CI
cd0af18851
Build pipeline: vsh-ci-dev-k8tz4
Source commit: 2dbe3b7231
Source message: Fix pointers to test resources
135 lines
4.5 KiB
Bash
Executable File
135 lines
4.5 KiB
Bash
Executable File
#!/bin/bash
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set -eo pipefail
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# ensure that the command below is run from the root of the repository
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REPO_ROOT=$(git rev-parse --show-toplevel)
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cd "$REPO_ROOT"
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# settings
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ID=10x_5k_lung_crispr
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OUT="resources_test/$ID"
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# create raw directory
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raw_dir="$OUT/raw"
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mkdir -p "$raw_dir"
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# Check whether seqkit is available
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if ! command -v seqkit &> /dev/null; then
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echo "This script requires seqkit. Please make sure the binary is added to your PATH."
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exit 1
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fi
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# check whether reference is available
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reference_dir="resources_test/reference_gencodev41_chr1/"
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genome_tar="$reference_dir/reference_cellranger.tar.gz"
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if [[ ! -f "$genome_tar" ]]; then
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echo "$genome_tar does not exist. Please create the reference genome first"
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exit 1
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fi
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# dataset page:
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# https://www.10xgenomics.com/resources/datasets/5-k-a-549-lung-carcinoma-cells-no-treatment-transduced-with-a-crispr-pool-3-1-standard-6-0-0
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# download and untar source fastq files
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tar_dir="$HOME/.cache/openpipeline/SC3_v3_NextGem_DI_CRISPR_A549_5K_Multiplex"
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if [[ ! -d "$tar_dir" ]]; then
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mkdir -p "$tar_dir"
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# download fastqs and untar
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wget "https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-exp/6.0.0/SC3_v3_NextGem_DI_CRISPR_A549_5K_Multiplex/SC3_v3_NextGem_DI_CRISPR_A549_5K_Multiplex_fastqs.tar" -O "$tar_dir.tar"
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tar -xvf "$tar_dir.tar" -C "$tar_dir" --strip-components=1
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rm "$tar_dir.tar"
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fi
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function seqkit_head {
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input="$1"
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output="$2"
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if [[ ! -f "$output" ]]; then
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echo "> Processing `basename $input`"
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seqkit head -n 200000 "$input" | gzip > "$output"
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fi
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}
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orig_sample_id="SC3_v3_NextGem_DI_CRISPR_A549_5K"
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seqkit_head "$tar_dir/${orig_sample_id}_gex/${orig_sample_id}_gex_S5_L001_R1_001.fastq.gz" "$raw_dir/${orig_sample_id}_gex_subset_S5_L001_R1_001.fastq.gz"
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seqkit_head "$tar_dir/${orig_sample_id}_gex/${orig_sample_id}_gex_S5_L001_R2_001.fastq.gz" "$raw_dir/${orig_sample_id}_gex_subset_S5_L001_R2_001.fastq.gz"
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seqkit_head "$tar_dir/${orig_sample_id}_crispr/${orig_sample_id}_crispr_S4_L001_R1_001.fastq.gz" "$raw_dir/${orig_sample_id}_crispr_subset_S4_L001_R1_001.fastq.gz"
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seqkit_head "$tar_dir/${orig_sample_id}_crispr/${orig_sample_id}_crispr_S4_L001_R2_001.fastq.gz" "$raw_dir/${orig_sample_id}_crispr_subset_S4_L001_R2_001.fastq.gz"
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# download crispr feature reference
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crispr_ref="$raw_dir/SC3_v3_NextGem_DI_CRISPR_A549_5K_Multiplex_count_feature_reference.csv"
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if [[ ! -f "$crisp_ref" ]]; then
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wget "https://cf.10xgenomics.com/samples/cell-exp/6.0.0/SC3_v3_NextGem_DI_CRISPR_A549_5K_Multiplex/SC3_v3_NextGem_DI_CRISPR_A549_5K_Multiplex_count_feature_reference.csv" -O "$crispr_ref"
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fi
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crispr_ref_adjusted="$raw_dir/SC3_v3_NextGem_DI_CRISPR_A549_5K_Multiplex_count_feature_reference_corrected.csv"
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reference_gtf="resources_test/reference_gencodev41_chr1/reference.gtf.gz"
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cat "$crispr_ref" | while read line || [[ -n $line ]];
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do
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echo "Line: $line"
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old_id=$( printf "%s\n" "$line" | awk -F',' '{print $7}' )
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echo "Old ID: $old_id"
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if [ "$old_id" = "Non-Targeting" ] || [ "$old_id" = "target_gene_id" ] ; then
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echo "Just writing line"
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printf "%s\n" "$line" >> "$crispr_ref_adjusted"
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else
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gtf_lookup=$(zgrep "$old_id" "$reference_gtf" || test $? = 1;)
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if [ ! -z "$gtf_lookup" ]; then
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echo "Found hit"
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new_id=$(echo "$gtf_lookup" | awk '{if ($3 == "gene") print $10;}' | sed -e "s/^\"//" -e "s/\";$//")
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echo "New ID: $new_id"
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new_line=${line/"$old_id"/"$new_id"}
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printf "%s\n" "$new_line" >> "$crispr_ref_adjusted"
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else
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echo "Did not find hit"
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fi
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fi
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done
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# Run mapping pipeline
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# TODO: Also include conversion to h5mu
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cat > /tmp/params.yaml << HERE
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param_list:
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- id: "$ID"
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input: "$raw_dir"
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library_id:
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- "${orig_sample_id}_gex_subset"
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- "${orig_sample_id}_crispr_subset"
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library_type:
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- "Gene Expression"
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- "CRISPR Guide Capture"
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gex_reference: "$genome_tar"
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feature_reference: "$crispr_ref_adjusted"
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publish_dir: "$OUT/processed"
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HERE
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nextflow \
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run . \
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-main-script target/nextflow/mapping/cellranger_multi/main.nf \
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-resume \
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-profile docker,mount_temp \
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-params-file /tmp/params.yaml \
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-c src/workflows/utils/labels.config
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# Create h5mu
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cat > /tmp/params.yaml << HERE
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id: "$ID"
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input: "$OUT/processed/10x_5k_lung_crispr.cellranger_multi.output"
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publish_dir: "$OUT/"
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output: "$orig_sample_id.h5mu"
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HERE
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nextflow \
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run . \
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-main-script target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf \
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-resume \
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-profile docker,mount_temp \
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-params-file /tmp/params.yaml \
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-c src/workflows/utils/labels.config
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