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Implemented lineage only mode #54

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merged 10 commits into from
Oct 10, 2023
Merged

Implemented lineage only mode #54

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9d75700
Implemented lineage only mode
johausmann Sep 28, 2023
27386e7
Updated pangolin task to accept vcf with caller == input
johausmann Oct 5, 2023
3fa96e2
Update Makefile
johausmann Oct 5, 2023
7b0482e
Replace whitespace with tab in Makefile
johausmann Oct 5, 2023
5e90601
Updated path in test_14.sh
johausmann Oct 5, 2023
ea09b0b
Update test_15.sh
johausmann Oct 10, 2023
d41a5f0
Update test_16.sh
johausmann Oct 10, 2023
07b3c52
Update test_14.sh
johausmann Oct 10, 2023
ce941c1
Updated lineage test files and added new VCF file as lofreq VCF gives…
johausmann Oct 10, 2023
16011f7
Last push did not include updated test scripts
johausmann Oct 10, 2023
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230 changes: 133 additions & 97 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,7 @@ params.skip_bcftools = false
params.skip_gatk = false
params.skip_pangolin = false
params.skip_normalization = false
params.lineage_mode = false

// references
params.reference = false
Expand All @@ -39,7 +40,7 @@ params.gff = false
//params.snpeff_config = false
params.snpeff_organism = false
params.primers = false
params.different_virus = false
params.reference_generate = false

params.output = "."
params.min_mapping_quality = 20
Expand Down Expand Up @@ -206,6 +207,11 @@ else if (params.input_vcfs_list != false || params.vcf != false) {
.set { input_vcfs }
}
}
else if(params.reference_generate) {
genome = params.reference
annotation = gff
annotation_name = snpeff_organism
}
else {
log.error "missing some input data"
exit 1
Expand Down Expand Up @@ -240,119 +246,149 @@ if (params.skip_bcftools && params.skip_gatk && params.skip_ivar && params.skip_
exit 1
}

// Lineage mode should only be used when running with assembly or VCF input
// For FASTQ input we can run pangolin as regular rule
if (params.lineage_mode && input_fastqs) {
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log.error "lineage mode is only supported with fasta or VCF input"
exit 1
}

workflow {
if (params.reference) {
if (! skip_snpeff && gff) {
SNPEFF_DATABASE(reference, gff, snpeff_organism)
snpeff_data = SNPEFF_DATABASE.out.snpeff_data
snpeff_config = SNPEFF_DATABASE.out.snpeff_config
}

}
if (input_fastqs) {
if (params.reference) {
BWA_INDEX(reference)
reference = BWA_INDEX.out.reference
if (params.lineage_mode) {
log.info "Running lineage mode. In this mode only Pangolin is executed on either fasta or VCF"
if (input_fastas) {
PANGOLIN_LINEAGE(input_fastas)
}
if (library == "paired") {
READ_TRIMMING_PAIRED_END(input_fastqs)
ALIGNMENT_PAIRED_END(READ_TRIMMING_PAIRED_END.out[0], reference)
bam_files = ALIGNMENT_PAIRED_END.out
else if (input_vcfs) {
VARIANT_NORMALIZATION(input_vcfs, reference)
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normalized_vcfs = VARIANT_NORMALIZATION.out
VCF2FASTA(normalized_vcfs, reference)
PANGOLIN_LINEAGE(VCF2FASTA.out)
}
else {
READ_TRIMMING_SINGLE_END(input_fastqs)
ALIGNMENT_SINGLE_END(READ_TRIMMING_SINGLE_END.out[0], reference)
bam_files = ALIGNMENT_SINGLE_END.out
}
else if (params.reference_generate) {
log.info "Running genome/annotation generate mode. This step generates only bwa and snpEff databases..."
// Custom reference mode. This mode is added to prepare the reference just once when processing many samples
if (genome) {
BWA_INDEX(genome)
if (!skip_snpeff) {
SNPEFF_DATABASE(genome, gff, snpeff_organism)
}
}
BAM_PREPROCESSING(bam_files, reference)
preprocessed_bams = BAM_PREPROCESSING.out.preprocessed_bams
}
else {
// Run genome and annotation steps for single sample
if (params.reference) {
if (! skip_snpeff && gff) {
SNPEFF_DATABASE(reference, gff, snpeff_organism)
snpeff_data = SNPEFF_DATABASE.out.snpeff_data
snpeff_config = SNPEFF_DATABASE.out.snpeff_config
}

if (primers) {
PRIMER_TRIMMING_IVAR(preprocessed_bams, primers)
preprocessed_bams = PRIMER_TRIMMING_IVAR.out.trimmed_bam
}
COVERAGE_ANALYSIS(preprocessed_bams)

