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Merge pull request #252 from replikation/MarieLataretu/issue245
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[Enhancment] publish more logs/intermediate files from ARTIC
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@replikation
replikation authored Aug 3, 2023
2 parents a618015 + 80ae629 commit 19b87bf
Showing 1 changed file with 41 additions and 4 deletions.
45 changes: 41 additions & 4 deletions workflows/process/artic.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,10 @@ process artic_medaka {
publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "${name}_mapped_*.primertrimmed.sorted.bam*"
publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "${name}.trimmed.rg.sorted.bam"
publishDir "${params.output}/${params.genomedir}/all_consensus_sequences/", mode: 'copy', pattern: "*.consensus.fasta"
publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "${name}.primersitereport.txt"
publishDir "${params.output}/${params.lineagedir}/${name}/", mode: 'copy', pattern: "SNP_${name}.pass.vcf"
publishDir "${params.output}/${params.lineagedir}/${name}/", mode: 'copy', pattern: "${name}.coverage_mask.txt"
publishDir "${params.output}/${params.lineagedir}/${name}/", mode: 'copy', pattern: "${name}.fail.vcf"

input:
tuple val(name), path(reads), path(external_scheme)
Expand All @@ -14,6 +17,10 @@ process artic_medaka {
tuple val(name), path("SNP_${name}.pass.vcf"), emit: vcf
tuple val(name), path("${name}.pass.vcf.gz"), path("${name}.coverage_mask.txt.*1.depths"), path("${name}.coverage_mask.txt.*2.depths"), emit: covarplot
tuple val(name), path("${name}.trimmed.rg.sorted.bam"), emit: fullbam
tuple val(name), path("${name}.primersitereport.txt"), emit: primersitereport
tuple val(name), path("${name}.coverage_mask.txt"), emit: coverage_mask
tuple val(name), path("${name}.fail.vcf"), emit: vcf_fail

script:
"""
artic minion --medaka \
Expand Down Expand Up @@ -49,7 +56,10 @@ process artic_medaka {
${name}.pass.vcf.gz \
${name}.coverage_mask.txt.nCoV-2019_1.depths \
${name}.coverage_mask.txt.nCoV-2019_2.depths \
${name}.trimmed.rg.sorted.bam
${name}.trimmed.rg.sorted.bam \
${name}.primersitereport.txt \
${name}.coverage_mask.txt \
${name}.fail.vcf
"""
}

Expand All @@ -59,7 +69,10 @@ process artic_medaka_custom_bed {
publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "${name}_mapped_*.primertrimmed.sorted.bam*"
publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "${name}.trimmed.rg.sorted.bam"
publishDir "${params.output}/${params.genomedir}/all_consensus_sequences/", mode: 'copy', pattern: "*.consensus.fasta"
publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "${name}.primersitereport.txt"
publishDir "${params.output}/${params.lineagedir}/${name}/", mode: 'copy', pattern: "SNP_${name}.pass.vcf"
publishDir "${params.output}/${params.lineagedir}/${name}/", mode: 'copy', pattern: "${name}.coverage_mask.txt"
publishDir "${params.output}/${params.lineagedir}/${name}/", mode: 'copy', pattern: "${name}.fail.vcf"

input:
tuple val(name), path(reads), path(external_scheme), path(primerBed)
Expand All @@ -69,6 +82,9 @@ process artic_medaka_custom_bed {
tuple val(name), path("SNP_${name}.pass.vcf"), emit: vcf
tuple val(name), path("${name}.pass.vcf.gz"), path("${name}.coverage_mask.txt.*1.depths"), path("${name}.coverage_mask.txt.*2.depths"), emit: covarplot
tuple val(name), path("${name}.trimmed.rg.sorted.bam"), emit: fullbam
tuple val(name), path("${name}.primersitereport.txt"), emit: primersitereport
tuple val(name), path("${name}.coverage_mask.txt"), emit: coverage_mask
tuple val(name), path("${name}.fail.vcf"), emit: vcf_fail
script:
"""
# create a new primer dir as input for artic
Expand Down Expand Up @@ -115,7 +131,10 @@ process artic_medaka_custom_bed {
${name}.pass.vcf.gz \
${name}.coverage_mask.txt.nCoV-2019_1.depths \
${name}.coverage_mask.txt.nCoV-2019_2.depths \
${name}.trimmed.rg.sorted.bam
${name}.trimmed.rg.sorted.bam \
${name}.primersitereport.txt \
${name}.coverage_mask.txt \
${name}.fail.vcf
"""
}

