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PD-2501 StarSolo on one machine #1194

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PD-2501 StarSolo on one machine #1194

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9014452
Change machine type and number of output files for fastqprocess optimus
aawdeh Feb 2, 2024
fca8f9c
Merge branch 'develop' into aa-starsolo-one
aawdeh Feb 6, 2024
b0ba813
Merge branch 'develop' into aa-starsolo-one
aawdeh Feb 6, 2024
b6eb327
Merge branch 'develop' into aa-starsolo-one
aawdeh Mar 18, 2024
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2 changes: 1 addition & 1 deletion tasks/skylab/FastqProcessing.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -102,7 +102,7 @@ task FastqProcessing {
fi

fastqprocess \
--bam-size 30.0 \
--num-output-files 1 \
--sample-id "~{sample_id}" \
$FASTQS \
--white-list "~{whitelist}" \
Expand Down
86 changes: 27 additions & 59 deletions tasks/skylab/StarAlign.wdl
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Expand Up @@ -227,12 +227,15 @@ task STARsoloFastq {

# runtime values
String docker = "us.gcr.io/broad-gotc-prod/star:1.0.1-2.7.11a-1692706072"
Int machine_mem_mb = 64000
Int cpu = 8

String cpu_platform = "Intel Ice Lake"
Int machine_mem_mb = 512000
Int cpu = 128
Int disk = 2000
# multiply input size by 2.2 to account for output bam file + 20% overhead, add size of reference.
Int disk = ceil((size(tar_star_reference, "Gi") * 3)) + ceil(size(r1_fastq, "Gi") * 20) + ceil(size(r2_fastq, "Gi") * 20)
# Int disk = ceil((size(tar_star_reference, "Gi") * 3)) + ceil(size(r1_fastq, "Gi") * 20) + ceil(size(r2_fastq, "Gi") * 20)
# by default request non preemptible machine to make sure the slow star alignment step completes
Int preemptible = 3
Int preemptible = 1
}

meta {
Expand Down Expand Up @@ -292,7 +295,23 @@ task STARsoloFastq {
## single cell or whole cell
COUNTING_MODE="Gene"
echo "Running in ~{counting_mode} mode. The Star parameter --soloFeatures will be set to $COUNTING_MODE"
STAR \
elif [[ "~{counting_mode}" == "sn_rna" ]]
then
## single nuclei
if [[ ~{count_exons} == false ]]
then
COUNTING_MODE="GeneFull_Ex50pAS"
echo "Running in ~{counting_mode} mode. Count_exons is false and the Star parameter --soloFeatures will be set to $COUNTING_MODE"
else
COUNTING_MODE="GeneFull_Ex50pAS Gene"
echo "Running in ~{counting_mode} mode. Count_exons is true and the Star parameter --soloFeatures will be set to $COUNTING_MODE"
fi
else
echo Error: unknown counting mode: "$counting_mode". Should be either sn_rna or sc_rna.
exit 1;
fi

STAR \
--soloType Droplet \
--soloStrand ~{star_strand_mode} \
--runThreadN ~{cpu} \
Expand All @@ -311,62 +330,10 @@ task STARsoloFastq {
--soloBarcodeReadLength 0 \
--soloCellReadStats Standard \
~{"--soloMultiMappers " + soloMultiMappers}
elif [[ "~{counting_mode}" == "sn_rna" ]]
then
## single nuclei
if [[ ~{count_exons} == false ]]
then
COUNTING_MODE="GeneFull_Ex50pAS"
echo "Running in ~{counting_mode} mode. Count_exons is false and the Star parameter --soloFeatures will be set to $COUNTING_MODE"
STAR \
--soloType Droplet \
--soloStrand ~{star_strand_mode} \
--runThreadN ~{cpu} \
--genomeDir genome_reference \
--readFilesIn "~{sep=',' r2_fastq}" "~{sep=',' r1_fastq}" \
--readFilesCommand "gunzip -c" \
--soloCBwhitelist ~{white_list} \
--soloUMIlen $UMILen --soloCBlen $CBLen \
--soloFeatures $COUNTING_MODE \
--clipAdapterType CellRanger4 \
--outFilterScoreMin 30 \
--soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts \
--soloUMIdedup 1MM_Directional_UMItools \
--outSAMtype BAM SortedByCoordinate \
--outSAMattributes UB UR UY CR CB CY NH GX GN sF \
--soloBarcodeReadLength 0 \
--soloCellReadStats Standard \
~{"--soloMultiMappers " + soloMultiMappers}
else
COUNTING_MODE="GeneFull_Ex50pAS Gene"
echo "Running in ~{counting_mode} mode. Count_exons is true and the Star parameter --soloFeatures will be set to $COUNTING_MODE"
STAR \
--soloType Droplet \
--soloStrand ~{star_strand_mode} \
--runThreadN ~{cpu} \
--genomeDir genome_reference \
--readFilesIn "~{sep=',' r2_fastq}" "~{sep=',' r1_fastq}" \
--readFilesCommand "gunzip -c" \
--soloCBwhitelist ~{white_list} \
--soloUMIlen $UMILen --soloCBlen $CBLen \
--soloFeatures $COUNTING_MODE \
--clipAdapterType CellRanger4 \
--outFilterScoreMin 30 \
--soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts \
--soloUMIdedup 1MM_Directional_UMItools \
--outSAMtype BAM SortedByCoordinate \
--outSAMattributes UB UR UY CR CB CY NH GX GN sF \
--soloBarcodeReadLength 0 \
--soloCellReadStats Standard \
~{"--soloMultiMappers " + soloMultiMappers}
fi
else
echo Error: unknown counting mode: "$counting_mode". Should be either sn_rna or sc_rna.
exit 1;
fi

echo "UMI LEN " $UMILen

# why is this here?
touch barcodes_sn_rna.tsv
touch features_sn_rna.tsv
touch matrix_sn_rna.mtx
Expand Down Expand Up @@ -434,10 +401,11 @@ task STARsoloFastq {
runtime {
docker: docker
memory: "~{machine_mem_mb} MiB"
disks: "local-disk ~{disk} HDD"
disks: "local-disk ~{disk} SSD"
disk: disk + " GB" # TES
cpu: cpu
preemptible: preemptible
cpuPlatform: cpu_platform
}

output {
Expand Down
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