Merge branch 'nf-core:master' into master

This commit is contained in:
FriederikeHanssen 2022-03-29 19:01:32 +02:00 committed by GitHub
commit 6dbf66421e
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41 changed files with 479 additions and 35 deletions

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@ -34,4 +34,15 @@ process BCFTOOLS_NORM {
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.vcf.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
} }

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@ -41,4 +41,15 @@ process BCFTOOLS_VIEW {
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.vcf.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
} }

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@ -31,4 +31,19 @@ process BWAMEM2_INDEX {
bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //') bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
END_VERSIONS END_VERSIONS
""" """
stub:
"""
mkdir bwamem2
touch bwamem2/${fasta}.0123
touch bwamem2/${fasta}.ann
touch bwamem2/${fasta}.pac
touch bwamem2/${fasta}.amb
touch bwamem2/${fasta}.bwt.2bit.64
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
END_VERSIONS
"""
} }

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@ -43,4 +43,15 @@ process BWAMEM2_MEM {
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.bam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
} }

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@ -47,4 +47,14 @@ process CAT_CAT {
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS END_VERSIONS
""" """
stub:
"""
touch $prefix
cat <<-END_VERSIONS > versions.yml
"${task.process}":
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
"""
} }

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@ -2,10 +2,10 @@ process CHROMAP_CHROMAP {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::chromap=0.2.0 bioconda::samtools=1.14" : null) conda (params.enable_conda ? "bioconda::chromap=0.2.1 bioconda::samtools=1.15" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:ed3529ef5253d7ccbc688b6a4c5c447152685757-0' : 'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:bd74d08a359024829a7aec1638a28607bbcd8a58-0' :
'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:ed3529ef5253d7ccbc688b6a4c5c447152685757-0' }" 'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:bd74d08a359024829a7aec1638a28607bbcd8a58-0' }"
input: input:
tuple val(meta), path(reads) tuple val(meta), path(reads)

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@ -1,11 +1,11 @@
process CHROMAP_INDEX { process CHROMAP_INDEX {
tag '$fasta' tag "$fasta"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::chromap=0.2.0" : null) conda (params.enable_conda ? "bioconda::chromap=0.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/chromap:0.2.0--hd03093a_1' : 'https://depot.galaxyproject.org/singularity/chromap:0.2.1--hd03093a_0' :
'quay.io/biocontainers/chromap:0.2.0--hd03093a_1' }" 'quay.io/biocontainers/chromap:0.2.1--hd03093a_0' }"
input: input:
path fasta path fasta

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@ -22,9 +22,10 @@ process DASTOOL_SCAFFOLDS2BIN {
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def file_extension = extension ? extension : "fasta" def file_extension = extension ? extension : "fasta"
def clean_fasta = fasta.toString() - ".gz"
def decompress_fasta = fasta.toString() == clean_fasta ? "" : "gunzip -q -f $fasta"
""" """
gunzip -f *.${file_extension}.gz $decompress_fasta
Fasta_to_Scaffolds2Bin.sh \\ Fasta_to_Scaffolds2Bin.sh \\
$args \\ $args \\

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@ -30,14 +30,11 @@ input:
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- fasta: - fasta:
type: file type: file
description: Fasta of list of fasta files recommended to be gathered via with .collect() of bins description: Fasta or list of fasta files recommended to be gathered via with .collect() of bins
pattern: "*.{fa,fas,fasta}" pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}"
- binner:
type: val
description: Name of the binning software (optional)
- extension: - extension:
type: val type: val
description: Fasta file extension (fa | fas | fasta | ...) description: Fasta file extension (fa | fas | fasta | ...), but without .gz suffix, even if gzipped input.
output: output:
- meta: - meta:

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@ -44,4 +44,16 @@ process DEEPVARIANT {
deepvariant: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' ) deepvariant: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' )
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.vcf.gz
touch ${prefix}.g.vcf.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
deepvariant: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' )
END_VERSIONS
"""
} }

