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Verified Commit 8afe54bb authored by Laurent Modolo's avatar Laurent Modolo
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nf_modules: update module from g2gtools to multiqc to match the CONTRIBUTING.md

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with 367 additions and 110 deletions
src/nf_modules/fastqc/main.nf
+ 16
− 51
View file @ 8afe54bb
......@@ -2,65 +2,30 @@ version = "0.11.5"
container_url = "lbmc/fastqc:${version}"
params.fastqc_fastq = ""
params.fastqc_fastq_out = ""
process fastqc_fastq {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$pair_id"
input:
tuple val(pair_id), path(reads)
output:
path "*.{zip,html}", emit: report
script:
if (reads instanceof List)
"""
fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ \
${params.fastqc_fastq} \
${reads[0]} ${reads[1]}
"""
else
"""
fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ ${reads}
"""
}
params.fastqc_fastq_pairedend = ""
process fastqc_fastq_pairedend {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$pair_id"
input:
tuple val(pair_id), path(reads)
output:
path "*.{zip,html}", emit: report
script:
"""
fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ \
${params.fastqc_fastq_pairedend} \
${reads[0]} ${reads[1]}
"""
}
params.fastqc_fastq_singleend = ""
process fastqc_fastq_singleend {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
if (params.fastqc_fastq_out != "") {
publishDir "results/${params.fastqc_fastq_out}", mode: 'copy'
}
input:
tuple val(file_id), path(reads)
output:
path "*.{zip,html}", emit: report
tuple val(file_id), path("*.{zip,html}"), emit: report
script:
"""
fastqc --quiet --threads ${task.cpus} ${params.fastqc_fastq_singleend} --format fastq --outdir ./ ${reads}
"""
}
if (reads.size() == 2)
"""
fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ \
${params.fastqc_fastq} \
${reads[0]} ${reads[1]}
"""
else if (reads.size() == 1)
"""
fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ ${params.fastqc_fastq} ${reads[0]}
"""
}
\ No newline at end of file
src/nf_modules/g2gtools/main.nf
+ 63
− 8
View file @ 8afe54bb
......@@ -2,10 +2,14 @@ version = "0.2.8"
container_url = "lbmc/g2gtools:${version}"
params.vci_build = ""
params.vci_build_out = ""
process vci_build {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
if (params.vci_build_out != "") {
publishDir "results/${params.vci_build_out}", mode: 'copy'
}
input:
tuple val(file_id), path(vcf)
......@@ -14,6 +18,12 @@ process vci_build {
tuple val(file_id), path("*.vci.gz"), path("*.vci.gz.tbi"), emit: vci
tuple val(file_id), path("*_report.txt"), emit: report
script:
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
input_vcf = ""
for (vcf_file in vcf) {
input_vcf += " -i ${vcf_file}"
......@@ -24,83 +34,114 @@ g2gtools vcf2vci \
-p ${task.cpus} \
-f ${fasta} \
${input_vcf} \
-s ${file_id} \
-o ${file_id}.vci 2> ${file_id}_g2gtools_vcf2vci_report.txt
-s ${file_prefix} \
-o ${file_prefix}.vci 2> ${file_prefix}_g2gtools_vcf2vci_report.txt
"""
}
params.incorporate_snp = ""
params.incorporate_snp_out = ""
process incorporate_snp {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
if (params.incorporate_snp_out != "") {
publishDir "results/${params.incorporate_snp_out}", mode: 'copy'
}
input:
tuple val(file_id), path(vci), path(tbi)
tuple val(ref_id), path(fasta)