Expand All @@ -126,7 +145,10 @@ process artic_nanopolish {
publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "${name}_mapped_*.primertrimmed.sorted.bam*"
publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "${name}.trimmed.rg.sorted.bam"
publishDir "${params.output}/${params.genomedir}/all_consensus_sequences/", mode: 'copy', pattern: "*.consensus.fasta"
publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "${name}.primersitereport.txt"
publishDir "${params.output}/${params.lineagedir}/${name}/", mode: 'copy', pattern: "SNP_${name}.pass.vcf"
publishDir "${params.output}/${params.lineagedir}/${name}/", mode: 'copy', pattern: "${name}.coverage_mask.txt"
publishDir "${params.output}/${params.lineagedir}/${name}/", mode: 'copy', pattern: "${name}.fail.vcf"

input:
tuple val(name), path(reads), path(external_scheme), path(fast5_dir), path(txt_files)
Expand All @@ -136,6 +158,9 @@ process artic_nanopolish {
tuple val(name), path("SNP_${name}.pass.vcf"), emit: vcf
tuple val(name), path("${name}.pass.vcf.gz"), path("${name}.coverage_mask.txt.*1.depths"), path("${name}.coverage_mask.txt.*2.depths"), emit: covarplot
tuple val(name), path("${name}.trimmed.rg.sorted.bam"), emit: fullbam
tuple val(name), path("${name}.primersitereport.txt"), emit: primersitereport
tuple val(name), path("${name}.coverage_mask.txt"), emit: coverage_mask
tuple val(name), path("${name}.fail.vcf"), emit: vcf_fail
script:
"""
artic minion --minimap2 --normalise 500 \
Expand Down Expand Up @@ -170,7 +195,10 @@ process artic_nanopolish {
${name}.pass.vcf.gz \
${name}.coverage_mask.txt.nCoV-2019_1.depths \
${name}.coverage_mask.txt.nCoV-2019_2.depths \
${name}.trimmed.rg.sorted.bam
${name}.trimmed.rg.sorted.bam \
${name}.primersitereport.txt \
${name}.coverage_mask.txt \
${name}.fail.vcf
"""
}

Expand All @@ -181,7 +209,10 @@ process artic_nanopolish_custom_bed {
publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "${name}_mapped_*.primertrimmed.sorted.bam*"
publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "${name}.trimmed.rg.sorted.bam"
publishDir "${params.output}/${params.genomedir}/all_consensus_sequences/", mode: 'copy', pattern: "*.consensus.fasta"
publishDir "${params.output}/${params.genomedir}/${name}/", mode: 'copy', pattern: "${name}.primersitereport.txt"
publishDir "${params.output}/${params.lineagedir}/${name}/", mode: 'copy', pattern: "SNP_${name}.pass.vcf"
publishDir "${params.output}/${params.lineagedir}/${name}/", mode: 'copy', pattern: "${name}.coverage_mask.txt"
publishDir "${params.output}/${params.lineagedir}/${name}/", mode: 'copy', pattern: "${name}.fail.vcf"

input:
tuple val(name), path(reads), path(external_scheme), path(fast5_dir), path(txt_files), path(primerBed)
Expand All @@ -191,6 +222,9 @@ process artic_nanopolish_custom_bed {
tuple val(name), path("SNP_${name}.pass.vcf"), emit: vcf
tuple val(name), path("${name}.pass.vcf.gz"), path("${name}.coverage_mask.txt.*1.depths"), path("${name}.coverage_mask.txt.*2.depths"), emit: covarplot
tuple val(name), path("${name}.trimmed.rg.sorted.bam"), emit: fullbam
tuple val(name), path("${name}.primersitereport.txt"), emit: primersitereport
tuple val(name), path("${name}.coverage_mask.txt"), emit: coverage_mask
tuple val(name), path("${name}.fail.vcf"), emit: vcf_fail
script:
"""
# create a new primer dir as input for artic
Expand Down Expand Up @@ -236,7 +270,10 @@ process artic_nanopolish_custom_bed {
${name}.pass.vcf.gz \
${name}.coverage_mask.txt.nCoV-2019_1.depths \
${name}.coverage_mask.txt.nCoV-2019_2.depths \
${name}.trimmed.rg.sorted.bam
${name}.trimmed.rg.sorted.bam \
${name}.primersitereport.txt \
${name}.coverage_mask.txt \
${name}.fail.vcf
"""
}

Expand Down

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