/Sex.DetERRmine/README.md"
tool_dev_url: "https://github.com/TCLamnidis/Sex.DetERRmine"
doi: "https://doi.org/10.1038/s41467-018-07483-5"
licence: "['GPL v3']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- depth:
type: file
description: Output from samtools depth (with header)
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"
- json:
type: file
description: JSON formatted table of relative coverages on the X and Y, with associated error bars.
pattern: "*.json"
- tsv:
type: file
description: TSV table of relative coverages on the X and Y, with associated error bars.
pattern: "*.tsv"
authors:
- "@TCLamnidis"

4
tests/config/pytest_modules.yml
View file

@ -1855,6 +1855,10 @@ seqwish/induce:
- modules/seqwish/induce/**
- tests/modules/seqwish/induce/**
sexdeterrmine:
- modules/sexdeterrmine/**
- tests/modules/sexdeterrmine/**
shasum:
- modules/shasum/**
- tests/modules/shasum/**

3
tests/config/test_data.config
View file

@ -232,10 +232,11 @@ params {
test2_paired_end_umi_unsorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam"
test2_paired_end_umi_unsorted_tagged_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam"
mitochon_standin_recalibrated_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam"
mitochon_standin_recalibrated_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai"
test3_single_end_markduplicates_sorted_bam = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test3.single_end.markduplicates.sorted.bam"
test_paired_end_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram"
test_paired_end_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai"
test_paired_end_markduplicates_sorted_cram = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram"

56
tests/modules/cellranger/count/test.yml
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@ -1,19 +1,65 @@
- name: cellranger count test_cellranger_count
command: nextflow run tests/modules/cellranger/count -entry test_cellranger_count -c tests/config/nextflow.config -c tests/modules/cellranger/count/nextflow.config
command: nextflow run ./tests/modules/cellranger/count -entry test_cellranger_count -c ./tests/config/nextflow.config -c ./tests/modules/cellranger/count/nextflow.config
tags:
- cellranger
- cellranger/count
- cellranger
files:
- path: output/cellranger/genome.filtered.gtf
md5sum: a8b8a7b5039e05d3a9cf9151ea138b5b
- path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa
md5sum: f315020d899597c1b57e5fe9f60f4c3e
- path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa.fai
md5sum: 3520cd30e1b100e55f578db9c855f685
- path: output/cellranger/homo_sapiens_chr22_reference/genes/genes.gtf.gz
md5sum: d1e05cd46684fa26d852b6bc9f05e31f
- path: output/cellranger/homo_sapiens_chr22_reference/reference.json
md5sum: 8405fd7f527a944eafb9c2909045840b
- path: output/cellranger/homo_sapiens_chr22_reference/star/Genome
md5sum: 897cec2d191945335f8b320438bd9135
- path: output/cellranger/homo_sapiens_chr22_reference/star/SA
md5sum: 7961129ac5d0e1706105be1d31c6b30c
- path: output/cellranger/homo_sapiens_chr22_reference/star/SAindex
md5sum: dcceb480b30cda93fb8c63ddc339093b
- path: output/cellranger/homo_sapiens_chr22_reference/star/chrLength.txt
md5sum: c81f40f27e72606d7d07097c1d56a5b5
- path: output/cellranger/homo_sapiens_chr22_reference/star/chrName.txt
md5sum: 5ae68a67b70976ee95342a7451cb5af1
- path: output/cellranger/homo_sapiens_chr22_reference/star/chrNameLength.txt
md5sum: b190587cae0531f3cf25552d8aa674db
- path: output/cellranger/homo_sapiens_chr22_reference/star/chrStart.txt
md5sum: bc73df776dd3d5bb9cfcbcba60880519
- path: output/cellranger/homo_sapiens_chr22_reference/star/exonGeTrInfo.tab
md5sum: 9129691eeb4ed0d02b17be879fa3edb0
- path: output/cellranger/homo_sapiens_chr22_reference/star/exonInfo.tab
md5sum: 209b82f0683efd03e17d2c729676554f
- path: output/cellranger/homo_sapiens_chr22_reference/star/geneInfo.tab
md5sum: 02a8f4575bdfcd4a42b4d8d07f2e9369
- path: output/cellranger/homo_sapiens_chr22_reference/star/genomeParameters.txt
- path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbInfo.txt
md5sum: 1082ab459363b3f2f7aabcef0979c1ed
- path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.fromGTF.out.tab
- path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.out.tab
- path: output/cellranger/homo_sapiens_chr22_reference/star/transcriptInfo.tab
md5sum: cedcb5f4e7d97bc548cd5daa022e092c
- path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix.h5
md5sum: f8b6b7cc8248151a98c46d4ebec450c6
- path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/barcodes.tsv.gz
- path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/features.tsv.gz
- path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/matrix.mtx.gz
- path: output/cellranger/sample-123/outs/metrics_summary.csv
md5sum: 707df0f101d479d93f412ca74f9c4131
- path: output/cellranger/sample-123/outs/molecule_info.h5
md5sum: 0e56836ef0725f2ab05f56ca5a71e55b
md5sum: a13bd7425f441c8d0eac8ffc50082996
- path: output/cellranger/sample-123/outs/possorted_genome_bam.bam
md5sum: 15441da9cfceea0bb48c8b66b1b860df
- path: output/cellranger/sample-123/outs/possorted_genome_bam.bam.bai
md5sum: 7c3d49c77016a09535aff61a027f750c
- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix
- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix.h5
md5sum: cdad1cd7b215d7137cf92515e81a8525
md5sum: a5290f3e300a4070f3d68a0c2e215f54
- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix/barcodes.tsv.gz
md5sum: 5cc39ef0c7ac85f2b758b164aabf9157
- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix/features.tsv.gz
md5sum: 07d497c7ce3e22f374af7b2cf9b97d72
- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix/matrix.mtx.gz
md5sum: bdce94a51f16e22d40301724080b76ee
- path: output/cellranger/sample-123/outs/web_summary.html