output:
tuple val(file_id), path("${file_id}_snp.fa"), path("${vci}"), path("${tbi}"), emit: fasta
tuple val(file_id), path("${file_prefix}_snp.fa"), path("${vci}"), path("${tbi}"), emit: fasta
tuple val(file_id), path("*_report.txt"), emit: report
script:
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
g2gtools patch \
${params.incorporate_snp} \
-p ${task.cpus} \
-i ${fasta} \
-c ${vci} \
-o ${file_id}_snp.fa 2> ${file_id}_g2gtools_path_report.txt
-o ${file_prefix}_snp.fa 2> ${file_prefix}_g2gtools_path_report.txt
"""
}
params.incorporate_indel = ""
params.incorporate_indel_out = ""
process incorporate_indel {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
if (params.incorporate_indel_out != "") {
publishDir "results/${params.incorporate_indel_out}", mode: 'copy'
}
input:
tuple val(file_id), path(fasta), path(vci), path(tbi)
output:
tuple val(file_id), path("${file_id}_snp_indel.fa"), path("${vci}"), path("${tbi}"), emit: fasta
tuple val(file_id), path("${file_prefix}_snp_indel.fa"), path("${vci}"), path("${tbi}"), emit: fasta
tuple val(file_id), path("*_report.txt"), emit: report
script:
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
g2gtools transform \
${params.incorporate_indel} \
-p ${task.cpus} \
-i ${fasta} \
-c ${vci} \
-o ${file_id}_snp_indel.fa 2> ${file_id}_g2gtools_transform_report.txt
-o ${file_prefix}_snp_indel.fa 2> ${file_prefix}_g2gtools_transform_report.txt
"""
}
params.convert_gtf = ""
params.convert_gtf_out = ""
process convert_gtf {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
if (params.convert_gtf_out != "") {
publishDir "results/${params.convert_gtf_out}", mode: 'copy'
}
input:
tuple val(file_id), path(vci), path(tbi)
tuple val(annot_id), path(gtf)
output:
tuple val(file_id), path("${file_id}.gtf"), emit: gtf
tuple val(file_id), path("${file_prefix}.gtf"), emit: gtf
tuple val(file_id), path("*_report.txt"), emit: report
script:
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
g2gtools convert \
${params.convert_gtf} \
-i ${gtf} \
-c ${vci} \
-o ${file_id}.gtf 2> ${file_id}_g2gtools_convert_report.txt
-o ${file_prefix}.gtf 2> ${file_prefix}_g2gtools_convert_report.txt
"""
}
params.convert_bed = ""
params.convert_bed_out = ""
process convert_bed {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
if (params.convert_bed_out != "") {
publishDir "results/${params.convert_bed_out}", mode: 'copy'
}
input:
tuple val(file_id), path(vci), path(tbi)
......@@ -109,6 +150,11 @@ process convert_bed {
tuple val(file_id), path("${file_id}.bed"), emit: bed
tuple val(file_id), path("*_report.txt"), emit: report
script:
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
g2gtools convert \
${params.convert_bed} \
......@@ -119,10 +165,14 @@ g2gtools convert \
}
params.convert_bam = ""
params.convert_bam_out = ""
process convert_bam {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "${bam_id} ${file_id}"
if (params.convert_bam_out != "") {
publishDir "results/${params.convert_bam_out}", mode: 'copy'
}
input:
tuple val(file_id), path(vci), path(tbi)
......@@ -131,6 +181,11 @@ process convert_bam {
tuple val(file_id), path("${file_id}_${bam_id.baseName}.bam"), emit: bam
tuple val(file_id), path("*_report.txt"), emit: report
script:
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
g2gtools convert \
${params.convert_bam} \
......
