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Merge branch 'master' into antismashlite

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James A. Fellows Yates 2022-05-12 14:53:52 +02:00 committed by GitHub
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111
modules/bowtie2/align/main.nf
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@ -1,11 +1,11 @@
process BOWTIE2_ALIGN {
tag "$meta.id"
label 'process_high'
label "process_high"
conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0' :
'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0' }"
conda (params.enable_conda ? "bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6" : null)
container "${ workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ?
"https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" :
"quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" }"
input:
tuple val(meta), path(reads)
@ -13,69 +13,60 @@ process BOWTIE2_ALIGN {
val save_unaligned
output:
tuple val(meta), path('*.bam') , emit: bam
tuple val(meta), path('*.log') , emit: log
tuple val(meta), path('*fastq.gz'), emit: fastq, optional:true
tuple val(meta), path("*.bam") , emit: bam
tuple val(meta), path("*.log") , emit: log
tuple val(meta), path("*fastq.gz"), emit: fastq, optional:true
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def args = task.ext.args ?: ""
def args2 = task.ext.args2 ?: ""
def prefix = task.ext.prefix ?: "${meta.id}"
def unaligned = ""
def reads_args = ""
if (meta.single_end) {
def unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
"""
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'`
[ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
bowtie2 \\
-x \$INDEX \\
-U $reads \\
--threads $task.cpus \\
$unaligned \\
$args \\
2> ${prefix}.bowtie2.log \\
| samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
"""
unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ""
reads_args = "-U ${reads}"
} else {
def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
"""
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed 's/.rev.1.bt2l//'`
[ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
bowtie2 \\
-x \$INDEX \\
-1 ${reads[0]} \\
-2 ${reads[1]} \\
--threads $task.cpus \\
$unaligned \\
$args \\
2> ${prefix}.bowtie2.log \\
| samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -
if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
fi
if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
fi
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
"""
unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ""
reads_args = "-1 ${reads[0]} -2 ${reads[1]}"
}
def samtools_command = "samtools view -@ $task.cpus --bam --with-header ${args2} > ${prefix}.bam"
"""
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/.rev.1.bt2//"`
[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/.rev.1.bt2l//"`
[ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1
bowtie2 \\
-x \$INDEX \\
$reads_args \\
--threads $task.cpus \\
$unaligned \\
$args \\
2> ${prefix}.bowtie2.log \\
| $samtools_command
if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
fi
if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
fi
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
"""
}

20
modules/custom/sratoolsncbisettings/main.nf Normal file
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@ -0,0 +1,20 @@
process CUSTOM_SRATOOLSNCBISETTINGS {
tag 'ncbi-settings'
label 'process_low'
conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' :
'quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
output:
path('*.mkfg') , emit: ncbi_settings
path 'versions.yml', emit: versions
when:
task.ext.when == null || task.ext.when
shell:
config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
template 'detect_ncbi_settings.sh'
}

28
modules/custom/sratoolsncbisettings/meta.yml Normal file
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@ -0,0 +1,28 @@
name: "sratoolsncbisettings"
description: Test for the presence of suitable NCBI settings or create them on the fly.
keywords:
- NCBI
- settings
- sra-tools
- prefetch
- fasterq-dump
tools:
- "sratools":
description: "SRA Toolkit and SDK from NCBI"
homepage: https://github.com/ncbi/sra-tools
documentation: https://github.com/ncbi/sra-tools/wiki
tool_dev_url: https://github.com/ncbi/sra-tools
licence: "['Public Domain']"
output:
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- ncbi_settings:
type: file
description: An NCBI user settings file.
pattern: "*.mkfg"
authors:
- "@Midnighter"

