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update ncbi-scrub task (version 2.2.1) #202

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update ncbi-scrub task (version 2.2.1) #202

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0adf7f1
update ncbi/scrub task (version 2.2.1)
cimendes Oct 2, 2023
903b045
Merge branch 'main' into im-ncbi-scrub-update
cimendes Oct 11, 2023
9c15fc3
fixed ncbi scrub pe wf outputs to match task changes (#231)
frankambrosio3 Nov 7, 2023
9977656
Merge branch 'main' into im-ncbi-scrub-update
Dec 6, 2023
ca0f002
HOSTILE: For TheiaCoV_Illumina_PE_PHB and TheiaCoV_ONT_PHB (#256)
jrotieno Dec 11, 2023
9e8241d
adding option for dehosting tool to theiaprok
jrotieno Dec 11, 2023
33cdb03
adding seq_method to theiaprok call for qc_trim
jrotieno Dec 11, 2023
e4cf608
force sting output
cimendes Dec 22, 2023
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45 changes: 11 additions & 34 deletions tasks/quality_control/task_ncbi_scrub.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -5,51 +5,29 @@ task ncbi_scrub_pe {
File read1
File read2
String samplename
String docker = "us-docker.pkg.dev/general-theiagen/ncbi/sra-human-scrubber:1.0.2021-05-05"
String docker = "us-docker.pkg.dev/general-theiagen/ncbi/sra-human-scrubber:2.2.1"
Int disk_size = 100
}
String r1_filename = basename(read1)
String r2_filename = basename(read2)
command <<<
# date and version control
date | tee DATE

# unzip fwd file as scrub tool does not take in .gz fastq files
if [[ "~{read1}" == *.gz ]]
then
gunzip -c ~{read1} > r1.fastq
read1_unzip=r1.fastq
else
read1_unzip=~{read1}
fi

# dehost reads
/opt/scrubber/scripts/scrub.sh -n ${read1_unzip} |& tail -n1 | awk -F" " '{print $1}' > FWD_SPOTS_REMOVED

# gzip dehosted reads
gzip ${read1_unzip}.clean -c > ~{samplename}_R1_dehosted.fastq.gz

# do the same on read
# unzip file if necessary
if [[ "~{read2}" == *.gz ]]
then
gunzip -c ~{read2} > r2.fastq
read2_unzip=r2.fastq
else
read2_unzip=~{read2}
fi
# unzip read files as scrub tool does not take in .gz fastq files, and interleave them
paste <(zcat ~{read1} | paste - - - -) <(zcat ~{read2} | paste - - - -) | tr '\t' '\n' > interleaved.fastq
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Will this work if there are uneven reads in ~{read1} and ~{read2}?


# dehost reads
/opt/scrubber/scripts/scrub.sh -n ${read2_unzip} |& tail -n1 | awk -F" " '{print $1}' > REV_SPOTS_REMOVED
/opt/scrubber/scripts/scrub.sh -i interleaved.fastq |& tail -n1 | awk -F" " '{print $1}' > SPOTS_REMOVED

# gzip dehosted reads
gzip ${read2_unzip}.clean -c > ~{samplename}_R2_dehosted.fastq.gz
# split interleaved reads and compress files
paste - - - - - - - - < interleaved.fastq.clean \
| tee >(cut -f 1-4 | tr '\t' '\n' | gzip > ~{samplename}_R1_dehosted.fastq.gz) \
| cut -f 5-8 | tr '\t' '\n' | gzip > ~{samplename}_R2_dehosted.fastq.gz

>>>
output {
File read1_dehosted = "~{samplename}_R1_dehosted.fastq.gz"
File read2_dehosted = "~{samplename}_R2_dehosted.fastq.gz"
Int read1_human_spots_removed = read_int("FWD_SPOTS_REMOVED")
Int read2_human_spots_removed = read_int("REV_SPOTS_REMOVED")
Int human_spots_removed = read_int("SPOTS_REMOVED")
String ncbi_scrub_docker = docker
}
runtime {
Expand All @@ -67,10 +45,9 @@ task ncbi_scrub_se {
input {
File read1
String samplename
String docker = "us-docker.pkg.dev/general-theiagen/ncbi/sra-human-scrubber:1.0.2021-05-05"
String docker = "us-docker.pkg.dev/general-theiagen/ncbi/sra-human-scrubber:2.2.1"
Int disk_size = 100
}
String r1_filename = basename(read1)
command <<<
# date and version control
date | tee DATE
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3 changes: 1 addition & 2 deletions workflows/utilities/wf_read_QC_trim_pe.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -118,8 +118,7 @@ workflow read_QC_trim_pe {
# NCBI scrubber
File? read1_dehosted = ncbi_scrub_pe.read1_dehosted
File? read2_dehosted = ncbi_scrub_pe.read2_dehosted
Int? read1_human_spots_removed = ncbi_scrub_pe.read1_human_spots_removed
Int? read2_human_spots_removed = ncbi_scrub_pe.read2_human_spots_removed
Int? ncbi_scrub_human_spots_removed = ncbi_scrub_pe.human_spots_removed
String? ncbi_scrub_docker = ncbi_scrub_pe.ncbi_scrub_docker

# bbduk
Expand Down