src/nf_modules/gatk3/main.nf
+ 114
− 12
View file @ 8afe54bb
......@@ -2,10 +2,14 @@ version = "3.8.0"
container_url = "lbmc/gatk:${version}"
params.variant_calling = ""
params.variant_calling_out = ""
process variant_calling {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
if (params.variant_calling_out != "") {
publishDir "results/${params.variant_calling_out}", mode: 'copy'
}
input:
tuple val(file_id), path(bam), path(bai)
......@@ -14,21 +18,30 @@ process variant_calling {
tuple val(file_id), path("*.vcf"), emit: vcf
script:
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk3 -T HaplotypeCaller \
-nct ${task.cpus} \
${params.variant_calling} \
-R ${fasta} \
-I ${bam} \
-o ${file_id}.vcf
-o ${file_prefix}.vcf
"""
}
params.filter_snp = ""
params.filter_snp_out = ""
process filter_snp {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
if (params.filter_snp_out != "") {
publishDir "results/${params.filter_snp_out}", mode: 'copy'
}
input:
tuple val(file_id), path(vcf)
......@@ -36,6 +49,11 @@ process filter_snp {
output:
tuple val(file_id), path("*_snp.vcf"), emit: vcf
script:
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk3 -T SelectVariants \
-nct ${task.cpus} \
......@@ -43,15 +61,19 @@ gatk3 -T SelectVariants \
-R ${fasta} \
-V ${vcf} \
-selectType SNP \
-o ${file_id}_snp.vcf
-o ${file_prefix}_snp.vcf
"""
}
params.filter_indels = ""
params.filter_indels_out = ""
process filter_indels {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
if (params.filter_indels_out != "") {
publishDir "results/${params.filter_indels_out}", mode: 'copy'
}
input:
tuple val(file_id), path(vcf)
......@@ -59,6 +81,11 @@ process filter_indels {
output:
tuple val(file_id), path("*_indel.vcf"), emit: vcf
script:
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk3 -T SelectVariants \
-nct ${task.cpus} \
......@@ -66,16 +93,20 @@ gatk3 -T SelectVariants \
-R ${fasta} \
-V ${vcf} \
-selectType INDEL \
-o ${file_id}_indel.vcf
-o ${file_prefix}_indel.vcf
"""
}
high_confidence_snp_filter = "(QD < 2.0) || (FS > 60.0) || (MQ < 40.0) || (MQRankSum < -12.5) || (ReadPosRankSum < -8.0) || (SOR > 4.0)"
params.high_confidence_snp = "--filterExpression \"${high_confidence_snp_filter}\" --filterName \"basic_snp_filter\""
params.high_confidence_snp_out = ""
process high_confidence_snp {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
if (params.high_confidence_snp_out != "") {
publishDir "results/${params.high_confidence_snp_out}", mode: 'copy'
}
input:
tuple val(file_id), path(vcf)
......@@ -83,22 +114,31 @@ process high_confidence_snp {
output:
tuple val(file_id), path("*_snp.vcf"), emit: vcf
script:
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk3 -T VariantFiltration \
-nct ${task.cpus} \
-R ${fasta} \
-V ${vcf} \
${params.high_confidence_snp} \
-o ${file_id}_filtered_snp.vcf
-o ${file_prefix}_filtered_snp.vcf
"""
}
high_confidence_indel_filter = "QD < 3.0 || FS > 200.0 || ReadPosRankSum < -20.0 || SOR > 10.0"
params.high_confidence_indels = "--filterExpression \"${high_confidence_indel_filter}\" --filterName \"basic_indel_filter\""
params.high_confidence_indels_out = ""
process high_confidence_indels {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
if (params.high_confidence_indels_out != "") {
publishDir "results/${params.high_confidence_indels_out}", mode: 'copy'
}
input:
tuple val(file_id), path(vcf)
......@@ -106,21 +146,30 @@ process high_confidence_indels {
output:
tuple val(file_id), path("*_indel.vcf"), emit: vcf
script:
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk3 -T VariantFiltration \
-nct ${task.cpus} \
-R ${fasta} \
-V ${vcf} \
${params.high_confidence_indels} \
-o ${file_id}_filtered_indel.vcf
-o ${file_prefix}_filtered_indel.vcf
"""
}
params.recalibrate_snp_table = ""
params.recalibrate_snp_table_out = ""
process recalibrate_snp_table {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
if (params.recalibrate_snp_table_out != "") {
publishDir "results/${params.recalibrate_snp_table_out}", mode: 'copy'
}
input:
tuple val(file_id), path(snp_file), path(indel_file), path(bam), path(bam_idx)
......@@ -141,10 +190,14 @@ gatk3 -T BaseRecalibrator \
}
params.recalibrate_snp = ""
params.recalibrate_snp_out = ""