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@ -37,4 +37,15 @@ process EXPANSIONHUNTER {
expansionhunter: \$( echo \$(ExpansionHunter --version 2>&1) | sed 's/^.*ExpansionHunter v//') expansionhunter: \$( echo \$(ExpansionHunter --version 2>&1) | sed 's/^.*ExpansionHunter v//')
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.vcf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
expansionhunter: \$( echo \$(ExpansionHunter --version 2>&1) | sed 's/^.*ExpansionHunter v//')
END_VERSIONS
"""
} }

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@ -44,4 +44,16 @@ process FASTQC {
END_VERSIONS END_VERSIONS
""" """
} }
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.html
touch ${prefix}.zip
cat <<-END_VERSIONS > versions.yml
"${task.process}":
fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
END_VERSIONS
"""
} }

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@ -39,4 +39,15 @@ process GATK4_BEDTOINTERVALLIST {
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.interval_list
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
} }

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@ -37,4 +37,15 @@ process GATK4_CREATESEQUENCEDICTIONARY {
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.dict
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
} }

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@ -51,4 +51,22 @@ process GATK4_INTERVALLISTTOOLS {
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
mkdir -p ${prefix}_split/temp_0001_of_6
mkdir -p ${prefix}_split/temp_0002_of_6
mkdir -p ${prefix}_split/temp_0003_of_6
mkdir -p ${prefix}_split/temp_0004_of_6
touch ${prefix}_split/temp_0001_of_6/1scattered.interval_list
touch ${prefix}_split/temp_0002_of_6/2scattered.interval_list
touch ${prefix}_split/temp_0003_of_6/3scattered.interval_list
touch ${prefix}_split/temp_0004_of_6/4scattered.interval_list
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
} }

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@ -42,4 +42,15 @@ process GLNEXUS {
glnexus: \$( echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release v//; s/ .*\$//') glnexus: \$( echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release v//; s/ .*\$//')
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.bcf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
glnexus: \$( echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release v//; s/ .*\$//')
END_VERSIONS
"""
} }

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@ -28,4 +28,16 @@ process MULTIQC {
multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
END_VERSIONS END_VERSIONS
""" """
stub:
"""
touch multiqc_data
touch multiqc_plots
touch multiqc_report.html
cat <<-END_VERSIONS > versions.yml
"${task.process}":
multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
END_VERSIONS
"""
} }

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@ -48,4 +48,15 @@ process PICARD_COLLECTHSMETRICS {
picard: \$(echo \$(picard CollectHsMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) picard: \$(echo \$(picard CollectHsMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}_collecthsmetrics.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
picard: \$(echo \$(picard CollectHsMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
} }

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@ -42,4 +42,24 @@ process PICARD_COLLECTMULTIPLEMETRICS {
picard: \$(picard CollectMultipleMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:) picard: \$(picard CollectMultipleMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.CollectMultipleMetrics.alignment_summary_metrics
touch ${prefix}.CollectMultipleMetrics.insert_size_metrics
touch ${prefix}.CollectMultipleMetrics.quality_distribution.pdf
touch ${prefix}.CollectMultipleMetrics.base_distribution_by_cycle_metrics
touch ${prefix}.CollectMultipleMetrics.quality_by_cycle_metrics
touch ${prefix}.CollectMultipleMetrics.read_length_histogram.pdf
touch ${prefix}.CollectMultipleMetrics.base_distribution_by_cycle.pdf
touch ${prefix}.CollectMultipleMetrics.quality_by_cycle.pdf
touch ${prefix}.CollectMultipleMetrics.insert_size_histogram.pdf
touch ${prefix}.CollectMultipleMetrics.quality_distribution_metrics
cat <<-END_VERSIONS > versions.yml
"${task.process}":
picard: \$(echo \$(picard CollectMultipleMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
} }