2
tests/modules/cellranger/mkfastq/test.yml
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@ -5,7 +5,6 @@
- cellranger/mkfastq
files:
- path: output/cellranger/cellranger-tiny-bcl-1/outs/fastq_path/fake_file.fastq.gz
md5sum: d41d8cd98f00b204e9800998ecf8427e
- name: cellranger mkfastq test_cellranger_mkfastq_illumina
command: nextflow run tests/modules/cellranger/mkfastq -entry test_cellranger_mkfastq_illumina -c tests/config/nextflow.config -c ./tests/modules/cellranger/mkfastq/nextflow.config -stub-run
tags:
@ -13,4 +12,3 @@
- cellranger/mkfastq
files:
- path: output/cellranger/cellranger-tiny-bcl-1/outs/fastq_path/fake_file.fastq.gz
md5sum: d41d8cd98f00b204e9800998ecf8427e

4
tests/modules/cellranger/mkgtf/test.yml
View file

@ -1,8 +1,8 @@
- name: cellranger mkgtf test_cellranger_mkgtf
command: nextflow run tests/modules/cellranger/mkgtf -entry test_cellranger_mkgtf -c tests/config/nextflow.config -c tests/modules/cellranger/mkgtf/nextflow.config
command: nextflow run ./tests/modules/cellranger/mkgtf -entry test_cellranger_mkgtf -c ./tests/config/nextflow.config -c ./tests/modules/cellranger/mkgtf/nextflow.config
tags:
- cellranger
- cellranger/mkgtf
- cellranger
files:
- path: output/cellranger/genome.filtered.gtf
md5sum: a8b8a7b5039e05d3a9cf9151ea138b5b