process recalibrate_snp {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
if (params.recalibrate_snp_out != "") {
publishDir "results/${params.recalibrate_snp_out}", mode: 'copy'
}
input:
tuple val(file_id), path(snp_file), path(indel_file), path(bam), path(bam_idx)
......@@ -153,6 +206,11 @@ process recalibrate_snp {
output:
tuple val(file_id), path("*.bam"), emit: bam
script:
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk3 -T PrintReads \
--use_jdk_deflater \
......@@ -162,15 +220,19 @@ gatk3 -T PrintReads \
-R ${fasta} \
-I ${bam} \
-BQSR recal_data_table \
-o ${file_id}_recal.bam
-o ${file_prefix}_recal.bam
"""
}
params.haplotype_caller = ""
params.haplotype_caller_out = ""
process haplotype_caller {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
if (params.haplotype_caller_out != "") {
publishDir "results/${params.haplotype_caller_out}", mode: 'copy'
}
input:
tuple val(file_id), path(bam)
......@@ -178,6 +240,11 @@ process haplotype_caller {
output:
tuple val(file_id), path("*.gvcf"), emit: gvcf
script:
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk3 -T HaplotypeCaller \
-nct ${task.cpus} \
......@@ -186,15 +253,19 @@ gatk3 -T HaplotypeCaller \
-I ${bam} \
-ERC GVCF \
-variant_index_type LINEAR -variant_index_parameter 128000 \
-o ${file_id}.gvcf
-o ${file_prefix}.gvcf
"""
}
params.gvcf_genotyping = ""
params.gvcf_genotyping_out = ""
process gvcf_genotyping {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
if (params.gvcf_genotyping_out != "") {
publishDir "results/${params.gvcf_genotyping_out}", mode: 'copy'
}
input:
tuple val(file_id), path(gvcf)
......@@ -202,21 +273,30 @@ process gvcf_genotyping {
output:
tuple val(file_id), path("*.vcf"), emit: vcf
script:
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk3 -T GenotypeGVCFs \
-nct ${task.cpus} \
${params.gvcf_genotyping} \
-R ${fasta} \
-V ${gvcf} \
-o ${file_id}_joint.vcf
-o ${file_prefix}_joint.vcf
"""
}
params.select_variants_snp = ""
params.select_variants_snp_out = ""
process select_variants_snp {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
if (params.select_variants_snp_out != "") {
publishDir "results/${params.select_variants_snp_out}", mode: 'copy'
}
input:
tuple val(file_id), path(vcf)
......@@ -224,6 +304,11 @@ process select_variants_snp {
output:
tuple val(file_id), path("*_joint_snp.vcf"), emit: vcf
script:
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk3 -T SelectVariants \
-nct ${task.cpus} \
......@@ -231,15 +316,19 @@ gatk3 -T SelectVariants \
-R ${fasta} \
-V ${vcf} \
-selectType SNP \
-o ${file_id}_joint_snp.vcf
-o ${file_prefix}_joint_snp.vcf
"""
}
params.select_variants_indels = ""
params.select_variants_indels_out = ""
process select_variants_indels {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
if (params.select_variants_indels_out != "") {
publishDir "results/${params.select_variants_indels_out}", mode: 'copy'
}
input:
tuple val(file_id), path(vcf)
......@@ -247,6 +336,11 @@ process select_variants_indels {
output:
tuple val(file_id), path("*_joint_indel.vcf"), emit: vcf
script:
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk3 -T SelectVariants \
-nct ${task.cpus} \
......@@ -254,15 +348,19 @@ gatk3 -T SelectVariants \
-R ${fasta} \
-V ${vcf} \
-selectType INDEL \
-o ${file_id}_joint_indel.vcf
-o ${file_prefix}_joint_indel.vcf
"""
}
params.personalized_genome = ""
params.personalized_genome_out = ""
process personalized_genome {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
if (params.personalized_genome_out != "") {
publishDir "results/${params.personalized_genome_out}", mode: 'copy'
}
input:
tuple val(file_id), path(vcf)
......@@ -271,13 +369,17 @@ process personalized_genome {
tuple val(file_id), path("*_genome.fasta"), emit: fasta
script:
library = pick_library(file_id, library_list)
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk3 -T FastaAlternateReferenceMaker\
${params.personalized_genome} \
-R ${reference} \
-V ${vcf} \
-o ${library}_genome.fasta
-o ${file_prefix}_genome.fasta
"""
}
src/nf_modules/gatk4/main.nf
+ 111
− 5
View file @ 8afe54bb
......@@ -2,11 +2,14 @@ version = "4.2.0.0"
container_url = "broadinstitute/gatk:${version}"
params.variant_calling = ""