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@ -42,4 +42,17 @@ process PICARD_MARKDUPLICATES {
picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.bam
touch ${prefix}.bam.bai
touch ${prefix}.MarkDuplicates.metrics.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
} }

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@ -46,4 +46,17 @@ process PICARD_SORTVCF {
picard: \$(picard SortVcf --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:) picard: \$(picard SortVcf --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}_sorted.vcf.gz
touch ${prefix}.bam.bai
touch ${prefix}.MarkDuplicates.metrics.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
picard: \$(picard SortVcf --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
} }

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@ -52,4 +52,72 @@ process QUALIMAP_BAMQC {
qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//') qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
END_VERSIONS END_VERSIONS
""" """
stub:
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
mkdir -p $prefix/css
mkdir $prefix/images_qualimapReport
mkdir $prefix/raw_data_qualimapReport
cd $prefix/css
touch agogo.css
touch basic.css
touch bgtop.png
touch comment-close.png
touch doctools.js
touch down-pressed.png
touch jquery.js
touch plus.png
touch qualimap_logo_small.png
touch searchtools.js
touch up.png
touch websupport.js
touch ajax-loader.gif
touch bgfooter.png
touch comment-bright.png
touch comment.png
touch down.png
touch file.png
touch minus.png
touch pygments.css
touch report.css
touch underscore.js
touch up-pressed.png
cd ../images_qualimapReport/
touch genome_coverage_0to50_histogram.png
touch genome_coverage_quotes.png
touch genome_insert_size_across_reference.png
touch genome_mapping_quality_histogram.png
touch genome_uniq_read_starts_histogram.png
touch genome_coverage_across_reference.png
touch genome_gc_content_per_window.png
touch genome_insert_size_histogram.png
touch genome_reads_clipping_profile.png
touch genome_coverage_histogram.png
touch genome_homopolymer_indels.png
touch genome_mapping_quality_across_reference.png
touch genome_reads_content_per_read_position.png
cd ../raw_data_qualimapReport
touch coverage_across_reference.txt
touch genome_fraction_coverage.txt
touch insert_size_histogram.txt
touch mapped_reads_nucleotide_content.txt
touch coverage_histogram.txt
touch homopolymer_indels.txt
touch mapped_reads_clipping_profile.txt
touch mapping_quality_across_reference.txt
touch duplication_rate_histogram.txt
touch insert_size_across_reference.txt
touch mapped_reads_gc-content_distribution.txt
touch mapping_quality_histogram.txt
cd ../
touch genome_results.txt
touch qualimapReport.html
cd ../
cat <<-END_VERSIONS > versions.yml
"${task.process}":
qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
END_VERSIONS
"""
} }

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@ -29,4 +29,14 @@ process SAMTOOLS_FAIDX {
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS END_VERSIONS
""" """
stub:
"""
touch ${fasta}.fai
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
} }

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@ -33,4 +33,16 @@ process SAMTOOLS_INDEX {
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS END_VERSIONS
""" """
stub:
"""
touch ${input}.bai
touch ${input}.crai
touch ${input}.csi
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
} }

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@ -38,4 +38,16 @@ process SAMTOOLS_MERGE {
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS END_VERSIONS
""" """
stub:
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def file_type = input_files[0].getExtension()
"""
touch ${prefix}.${file_type}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
} }

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@ -28,4 +28,15 @@ process SAMTOOLS_SORT {
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.bam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
} }

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@ -34,4 +34,15 @@ process SAMTOOLS_STATS {
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${input}.stats
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
} }

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@ -70,5 +70,4 @@ process SVDB_QUERY {
svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' ) svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
END_VERSIONS END_VERSIONS
""" """
} }

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@ -30,4 +30,16 @@ process TABIX_BGZIPTABIX {
tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.gz
touch ${prefix}.gz.tbi
cat <<-END_VERSIONS > versions.yml
"${task.process}":
tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
} }

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@ -27,4 +27,15 @@ process TABIX_TABIX {
tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${tab}.tbi
cat <<-END_VERSIONS > versions.yml
"${task.process}":
tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
} }