6
tests/modules/cellranger/mkref/test.yml
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@ -1,8 +1,8 @@
- name: cellranger mkref test_cellranger_mkref
command: nextflow run ./tests/modules/cellranger/mkref -entry test_cellranger_mkref -c ./tests/config/nextflow.config -c ./tests/modules/cellranger/mkref/nextflow.config
command: nextflow run ./tests/modules/cellranger/mkref -entry test_cellranger_mkref -c ./tests/config/nextflow.config -c ./tests/modules/cellranger/mkref/nextflow.config
tags:
- cellranger
- cellranger/mkref
- cellranger
files:
- path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa
md5sum: f315020d899597c1b57e5fe9f60f4c3e
@ -11,7 +11,7 @@
- path: output/cellranger/homo_sapiens_chr22_reference/genes/genes.gtf.gz
md5sum: 6d9b5f409bfea95022bc25b9590e194e
- path: output/cellranger/homo_sapiens_chr22_reference/reference.json
md5sum: 5d8d1669cd251433505f183e1c9ed6bc
md5sum: 6cc817f0923062e780e6573806840cea
- path: output/cellranger/homo_sapiens_chr22_reference/star/Genome
md5sum: 22102926fadf5890e905ca71b2da3f35
- path: output/cellranger/homo_sapiens_chr22_reference/star/SA

16
tests/modules/sexdeterrmine/main.nf Normal file
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@ -0,0 +1,16 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_DEPTH } from '../../../modules/samtools/depth/main.nf'
include { SEXDETERRMINE } from '../../../modules/sexdeterrmine/main.nf'
workflow test_sexdeterrmine {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test3_single_end_markduplicates_sorted_bam'], checkIfExists: true) ]
SAMTOOLS_DEPTH ( input )
SEXDETERRMINE ( SAMTOOLS_DEPTH.out.tsv, [] )
}

12
tests/modules/sexdeterrmine/nextflow.config Normal file
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@ -0,0 +1,12 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName:SAMTOOLS_DEPTH {
ext.args = "-H"
}
withName:SEXDETERRMINE {
ext.prefix = { "${meta.id}_sexdet" }
}
}

15
tests/modules/sexdeterrmine/test.yml Normal file
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@ -0,0 +1,15 @@
- name: sexdeterrmine test_sexdeterrmine
command: nextflow run tests/modules/sexdeterrmine -entry test_sexdeterrmine -c tests/config/nextflow.config
tags:
- sexdeterrmine
files:
- path: output/samtools/test.tsv
md5sum: fa2992ca1ea93a6e1b3e838476191935
- path: output/samtools/versions.yml
md5sum: dbd04b700335c8ad236bd667254c8dd8
- path: output/sexdeterrmine/sexdeterrmine.json
md5sum: bafb2419bb8630eda29a251c20e97166
- path: output/sexdeterrmine/test_sexdet.tsv
md5sum: 1cf8a2b97b38353eb97a96ab872dcca9
- path: output/sexdeterrmine/versions.yml
md5sum: 077361101e8e7997aec3da8a01e59eee

8
tests/test_versions_yml.py
View file

@ -16,9 +16,9 @@ def _get_workflow_names():
# test_config = yaml.safe_load(f.read_text())
test_config = yaml.load(f.read_text(), Loader=yaml.BaseLoader)
for workflow in test_config:
# https://github.com/nf-core/modules/pull/1242 - added to cover tests
# https://github.com/nf-core/modules/pull/1242 - added to cover tests
# that expect an error and therefore will not generate a versions.yml
if 'exit_code' not in workflow:
if 'exit_code' not in workflow:
yield workflow["name"]
@ -56,5 +56,5 @@ def test_ensure_valid_version_yml(workflow_dir):
assert len(software_versions), "There must be at least one version emitted."
for tool, version in software_versions.items():
assert re.match(
r"^\d+.*", str(version)
), f"Version number for {tool} must start with a number. "
r"^\d.*|^[a-f0-9]{40}$", str(version)
), f"Version number for {tool} must start with a number, or be a Git SHA commit id. "