params.variant_calling_out = ""
process variant_calling {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
if (params.variant_calling_out != "") {
publishDir "results/${params.variant_calling_out}", mode: 'copy'
}
input:
tuple val(file_id), path(bam), path(bai)
......@@ -16,6 +19,11 @@ process variant_calling {
script:
xmx_memory = "${task.memory}" - ~/\s*GB/
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk --java-options "-Xmx${xmx_memory}G" HaplotypeCaller \
${params.variant_calling} \
......@@ -26,10 +34,14 @@ gatk --java-options "-Xmx${xmx_memory}G" HaplotypeCaller \
}
params.filter_snp = ""
params.filter_snp_out = ""
process filter_snp {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
if (params.filter_snp_out != "") {
publishDir "results/${params.filter_snp_out}", mode: 'copy'
}
input:
tuple val(file_id), path(vcf)
......@@ -38,6 +50,11 @@ process filter_snp {
tuple val(file_id), path("*_snp.vcf"), emit: vcf
script:
xmx_memory = "${task.memory}" - ~/\s*GB/
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk --java-options "-Xmx${xmx_memory}G" SelectVariants \
${params.filter_snp} \
......@@ -49,10 +66,14 @@ gatk --java-options "-Xmx${xmx_memory}G" SelectVariants \
}
params.filter_indels = ""
params.filter_indels_out = ""
process filter_indels {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
if (params.filter_indels_out != "") {
publishDir "results/${params.filter_indels_out}", mode: 'copy'
}
input:
tuple val(file_id), path(vcf)
......@@ -61,6 +82,11 @@ process filter_indels {
tuple val(file_id), path("*_indel.vcf"), emit: vcf
script:
xmx_memory = "${task.memory}" - ~/\s*GB/
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk --java-options "-Xmx${xmx_memory}G" SelectVariants \
${params.filter_indels} \
......@@ -71,13 +97,16 @@ gatk --java-options "-Xmx${xmx_memory}G" SelectVariants \
"""
}
high_confidence_snp_filter = "(QD < 2.0) || (FS > 60.0) || (MQ < 40.0) || (MQRankSum < -12.5) || (ReadPosRankSum < -8.0) || (SOR > 4.0)"
params.high_confidence_snp_filter = ""
params.high_confidence_snp_filter = "(QD < 2.0) || (FS > 60.0) || (MQ < 40.0) || (MQRankSum < -12.5) || (ReadPosRankSum < -8.0) || (SOR > 4.0)"
params.high_confidence_snp = ""
params.high_confidence_snp_out = ""
process high_confidence_snp {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
if (params.high_confidence_snp_out != "") {
publishDir "results/${params.high_confidence_snp_out}", mode: 'copy'
}
input:
tuple val(file_id), path(vcf)
......@@ -86,6 +115,11 @@ process high_confidence_snp {
tuple val(file_id), path("*_snp.vcf"), emit: vcf
script:
xmx_memory = "${task.memory}" - ~/\s*GB/
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk --java-options "-Xmx${xmx_memory}G" VariantFiltration \
-R ${fasta} \
......@@ -100,10 +134,14 @@ gatk --java-options "-Xmx${xmx_memory}G" VariantFiltration \
high_confidence_indel_filter = "QD < 3.0 || FS > 200.0 || ReadPosRankSum < -20.0 || SOR > 10.0"
params.high_confidence_indels = ""
params.high_confidence_indels_out = ""
process high_confidence_indels {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
if (params.high_confidence_indels_out != "") {
publishDir "results/${params.high_confidence_indels_out}", mode: 'copy'
}
input:
tuple val(file_id), path(vcf)
......@@ -112,6 +150,11 @@ process high_confidence_indels {
tuple val(file_id), path("*_indel.vcf"), emit: vcf
script:
xmx_memory = "${task.memory}" - ~/\s*GB/
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk --java-options "-Xmx${xmx_memory}G" VariantFiltration \
-R ${fasta} \
......@@ -124,10 +167,14 @@ gatk --java-options "-Xmx${xmx_memory}G" VariantFiltration \
}
params.recalibrate_snp_table = ""
params.recalibrate_snp_table_out = ""
process recalibrate_snp_table {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
if (params.recalibrate_snp_table_out != "") {
publishDir "results/${params.recalibrate_snp_table_out}", mode: 'copy'
}
input:
tuple val(file_id), path(snp_file), path(indel_file), path(bam), path(bam_idx)
......@@ -136,6 +183,11 @@ process recalibrate_snp_table {
tuple val(file_id), path("recal_data_table"), emit: recal_table
script:
xmx_memory = "${task.memory}" - ~/\s*GB/