// variant calling
vcfs_to_normalize = null
if (!params.skip_bcftools) {
VARIANT_CALLING_BCFTOOLS(preprocessed_bams, reference)
vcfs_to_normalize = vcfs_to_normalize == null?
VARIANT_CALLING_BCFTOOLS.out : vcfs_to_normalize.concat(VARIANT_CALLING_BCFTOOLS.out)
if (input_fastqs) {
if (params.reference) {
BWA_INDEX(reference)
reference = BWA_INDEX.out.reference
}
if (library == "paired") {
READ_TRIMMING_PAIRED_END(input_fastqs)
ALIGNMENT_PAIRED_END(READ_TRIMMING_PAIRED_END.out[0], reference)
bam_files = ALIGNMENT_PAIRED_END.out
}
else {
READ_TRIMMING_SINGLE_END(input_fastqs)
ALIGNMENT_SINGLE_END(READ_TRIMMING_SINGLE_END.out[0], reference)
bam_files = ALIGNMENT_SINGLE_END.out
}
BAM_PREPROCESSING(bam_files, reference)
preprocessed_bams = BAM_PREPROCESSING.out.preprocessed_bams

if (primers) {
PRIMER_TRIMMING_IVAR(preprocessed_bams, primers)
preprocessed_bams = PRIMER_TRIMMING_IVAR.out.trimmed_bam
}
COVERAGE_ANALYSIS(preprocessed_bams)

// variant calling
vcfs_to_normalize = null
if (!params.skip_bcftools) {
VARIANT_CALLING_BCFTOOLS(preprocessed_bams, reference)
vcfs_to_normalize = vcfs_to_normalize == null?
VARIANT_CALLING_BCFTOOLS.out : vcfs_to_normalize.concat(VARIANT_CALLING_BCFTOOLS.out)
}
if (!params.skip_lofreq) {
VARIANT_CALLING_LOFREQ(preprocessed_bams, reference)
vcfs_to_normalize = vcfs_to_normalize == null?
VARIANT_CALLING_LOFREQ.out : vcfs_to_normalize.concat(VARIANT_CALLING_LOFREQ.out)
}
if (!params.skip_gatk) {
VARIANT_CALLING_GATK(preprocessed_bams, reference)
vcfs_to_normalize = vcfs_to_normalize == null?
VARIANT_CALLING_GATK.out : vcfs_to_normalize.concat(VARIANT_CALLING_GATK.out)
}
if (!params.skip_ivar && gff) {
VARIANT_CALLING_IVAR(preprocessed_bams, reference, gff)
IVAR2VCF(VARIANT_CALLING_IVAR.out, reference)
vcfs_to_normalize = vcfs_to_normalize == null?
IVAR2VCF.out : vcfs_to_normalize.concat(IVAR2VCF.out)
}
}
if (!params.skip_lofreq) {
VARIANT_CALLING_LOFREQ(preprocessed_bams, reference)
vcfs_to_normalize = vcfs_to_normalize == null?
VARIANT_CALLING_LOFREQ.out : vcfs_to_normalize.concat(VARIANT_CALLING_LOFREQ.out)
else if (input_fastas) {
if (!params.skip_pangolin) {
// pangolin from fasta
PANGOLIN_LINEAGE(input_fastas)
}
// assembly variant calling
VARIANT_CALLING_ASSEMBLY(input_fastas, reference)
vcfs_to_normalize = VARIANT_CALLING_ASSEMBLY.out
}
if (!params.skip_gatk) {
VARIANT_CALLING_GATK(preprocessed_bams, reference)
vcfs_to_normalize = vcfs_to_normalize == null?
VARIANT_CALLING_GATK.out : vcfs_to_normalize.concat(VARIANT_CALLING_GATK.out)
else if (input_vcfs) {
vcfs_to_normalize = input_vcfs
}
if (!params.skip_ivar && gff) {
VARIANT_CALLING_IVAR(preprocessed_bams, reference, gff)
IVAR2VCF(VARIANT_CALLING_IVAR.out, reference)
vcfs_to_normalize = vcfs_to_normalize == null?
IVAR2VCF.out : vcfs_to_normalize.concat(IVAR2VCF.out)

if (! params.skip_normalization) {
VARIANT_NORMALIZATION(vcfs_to_normalize, reference)
normalized_vcfs = VARIANT_NORMALIZATION.out
}
}
else if (input_fastas) {
if (!params.skip_pangolin) {
// pangolin from fasta
PANGOLIN_LINEAGE(input_fastas)
else {
normalized_vcfs = vcfs_to_normalize
}