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@ -36,4 +36,16 @@ process TIDDIT_COV {
tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//') tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch $prefix.wig
touch $prefix.tab
cat <<-END_VERSIONS > versions.yml
"${task.process}":
tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
END_VERSIONS
"""
} }

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@ -38,4 +38,17 @@ process TIDDIT_SV {
tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//') tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch $prefix.vcf
touch $prefix.ploidy.tab
touch $prefix.signals.tab
cat <<-END_VERSIONS > versions.yml
"${task.process}":
tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
END_VERSIONS
"""
} }

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@ -35,4 +35,15 @@ process UCSC_WIGTOBIGWIG {
ucsc: $VERSION ucsc: $VERSION
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.bw
cat <<-END_VERSIONS > versions.yml
"${task.process}":
ucsc: $VERSION
END_VERSIONS
"""
} }

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@ -33,4 +33,15 @@ process UNTAR {
untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//') untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
END_VERSIONS END_VERSIONS
""" """
stub:
untar = archive.toString() - '.tar.gz'
"""
touch $untar
cat <<-END_VERSIONS > versions.yml
"${task.process}":
untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
END_VERSIONS
"""
} }

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@ -39,4 +39,15 @@ process VCFANNO {
vcfanno: \$(echo \$(vcfanno 2>&1 | grep version | cut -f3 -d' ' )) vcfanno: \$(echo \$(vcfanno 2>&1 | grep version | cut -f3 -d' ' ))
END_VERSIONS END_VERSIONS
""" """
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}_annotated.vcf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
vcfanno: \$(echo \$(vcfanno 2>&1 | grep version | cut -f3 -d' ' ))
END_VERSIONS
"""
} }

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@ -8,7 +8,7 @@
- path: output/chromap/test.bed.gz - path: output/chromap/test.bed.gz
md5sum: 25e40bde24c7b447292cd68573728694 md5sum: 25e40bde24c7b447292cd68573728694
- path: output/chromap/versions.yml - path: output/chromap/versions.yml
md5sum: 2d3d2959ac20d98036807964896829e7 md5sum: d24cfc35ad958206a5bc5694221b4fae
- name: chromap chromap test_chromap_chromap_paired_end - name: chromap chromap test_chromap_chromap_paired_end
command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
@ -20,7 +20,7 @@
- path: output/chromap/test.bed.gz - path: output/chromap/test.bed.gz
md5sum: 7cdc8448882b75811e0c784f5f20aef2 md5sum: 7cdc8448882b75811e0c784f5f20aef2
- path: output/chromap/versions.yml - path: output/chromap/versions.yml
md5sum: 51cff66779161d8a602cce5989017395 md5sum: 68ffe268a9d460956de4aad2a55ffd68
- name: chromap chromap test_chromap_chromap_paired_bam - name: chromap chromap test_chromap_chromap_paired_bam
command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_bam -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_bam -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
@ -30,6 +30,6 @@
files: files:
- path: output/chromap/genome.index - path: output/chromap/genome.index
- path: output/chromap/test.bam - path: output/chromap/test.bam
md5sum: f255c7441d5a1f307fc642d2aa19647e md5sum: df467417407408e42992dc3dd15b22f5
- path: output/chromap/versions.yml - path: output/chromap/versions.yml
md5sum: f91910c44169549c3923931de5c3afcb md5sum: ea732b4c6f1312d09745b66c3963dd3f

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@ -6,4 +6,4 @@
files: files:
- path: output/chromap/genome.index - path: output/chromap/genome.index
- path: output/chromap/versions.yml - path: output/chromap/versions.yml
md5sum: b75dec647f9dc5f4887f36d1db7a9ccd md5sum: fc5c80190d0622ea3e979e6862f8e32b