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk --java-options "-Xmx${xmx_memory}G" IndexFeatureFile \
-I ${snp_file}
......@@ -152,10 +204,14 @@ gatk --java-options "-Xmx${xmx_memory}G" BaseRecalibrator \
}
params.recalibrate_snp = ""
params.recalibrate_snp_out = ""
process recalibrate_snp {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
if (params.recalibrate_snp_out != "") {
publishDir "results/${params.recalibrate_snp_out}", mode: 'copy'
}
input:
tuple val(file_id), path(snp_file), path(indel_file), path(bam), path(bam_idx), path(recal_table)
......@@ -164,6 +220,11 @@ process recalibrate_snp {
tuple val(file_id), path("*.bam"), emit: bam
script:
xmx_memory = "${task.memory}" - ~/\s*GB/
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk --java-options "-Xmx${xmx_memory}G" ApplyBQSR \
${params.recalibrate_snp} \
......@@ -175,10 +236,14 @@ gatk --java-options "-Xmx${xmx_memory}G" ApplyBQSR \
}
params.haplotype_caller = ""
params.haplotype_caller_out = ""
process haplotype_caller {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
if (params.haplotype_caller_out != "") {
publishDir "results/${params.haplotype_caller_out}", mode: 'copy'
}
input:
tuple val(file_id), path(bam)
......@@ -187,6 +252,11 @@ process haplotype_caller {
tuple val(file_id), path("*.gvcf"), emit: gvcf
script:
xmx_memory = "${task.memory}" - ~/\s*GB/
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk --java-options "-Xmx${xmx_memory}G" HaplotypeCaller \
${params.haplotype_caller} \
......@@ -198,10 +268,14 @@ gatk --java-options "-Xmx${xmx_memory}G" HaplotypeCaller \
}
params.gvcf_genotyping = ""
params.gvcf_genotyping_out = ""
process gvcf_genotyping {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
if (params.gvcf_genotyping_out != "") {
publishDir "results/${params.gvcf_genotyping_out}", mode: 'copy'
}
input:
tuple val(file_id), path(gvcf)
......@@ -210,6 +284,11 @@ process gvcf_genotyping {
tuple val(file_id), path("*.vcf.gz"), emit: vcf
script:
xmx_memory = "${task.memory}" - ~/\s*GB/
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk --java-options "-Xmx${xmx_memory}G" GenotypeGVCFs \
${params.gvcf_genotyping} \
......@@ -220,10 +299,14 @@ gatk --java-options "-Xmx${xmx_memory}G" GenotypeGVCFs \
}
params.select_variants_snp = ""
params.select_variants_snp_out = ""
process select_variants_snp {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
if (params.select_variants_snp_out != "") {
publishDir "results/${params.select_variants_snp_out}", mode: 'copy'
}
input:
tuple val(file_id), path(vcf)
......@@ -232,6 +315,11 @@ process select_variants_snp {
tuple val(file_id), path("*_joint_snp.vcf"), emit: vcf
script:
xmx_memory = "${task.memory}" - ~/\s*GB/
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk --java-options "-Xmx${xmx_memory}GG" SelectVariants \
${params.select_variants_snp} \
......@@ -243,10 +331,14 @@ gatk --java-options "-Xmx${xmx_memory}GG" SelectVariants \
}
params.select_variants_indels = ""
params.select_variants_indels_out = ""
process select_variants_indels {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
if (params.select_variants_indels_out != "") {
publishDir "results/${params.select_variants_indels_out}", mode: 'copy'
}
input:
tuple val(file_id), path(vcf)
......@@ -255,21 +347,30 @@ process select_variants_indels {
tuple val(file_id), path("*_joint_indel.vcf"), emit: vcf
script:
xmx_memory = "${task.memory}" - ~/\s*GB/
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk --java-options "-Xmx${xmx_memory}G" SelectVariants \
${params.select_variants_indels} \
-R ${fasta} \
-V ${vcf} \
-select-type INDEL \
-O ${file_id}_joint_indel.vcf
-O ${file_prefix}_joint_indel.vcf
"""
}
params.personalized_genome = ""
params.personalized_genome_out = ""
process personalized_genome {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
if (params.personalized_genome_out != "") {
publishDir "results/${params.personalized_genome_out}", mode: 'copy'
}
input:
tuple val(file_id), path(vcf)
......@@ -279,6 +380,11 @@ process personalized_genome {
script:
xmx_memory = "${task.memory}" - ~/\s*GB/
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
"""
gatk --java-options "-Xmx${xmx_memory}G" FastaAlternateReferenceMaker\
${params.personalized_genome} \
......