45
modules/custom/sratoolsncbisettings/templates/detect_ncbi_settings.sh Normal file
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@ -0,0 +1,45 @@
#!/usr/bin/env bash
set -u
# Get the expected NCBI settings path and define the environment variable
# `NCBI_SETTINGS`.
eval "$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
# If the user settings do not exist yet, create a file suitable for `prefetch`
# and `fasterq-dump`. If an existing settings file does not contain the required
# values, error out with a helpful message.
if [[ ! -f "${NCBI_SETTINGS}" ]]; then
printf '!{config}' > 'user-settings.mkfg'
else
prefetch --help &> /dev/null
if [[ $? = 78 ]]; then
echo "You have an existing vdb-config at '${NCBI_SETTINGS}' but it is"\
"missing the required entries for /LIBS/GUID and"\
"/libs/cloud/report_instance_identity."\
"Feel free to add the following to your settings file:" >&2
echo "$(printf '!{config}')" >&2
exit 1
fi
fasterq-dump --help &> /dev/null
if [[ $? = 78 ]]; then
echo "You have an existing vdb-config at '${NCBI_SETTINGS}' but it is"\
"missing the required entries for /LIBS/GUID and"\
"/libs/cloud/report_instance_identity."\
"Feel free to add the following to your settings file:" >&2
echo "$(printf '!{config}')" >&2
exit 1
fi
if [[ "${NCBI_SETTINGS}" != *.mkfg ]]; then
echo "The detected settings '${NCBI_SETTINGS}' do not have the required"\
"file extension '.mkfg'." >&2
exit 1
fi
cp "${NCBI_SETTINGS}" ./
fi
cat <<-END_VERSIONS > versions.yml
"!{task.process}":
sratools: $(vdb-config --version 2>&1 | grep -Eo '[0-9.]+')
END_VERSIONS

8
modules/sratools/fasterqdump/main.nf
View file

@ -9,6 +9,7 @@ process SRATOOLS_FASTERQDUMP {
input:
tuple val(meta), path(sra)
path ncbi_settings
output:
tuple val(meta), path(output), emit: reads
@ -20,17 +21,12 @@ process SRATOOLS_FASTERQDUMP {
script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
// Paired-end data extracted by fasterq-dump (--split-3 the default) always creates
// *_1.fastq *_2.fastq files but sometimes also an additional *.fastq file
// for unpaired reads which we ignore here.
output = meta.single_end ? '*.fastq.gz' : '*_{1,2}.fastq.gz'
"""
eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
if [[ ! -f "\${NCBI_SETTINGS}" ]]; then
mkdir -p "\$(dirname "\${NCBI_SETTINGS}")"
printf '${config}' > "\${NCBI_SETTINGS}"
fi
export NCBI_SETTINGS="\$PWD/${ncbi_settings}"
fasterq-dump \\
$args \\

7
modules/sratools/fasterqdump/meta.yml
View file

@ -10,7 +10,7 @@ tools:
homepage: https://github.com/ncbi/sra-tools
documentation: https://github.com/ncbi/sra-tools/wiki
tool_dev_url: https://github.com/ncbi/sra-tools
licence: ["US-Government-Work"]
licence: ["Public Domain"]
input:
- meta:
@ -22,6 +22,11 @@ input:
type: directory
description: Directory containing ETL data for the given SRA.
pattern: "*/*.sra"
- ncbi_settings:
type: file
description: >
An NCBI user settings file.
pattern: "*.mkfg"
output:
- meta:

5
modules/sratools/prefetch/main.nf
View file

@ -9,10 +9,11 @@ process SRATOOLS_PREFETCH {
input:
tuple val(meta), val(id)
path ncbi_settings
output:
tuple val(meta), path(id), emit: sra
path "versions.yml" , emit: versions
path 'versions.yml' , emit: versions
when:
task.ext.when == null || task.ext.when
@ -20,7 +21,5 @@ process SRATOOLS_PREFETCH {
shell:
args = task.ext.args ?: ''
args2 = task.ext.args2 ?: '5 1 100' // <num retries> <base delay in seconds> <max delay in seconds>
config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
template 'retry_with_backoff.sh'
}

7
modules/sratools/prefetch/meta.yml
View file

@ -10,7 +10,7 @@ tools:
homepage: https://github.com/ncbi/sra-tools
documentation: https://github.com/ncbi/sra-tools/wiki
tool_dev_url: https://github.com/ncbi/sra-tools
licence: ["US-Government-Work"]
licence: ["Public Domain"]
input:
- meta:
@ -22,6 +22,11 @@ input:
type: val
description: >
A string denoting an SRA id.
- ncbi_settings:
type: file
description: >
An NCBI user settings file.
pattern: "*.mkfg"
output:
- meta:

6
modules/sratools/prefetch/templates/retry_with_backoff.sh
View file

@ -40,11 +40,7 @@ retry_with_backoff() {
echo "${output}"
}
eval "$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
if [[ ! -f "${NCBI_SETTINGS}" ]]; then
mkdir -p "$(dirname "${NCBI_SETTINGS}")"
printf '!{config}' > "${NCBI_SETTINGS}"
fi
export NCBI_SETTINGS="$PWD/!{ncbi_settings}"
retry_with_backoff !{args2} \
prefetch \

34
subworkflows/nf-core/sra_fastq/main.nf
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@ -1,34 +0,0 @@
//
// Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
//
params.prefetch_options = [:]
params.fasterqdump_options = [:]
include { SRATOOLS_PREFETCH } from '../../../modules/sratools/prefetch/main' addParams( options: params.prefetch_options )
include { SRATOOLS_FASTERQDUMP } from '../../../modules/sratools/fasterqdump/main' addParams( options: params.fasterqdump_options )
workflow SRA_FASTQ {
take:
sra_ids // channel: [ val(meta), val(id) ]
main:
ch_versions = Channel.empty()
//
// Prefetch sequencing reads in SRA format.
//
SRATOOLS_PREFETCH ( sra_ids )
ch_versions = ch_versions.mix( SRATOOLS_PREFETCH.out.versions.first() )
//
// Convert the SRA format into one or more compressed FASTQ files.
//
SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra )
ch_versions = ch_versions.mix( SRATOOLS_FASTERQDUMP.out.versions.first() )
emit:
reads = SRATOOLS_FASTERQDUMP.out.reads // channel: [ val(meta), [ reads ] ]
versions = ch_versions // channel: [ versions.yml ]
}

38
subworkflows/nf-core/srafastq/main.nf Normal file
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@ -0,0 +1,38 @@
include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../modules/custom/sratoolsncbisettings/main'
include { SRATOOLS_PREFETCH } from '../../../modules/sratools/prefetch/main'
include { SRATOOLS_FASTERQDUMP } from '../../../modules/sratools/fasterqdump/main'
/**
* Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
*/
workflow SRAFASTQ {
take:
sra_ids // channel: [ val(meta), val(id) ]
main:
ch_versions = Channel.empty()
//
// Detect existing NCBI user settings or create new ones.
//
CUSTOM_SRATOOLSNCBISETTINGS()
def settings = CUSTOM_SRATOOLSNCBISETTINGS.out.ncbi_settings
ch_versions = ch_versions.mix( CUSTOM_SRATOOLSNCBISETTINGS.out.versions )
//
// Prefetch sequencing reads in SRA format.
//
SRATOOLS_PREFETCH ( sra_ids, settings )
ch_versions = ch_versions.mix( SRATOOLS_PREFETCH.out.versions.first() )
//
// Convert the SRA format into one or more compressed FASTQ files.
//
SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra, settings )
ch_versions = ch_versions.mix( SRATOOLS_FASTERQDUMP.out.versions.first() )
emit:
reads = SRATOOLS_FASTERQDUMP.out.reads // channel: [ val(meta), [ reads ] ]
versions = ch_versions // channel: [ versions.yml ]
}

7
subworkflows/nf-core/sra_fastq/meta.yml → subworkflows/nf-core/srafastq/meta.yml
View file

@ -1,11 +1,14 @@
name: sra_fastq
description: Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
keywords:
- SRA
- NCBI
- sequencing
- FASTQ
- prefetch
- dump
- fasterq-dump
modules:
- custom/sratoolsncbisettings
- sratools/prefetch
- sratools/fasterqdump
input:
@ -17,7 +20,7 @@ input:
- id:
type: string
description: >
SRA identifier.
SRA run identifier.
# TODO Update when we decide on a standard for subworkflow docs
output:
- meta:

0
subworkflows/nf-core/sra_fastq/nextflow.config → subworkflows/nf-core/srafastq/nextflow.config
View file

4
tests/config/pytest_modules.yml
View file

@ -499,6 +499,10 @@ custom/getchromsizes:
- modules/custom/getchromsizes/**
- tests/modules/custom/getchromsizes/**
custom/sratoolsncbisettings:
- modules/custom/sratoolsncbisettings/**
- tests/modules/custom/sratoolsncbisettings/**
cutadapt:
- modules/cutadapt/**
- tests/modules/cutadapt/**