// assembly variant calling
VARIANT_CALLING_ASSEMBLY(input_fastas, reference)
vcfs_to_normalize = VARIANT_CALLING_ASSEMBLY.out
}
else if (input_vcfs) {
vcfs_to_normalize = input_vcfs
}

if (! params.skip_normalization) {
VARIANT_NORMALIZATION(vcfs_to_normalize, reference)
normalized_vcfs = VARIANT_NORMALIZATION.out
}
else {
normalized_vcfs = vcfs_to_normalize
}

if (input_fastqs || input_vcfs) {
// pangolin from VCF on the normalized VCFs
if (!params.skip_pangolin) {
VCF2FASTA(normalized_vcfs, reference)
PANGOLIN_LINEAGE(VCF2FASTA.out)
if (input_fastqs || input_vcfs) {
// pangolin from VCF on the normalized VCFs
if (!params.skip_pangolin) {
VCF2FASTA(normalized_vcfs, reference)
PANGOLIN_LINEAGE(VCF2FASTA.out)
}
}
}

if (! skip_sarscov2_annotations) {
// only optionally add SARS-CoV-2 specific annotations
VARIANT_SARSCOV2_ANNOTATION(normalized_vcfs)
normalized_vcfs = VARIANT_SARSCOV2_ANNOTATION.out.annotated_vcfs
}
if (! skip_sarscov2_annotations) {
// only optionally add SARS-CoV-2 specific annotations
VARIANT_SARSCOV2_ANNOTATION(normalized_vcfs)
normalized_vcfs = VARIANT_SARSCOV2_ANNOTATION.out.annotated_vcfs
}

if (preprocessed_bams) {
// we can only add technical annotations when we have the reads
VAFATOR(normalized_vcfs.combine(preprocessed_bams, by: 0))
VARIANT_VAF_ANNOTATION(VAFATOR.out.annotated_vcf)
normalized_vcfs = VARIANT_VAF_ANNOTATION.out.vaf_annotated
}
if (preprocessed_bams) {
// we can only add technical annotations when we have the reads
VAFATOR(normalized_vcfs.combine(preprocessed_bams, by: 0))
VARIANT_VAF_ANNOTATION(VAFATOR.out.annotated_vcf)
normalized_vcfs = VARIANT_VAF_ANNOTATION.out.vaf_annotated
}

// NOTE: phasing has to happen before SnpEff annotation for MNVs to be annotated correctly
if (gff) {
PHASING(normalized_vcfs, reference, gff)
normalized_vcfs = PHASING.out
}
// NOTE: phasing has to happen before SnpEff annotation for MNVs to be annotated correctly
if (gff) {
PHASING(normalized_vcfs, reference, gff)
normalized_vcfs = PHASING.out
}

if (! skip_snpeff) {
// only when configured we run SnpEff
VARIANT_ANNOTATION(normalized_vcfs, snpeff_data, snpeff_config, snpeff_organism)
normalized_vcfs = VARIANT_ANNOTATION.out.annotated_vcfs
}
else {
BGZIP(normalized_vcfs)
if (! skip_snpeff) {
// only when configured we run SnpEff
VARIANT_ANNOTATION(normalized_vcfs, snpeff_data, snpeff_config, snpeff_organism)
normalized_vcfs = VARIANT_ANNOTATION.out.annotated_vcfs
}
else {
BGZIP(normalized_vcfs)
}
}
}
5 changes: 4 additions & 1 deletion nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,10 @@ params.pfam_names_header = "$baseDir/reference/pfam_names.header.txt"
params.pfam_descriptions_header = "$baseDir/reference/pfam_descriptions.header.txt"

profiles {
conda { params.enable_conda = true }
conda {
params.enable_conda = true
conda.enabled = true
}
debug { process.beforeScript = 'echo $HOSTNAME' }
test {
params.cpus = 1
Expand Down
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