src/nf_modules/macs2/main.nf
+ 12
− 9
View file @ 8afe54bb
......@@ -3,12 +3,15 @@ container_url = "lbmc/macs2:${version}"
params.macs_gsize=3e9
params.macs_mfold="5 50"
params.peak_calling = ""
params.peak_calling = "--mfold ${params.macs_mfold} --gsize ${params.macs_gsize}"
params.peak_calling_out = ""
process peak_calling {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "${file_id}"
if (params.peak_calling_out != "") {
publishDir "results/${params.peak_calling_out}", mode: 'copy'
}
input:
tuple val(file_id), path(bam_ip), path(bam_control)
......@@ -27,9 +30,7 @@ macs2 callpeak \
--call-summits \
--control ${bam_control} \
--keep-dup all \
--name ${bam_ip.simpleName} \
--mfold ${params.macs_mfold} \
--gsize ${params.macs_gsize} 2> \
--name ${bam_ip.simpleName} 2> \
${bam_ip.simpleName}_macs2_report.txt
if grep -q "ERROR" ${bam_ip.simpleName}_macs2_report.txt; then
......@@ -39,11 +40,15 @@ fi
"""
}
params.peak_calling_bg = ""
params.peak_calling_bg = "--mfold ${params.macs_mfold} --gsize ${params.macs_gsize}"
params.peak_calling_bg_out = ""
process peak_calling_bg {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "${file_id}"
if (params.peak_calling_bg_out != "") {
publishDir "results/${params.peak_calling_bg_out}", mode: 'copy'
}
input:
tuple val(file_id), path(bg_ip), path(bg_control)
......@@ -66,9 +71,7 @@ macs2 callpeak \
--call-summits \
--control ${bg_control.simpleName}.bed \
--keep-dup all \
--name ${bg_ip.simpleName} \
--mfold ${params.macs_mfold} \
--gsize ${params.macs_gsize} 2> \
--name ${bg_ip.simpleName} 2> \
${bg_ip.simpleName}_macs2_report.txt
if grep -q "ERROR" ${bg_ip.simpleName}_macs2_report.txt; then
......
src/nf_modules/macs3/main.nf
+ 13
− 3
View file @ 8afe54bb
......@@ -2,12 +2,16 @@ version = "3.0.0a6"
container_url = "lbmc/macs3:${version}"
params.macs_gsize=3e9
params.macs_mfold=[5, 50]
params.macs_mfold="5 50"
params.peak_calling = "--mfold ${params.macs_mfold} --gsize ${params.macs_gsize}"
params.peak_calling_out = ""
process peak_calling {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "${file_id}"
if (params.peak_calling_out != "") {
publishDir "results/${params.peak_calling_out}", mode: 'copy'
}
input:
tuple val(file_id), path(bam_ip), path(bam_control)
......@@ -24,7 +28,7 @@ macs3 callpeak \
--call-summits \
--control ${bam_control} \
--keep-dup all \
--mfold params.macs_mfold[0] params.macs_mfold[1]
${params.peak_calling} \
--name ${bam_ip.simpleName} \
--gsize ${params.macs_gsize} 2> \
${bam_ip.simpleName}_macs3_report.txt
......@@ -36,10 +40,15 @@ fi
"""
}
params.peak_calling_bg = "--mfold ${params.macs_mfold} --gsize ${params.macs_gsize}"
params.peak_calling_bg_out = ""
process peak_calling_bg {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "${file_id}"
if (params.peak_calling_bg_out != "") {
publishDir "results/${params.peak_calling_bg_out}", mode: 'copy'
}
input:
tuple val(file_id), path(bg_ip), path(bg_control)
......@@ -56,6 +65,7 @@ awk '{print \$1"\t"\$2"\t"\$3"\t.\t+\t"\$4}' ${bg_ip} > \
awk '{print \$1"\t"\$2"\t"\$3"\t.\t+\t"\$4}' ${bg_control} > \
${bg_control.simpleName}.bed
macs3 callpeak \
${params.peak_calling_bg} \
--treatment ${bg_ip.simpleName}.bed \
--call-summits \
--control ${bg_control.simpleName}.bed \
......