5
tests/config/test_data.config
View file

@ -382,7 +382,7 @@ params {
test3_gff = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test3.gff"
}
'illumina' {
test_1_fastq_gz = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fasta/test_1.fastq.gz"
test_1_fastq_gz = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_1.fastq.gz"
test_2_fastq_gz = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_2.fastq.gz"
test_se_fastq_gz = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_se.fastq.gz"
}
@ -426,6 +426,9 @@ params {
test_merge_cool_cp2 = "${test_data_dir}/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cp2.cool"
}
'config' {
ncbi_user_settings = "${test_data_dir}/generic/config/ncbi_user_settings.mkfg"
}
}
}
}

84
tests/modules/bowtie2/align/test.yml
View file

@ -1,83 +1,21 @@
- name: bowtie2 align single-end
- name: bowtie2 align test_bowtie2_align_single_end
command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config
tags:
- bowtie2
- bowtie2/align
- bowtie2
files:
- path: ./output/bowtie2/test.bam
- path: ./output/bowtie2/test.bowtie2.log
- path: ./output/bowtie2/bowtie2/genome.3.bt2
md5sum: 4ed93abba181d8dfab2e303e33114777
- path: ./output/bowtie2/bowtie2/genome.2.bt2
md5sum: 47b153cd1319abc88dda532462651fcf
- path: ./output/bowtie2/bowtie2/genome.1.bt2
md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
- path: ./output/bowtie2/bowtie2/genome.4.bt2
md5sum: c25be5f8b0378abf7a58c8a880b87626
- path: ./output/bowtie2/bowtie2/genome.rev.1.bt2
md5sum: 52be6950579598a990570fbcf5372184
- path: ./output/bowtie2/bowtie2/genome.rev.2.bt2
md5sum: e3b4ef343dea4dd571642010a7d09597
- path: output/bowtie2/test.bam
- path: output/bowtie2/test.bowtie2.log
md5sum: 7b8a9e61b7646da1089b041333c41a87
- path: output/bowtie2/versions.yml
- name: bowtie2 align paired-end
- name: bowtie2 align test_bowtie2_align_paired_end
command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config
tags:
- bowtie2
- bowtie2/align
files:
- path: ./output/bowtie2/test.bam
- path: ./output/bowtie2/test.bowtie2.log
- path: ./output/bowtie2/bowtie2/genome.3.bt2
md5sum: 4ed93abba181d8dfab2e303e33114777
- path: ./output/bowtie2/bowtie2/genome.2.bt2
md5sum: 47b153cd1319abc88dda532462651fcf
- path: ./output/bowtie2/bowtie2/genome.1.bt2
md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
- path: ./output/bowtie2/bowtie2/genome.4.bt2
md5sum: c25be5f8b0378abf7a58c8a880b87626
- path: ./output/bowtie2/bowtie2/genome.rev.1.bt2
md5sum: 52be6950579598a990570fbcf5372184
- path: ./output/bowtie2/bowtie2/genome.rev.2.bt2
md5sum: e3b4ef343dea4dd571642010a7d09597
- name: bowtie2 align single-end large-index
command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config --force_large_index
tags:
- bowtie2
- bowtie2/align
files:
- path: ./output/bowtie2/test.bam
- path: ./output/bowtie2/test.bowtie2.log
- path: ./output/bowtie2/bowtie2/genome.3.bt2l
md5sum: 8952b3e0b1ce9a7a5916f2e147180853
- path: ./output/bowtie2/bowtie2/genome.2.bt2l
md5sum: 22c284084784a0720989595e0c9461fd
- path: ./output/bowtie2/bowtie2/genome.1.bt2l
md5sum: 07d811cd4e350d56267183d2ac7023a5
- path: ./output/bowtie2/bowtie2/genome.4.bt2l
md5sum: c25be5f8b0378abf7a58c8a880b87626
- path: ./output/bowtie2/bowtie2/genome.rev.1.bt2l
md5sum: fda48e35925fb24d1c0785f021981e25
- path: ./output/bowtie2/bowtie2/genome.rev.2.bt2l
md5sum: 802c26d32b970e1b105032b7ce7348b4
- name: bowtie2 align paired-end large-index
command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config --force_large_index
tags:
- bowtie2
- bowtie2/align
files:
- path: ./output/bowtie2/test.bam
- path: ./output/bowtie2/test.bowtie2.log
- path: ./output/bowtie2/bowtie2/genome.3.bt2l
md5sum: 8952b3e0b1ce9a7a5916f2e147180853
- path: ./output/bowtie2/bowtie2/genome.2.bt2l
md5sum: 22c284084784a0720989595e0c9461fd
- path: ./output/bowtie2/bowtie2/genome.1.bt2l
md5sum: 07d811cd4e350d56267183d2ac7023a5
- path: ./output/bowtie2/bowtie2/genome.4.bt2l
md5sum: c25be5f8b0378abf7a58c8a880b87626
- path: ./output/bowtie2/bowtie2/genome.rev.1.bt2l
md5sum: fda48e35925fb24d1c0785f021981e25
- path: ./output/bowtie2/bowtie2/genome.rev.2.bt2l
md5sum: 802c26d32b970e1b105032b7ce7348b4
- path: output/bowtie2/test.bam
- path: output/bowtie2/test.bowtie2.log
md5sum: bd89ce1b28c93bf822bae391ffcedd19
- path: output/bowtie2/versions.yml