View file

@ -2,9 +2,10 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf' include { GUNZIP } from '../../../../modules/gunzip/main.nf'
include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf' include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf'
include { DASTOOL_SCAFFOLDS2BIN } from '../../../../modules/dastool/scaffolds2bin/main.nf' include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf'
include { DASTOOL_SCAFFOLDS2BIN } from '../../../../modules/dastool/scaffolds2bin/main.nf'
workflow test_dastool_scaffolds2bin { workflow test_dastool_scaffolds2bin {
@ -22,4 +23,26 @@ workflow test_dastool_scaffolds2bin {
METABAT2_METABAT2 ( input_metabat2 ) METABAT2_METABAT2 ( input_metabat2 )
DASTOOL_SCAFFOLDS2BIN ( METABAT2_METABAT2.out.fasta.collect(), "fa") DASTOOL_SCAFFOLDS2BIN ( METABAT2_METABAT2.out.fasta.collect(), "fa")
} }
workflow test_dastool_scaffolds2bin_ungzipped {
input_depth = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam_bai'], checkIfExists: true) ]
METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )
Channel.fromPath(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
.map { it -> [[ id:'test', single_end:false ], it] }
.join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
.set { input_metabat2 }
METABAT2_METABAT2 ( input_metabat2 )
// TODO test unzipped input files
ch_input_2_scaffolds2bin = GUNZIP( METABAT2_METABAT2.out.fasta ).gunzip
DASTOOL_SCAFFOLDS2BIN ( ch_input_2_scaffolds2bin, "fa")
}

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@ -1,14 +1,20 @@
- name: dastool scaffolds2bin test_dastool_scaffolds2bin - name: dastool scaffolds2bin test_dastool_scaffolds2bin
command: nextflow run ./tests/modules/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin -c ./tests/config/nextflow.config -c ./tests/modules/dastool/scaffolds2bin/nextflow.config command: nextflow run tests/modules/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin -c tests/config/nextflow.config
tags: tags:
- dastool - dastool
- dastool/scaffolds2bin - dastool/scaffolds2bin
files: files:
- path: output/dastool/test.tsv - path: output/dastool/test.tsv
md5sum: 6e46c0be14dded7cb13af38f54feea47 md5sum: 6e46c0be14dded7cb13af38f54feea47
- path: output/metabat2/bins/test.1.fa.gz - path: output/dastool/versions.yml
md5sum: 2b297bf557cc3831b800348859331268 md5sum: d0831ed159eb5a1a1565d1d211012ad6
- path: output/metabat2/test.tsv.gz - name: dastool scaffolds2bin test_dastool_scaffolds2bin_ungzipped
md5sum: 619338fa5019e361d5545ce385a6961f command: nextflow run tests/modules/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin_ungzipped -c tests/config/nextflow.config
- path: output/metabat2/test.txt.gz tags:
md5sum: 745a0446af6ef68b930975e9ce5a95d6 - dastool
- dastool/scaffolds2bin
files:
- path: output/dastool/test.tsv
md5sum: 6e46c0be14dded7cb13af38f54feea47
- path: output/dastool/versions.yml
md5sum: da58e477b7f4c16a9ea495ec1a4a4d4f

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@ -7,8 +7,8 @@ include { EXPANSIONHUNTER } from '../../../modules/expansionhunter/main.nf'
workflow test_expansionhunter { workflow test_expansionhunter {
input = [ [ id:'test', gender:'male' ], // meta map input = [ [ id:'test', gender:'male' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
] ]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
variant_catalog = file(params.test_data['homo_sapiens']['genome']['repeat_expansions'], checkIfExists: true) variant_catalog = file(params.test_data['homo_sapiens']['genome']['repeat_expansions'], checkIfExists: true)

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@ -4,4 +4,4 @@
- expansionhunter - expansionhunter
files: files:
- path: output/expansionhunter/test.vcf - path: output/expansionhunter/test.vcf
md5sum: ef6c2101d7bd67211bb5a5a132690e02 md5sum: cfd4a1d35c0e469b99eb6aaa6d22de76