src/nf_modules/minimap2/main.nf
+ 30
− 17
View file @ 8afe54bb
......@@ -2,16 +2,20 @@ version = "2.17"
container_url = "lbmc/minimap2:${version}"
params.index_fasta = ""
params.index_fasta_out = ""
process index_fasta {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$fasta.baseName"
tag "$file_id"
if (params.index_fasta_out != "") {
publishDir "results/${params.index_fasta_out}", mode: 'copy'
}
input:
path fasta
tuple val(file_id), path(fasta)
output:
tuple path("${fasta}"), path("*.mmi*"), emit: index
tuple val(file_id), path("${fasta}"), path("*.mmi*"), emit: index
path "*_report.txt", emit: report
script:
......@@ -22,30 +26,39 @@ minimap2 ${params.index_fasta} -t ${task.cpus} -I ${memory}G -d ${fasta.baseName
}
params.mapping_fastq = "-ax sr"
params.mapping_fastq_out = ""
process mapping_fastq {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$pair_id"
tag "$file_id"
if (params.mapping_fastq_out != "") {
publishDir "results/${params.mapping_fastq_out}", mode: 'copy'
}
input:
tuple path(fasta), path(index)
tuple val(pair_id), path(reads)
tuple val(fasta_id), path(fasta), path(index)
tuple val(file_id), path(reads)
output:
tuple val(pair_id), path("*.bam"), emit: bam
tuple val(file_id), path("*.bam"), emit: bam
path "*_report.txt", emit: report
script:
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
memory = "${task.memory}" - ~/\s*GB/
memory = memory / (task.cpus + 1.0)
if (reads instanceof List)
"""
minimap2 ${params.mapping_fastq} -t ${task.cpus} -K ${memory} ${fasta} ${reads[0]} ${reads[1]} |
samtools view -Sb - > ${pair_id}.bam
"""
else
"""
minimap2 ${params.mapping_fastq} -t ${task.cpus} -K ${memory} ${fasta} ${reads} |
samtools view -Sb - > ${reads.baseName}.bam
"""
if (reads.size() == 2)
"""
minimap2 ${params.mapping_fastq} -t ${task.cpus} -K ${memory} ${fasta} ${reads[0]} ${reads[1]} |
samtools view -Sb - > ${pair_id}.bam
"""
else if (reads.size() == 1)
"""
minimap2 ${params.mapping_fastq} -t ${task.cpus} -K ${memory} ${fasta} ${reads} |
samtools view -Sb - > ${pair_id}.bam
"""
}
\ No newline at end of file
src/nf_modules/multiqc/main.nf
+ 5
− 2
View file @ 8afe54bb
......@@ -2,13 +2,16 @@ version = "1.9"
container_url = "lbmc/multiqc:${version}"
params.multiqc = ""
params.multiqc_out = ""
process multiqc {
container = "${container_url}"
label "big_mem_mono_cpus"
publishDir "results/QC/", mode: 'copy'
if (params.multiqc_out != "") {
publishDir "results/${params.multiqc_out}", mode: 'copy'
}
input:
path report
path report
output:
path "*multiqc_*", emit: report
......
src/solution_RNASeq.nf
+ 3
− 3
View file @ 8afe54bb
......@@ -8,17 +8,17 @@ log.info "fastq files : ${params.fastq}"
log.info "fasta file : ${params.fasta}"
log.info "bed file : ${params.bed}"
Channel
channel
.fromPath( params.fasta )
.ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
.map { it -> [it.simpleName, it]}
.set { fasta_files }
Channel
channel
.fromPath( params.bed )
.ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
.map { it -> [it.simpleName, it]}
.set { bed_files }
Channel
channel
.fromFilePairs( params.fastq, size: -1)
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
......
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