44
tests/modules/custom/sratoolsncbisettings/main.nf Normal file
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@ -0,0 +1,44 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../../modules/custom/sratoolsncbisettings/main.nf'
workflow test_sratoolsncbisettings_with_good_existing {
file(params.settings_path).mkdirs()
def settings = file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true)
settings.copyTo(params.settings_file)
CUSTOM_SRATOOLSNCBISETTINGS()
}
workflow test_sratoolsncbisettings_with_bad_existing {
file(params.settings_path).mkdirs()
def settings = file(params.settings_file)
settings.text = '''
## auto-generated configuration file - DO NOT EDIT ##
config/default = "false"
/repository/remote/main/CGI/resolver-cgi = "https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi"
/repository/remote/protected/CGI/resolver-cgi = "https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi"
/repository/user/ad/public/apps/file/volumes/flatAd = "."
/repository/user/ad/public/apps/refseq/volumes/refseqAd = "."
/repository/user/ad/public/apps/sra/volumes/sraAd = "."
/repository/user/ad/public/apps/sraPileup/volumes/ad = "."
/repository/user/ad/public/apps/sraRealign/volumes/ad = "."
/repository/user/ad/public/apps/wgs/volumes/wgsAd = "."
/repository/user/ad/public/root = "."
/repository/user/default-path = "/root/ncbi"
'''.stripIndent()
CUSTOM_SRATOOLSNCBISETTINGS()
}
workflow test_sratoolsncbisettings_with_nonexisting {
def settings = file(params.settings_file)
settings.delete()
CUSTOM_SRATOOLSNCBISETTINGS()
}

8
tests/modules/custom/sratoolsncbisettings/nextflow.config Normal file
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@ -0,0 +1,8 @@
params.settings_path = '/tmp/.ncbi'
params.settings_file = "${params.settings_path}/user-settings.mkfg"
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

17
tests/modules/custom/sratoolsncbisettings/nextflow_mount.config Normal file
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@ -0,0 +1,17 @@
params.settings_path = '/tmp/.ncbi'
params.settings_file = "${params.settings_path}/user-settings.mkfg"
env.NCBI_SETTINGS = params.settings_file
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: CUSTOM_SRATOOLSNCBISETTINGS {
containerOptions = {
(workflow.containerEngine == 'singularity') ?
"-B ${params.settings_path}:${params.settings_path}" :
"-v ${params.settings_path}:${params.settings_path}"
}
}
}

44
tests/modules/custom/sratoolsncbisettings/test.yml Normal file
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@ -0,0 +1,44 @@
- name: "custom sratoolsncbisettings test_sratoolsncbisettings_with_good_existing"
command: nextflow run ./tests/modules/custom/sratoolsncbisettings -entry test_sratoolsncbisettings_with_good_existing -c ./tests/config/nextflow.config -c ./tests/modules/custom/sratoolsncbisettings/nextflow_mount.config
tags:
- "custom"
- "custom/sratoolsncbisettings"
files:
- path: "output/custom/user-settings.mkfg"
md5sum: 955e27aff2c277c2f1f0943a098888c1
- path: output/custom/versions.yml
contains:
- "sratools: 2.11.0"
- name: "custom sratoolsncbisettings test_sratoolsncbisettings_with_bad_existing"
command: nextflow run ./tests/modules/custom/sratoolsncbisettings -entry test_sratoolsncbisettings_with_bad_existing -c ./tests/config/nextflow.config -c ./tests/modules/custom/sratoolsncbisettings/nextflow_mount.config
tags:
- "custom"
- "custom/sratoolsncbisettings"
exit_code: 1
stdout:
contains:
- "Command error:"
- "missing the required entries"
- "/LIBS/GUID"
- "/libs/cloud/report_instance_identity"
- "Feel free to add the following"
files:
- path: "output/custom/user-settings.mkfg"
should_exist: false
- path: output/custom/versions.yml
should_exist: false
- name: "custom sratoolsncbisettings test_sratoolsncbisettings_with_nonexisting"
command: nextflow run ./tests/modules/custom/sratoolsncbisettings -entry test_sratoolsncbisettings_with_nonexisting -c ./tests/config/nextflow.config -c ./tests/modules/custom/sratoolsncbisettings/nextflow.config
tags:
- "custom"
- "custom/sratoolsncbisettings"
files:
- path: "output/custom/user-settings.mkfg"
contains:
- "/LIBS/GUID"
- "/libs/cloud/report_instance_identity"
- path: output/custom/versions.yml
contains:
- "sratools: 2.11.0"

4
tests/modules/sratools/fasterqdump/main.nf
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@ -13,7 +13,7 @@ workflow test_sratools_fasterqdump_single_end {
def input = Channel.of([ id:'test_single_end', single_end:true ])
.combine(UNTAR.out.untar.map{ it[1] })
SRATOOLS_FASTERQDUMP ( input )
SRATOOLS_FASTERQDUMP(input, file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true))
}
workflow test_sratools_fasterqdump_paired_end {
@ -24,5 +24,5 @@ workflow test_sratools_fasterqdump_paired_end {
def input = Channel.of([ id:'test_paired_end', single_end:false ])
.combine(UNTAR.out.untar.map{ it[1] })
SRATOOLS_FASTERQDUMP ( input )
SRATOOLS_FASTERQDUMP(input, file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true))
}

6
tests/modules/sratools/fasterqdump/test.yml
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@ -8,6 +8,9 @@
md5sum: 1054c7b71884acdb5eed8a378f18be82
- path: output/untar/SRR13255544/SRR13255544.sra
md5sum: 466d05dafb2eec672150754168010b4d
- path: output/sratools/versions.yml
contains:
- "sratools: 2.11.0"
- name: sratools fasterqdump test_sratools_fasterqdump_paired_end
command: nextflow run ./tests/modules/sratools/fasterqdump -entry test_sratools_fasterqdump_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/sratools/fasterqdump/nextflow.config
@ -21,3 +24,6 @@
md5sum: 3e3b3af3413f50a1685fd7b3f1456d4e
- path: output/untar/SRR11140744/SRR11140744.sra
md5sum: 065666caf5b2d5dfb0cb25d5f3abe659
- path: output/sratools/versions.yml
contains:
- "sratools: 2.11.0"

4
tests/modules/sratools/prefetch/main.nf
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@ -8,8 +8,8 @@ workflow test_sratools_prefetch {
input = [
[ id:'test', single_end:false ], // meta map
'ERR2815334'
'DRR000774'
]
SRATOOLS_PREFETCH ( input )
SRATOOLS_PREFETCH(input, file(params.test_data['generic']['config']['ncbi_user_settings'], checkIfExists: true))
}

7
tests/modules/sratools/prefetch/test.yml
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@ -4,5 +4,8 @@
- sratools/prefetch
- sratools
files:
- path: output/sratools/ERR2815334/ERR2815334.sra
md5sum: 9a98c7f6f4774b7ef94aa915b92a54ea
- path: output/sratools/DRR000774/DRR000774.sra
md5sum: 7647dba20c89c0e3d7ad13842f060eb0
- path: output/sratools/versions.yml
contains:
- "sratools: 2.11.0"

23
tests/subworkflows/nf-core/sra_fastq/main.nf
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@ -1,23 +0,0 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SRA_FASTQ } from '../../../../subworkflows/nf-core/sra_fastq/main.nf' addParams( [:] )
workflow test_sra_fastq_single_end {
input = [
[ id:'test_single_end', single_end:true ], // meta map
'SRR13255544'
]
SRA_FASTQ ( input )
}
workflow test_sra_fastq_paired_end {
input = [
[ id:'test_paired_end', single_end:false ], // meta map
'SRR11140744'
]
SRA_FASTQ ( input )
}

27
tests/subworkflows/nf-core/sra_fastq/test.yml
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@ -1,27 +0,0 @@
- name: sra fastq single-end
command: nextflow run ./tests/subworkflows/nf-core/sra_fastq -entry test_sra_fastq_single_end -c tests/config/nextflow.config
tags:
- subworkflows
# - subworkflows/sra_fastq
# Modules
# - sratools
# - sratools/prefetch
# - sratools/fasterqdump
files:
- path: output/sratools/SRR13255544.fastq.gz
md5sum: 1054c7b71884acdb5eed8a378f18be82
- name: sra fastq paired-end
command: nextflow run ./tests/subworkflows/nf-core/sra_fastq -entry test_sra_fastq_paired_end -c tests/config/nextflow.config
tags:
- subworkflows
# - subworkflows/sra_fastq
# Modules
# - sratools
# - sratools/prefetch
# - sratools/fasterqdump
files:
- path: output/sratools/SRR11140744_1.fastq.gz
md5sum: 193809c784a4ea132ab2a253fa4f55b6
- path: output/sratools/SRR11140744_2.fastq.gz
md5sum: 3e3b3af3413f50a1685fd7b3f1456d4e

29
tests/subworkflows/nf-core/srafastq/main.nf Normal file
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@ -0,0 +1,29 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SRAFASTQ } from '../../../../subworkflows/nf-core/srafastq/main.nf'
workflow test_srafastq_single_end {
input = Channel.of(
[
[ id:'test_single_end1', single_end:true ], // meta map
'DRR000774'
],
[
[ id:'test_single_end2', single_end:true ], // meta map
'DRR000775'
]
)
SRAFASTQ ( input )
}
workflow test_srafastq_paired_end {
input = [
[ id:'test_paired_end', single_end:false ], // meta map
'SRR11140744'
]
SRAFASTQ ( input )
}

5
tests/subworkflows/nf-core/srafastq/nextflow.config Normal file
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@ -0,0 +1,5 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

29
tests/subworkflows/nf-core/srafastq/test.yml Normal file
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@ -0,0 +1,29 @@
- name: srafastq single-end
command: nextflow run ./tests/subworkflows/nf-core/srafastq -entry test_srafastq_single_end -c tests/config/nextflow.config -c tests/subworkflows/nf-core/srafastq/nextflow.config
tags:
- subworkflows
# - subworkflows/srafastq
# Modules
# - sratools
# - sratools/prefetch
# - sratools/fasterqdump
files:
- path: output/sratools/DRR000774.fastq.gz
md5sum: 19029a1132115b55277a0d79ee089b49
- path: output/sratools/DRR000775.fastq.gz
md5sum: 59ff24c86ecb260752668c059c2a1eaf
- name: srafastq paired-end
command: nextflow run ./tests/subworkflows/nf-core/srafastq -entry test_srafastq_paired_end -c tests/config/nextflow.config -c tests/subworkflows/nf-core/srafastq/nextflow.config
tags:
- subworkflows
# - subworkflows/srafastq
# Modules
# - sratools
# - sratools/prefetch
# - sratools/fasterqdump
files:
- path: output/sratools/SRR11140744_1.fastq.gz
md5sum: 193809c784a4ea132ab2a253fa4f55b6
- path: output/sratools/SRR11140744_2.fastq.gz
md5sum: 3e3b3af3413f50a1685fd7b3f1456d4e