113 lines
3.4 KiB
Bash
113 lines
3.4 KiB
Bash
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#!/bin/bash
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set -eo pipefail
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# get the root of the directory
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REPO_ROOT=$(git rev-parse --show-toplevel)
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# ensure that the command below is run from the root of the repository
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cd "$REPO_ROOT"
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# settings
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ID=cellranger_tiny_bcl
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OUT="resources_test/$ID/"
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DIR="$OUT"
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# create tempdir
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MY_TEMP="${VIASH_TEMP:-/tmp}"
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TMPDIR=$(mktemp -d "$MY_TEMP/$ID-XXXXXX")
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function clean_up {
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[[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
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}
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trap clean_up EXIT
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# download bcl data
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if [ ! -f "${OUT}/bcl/sample_sheet.csv" ]; then
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mkdir -p "$OUT/bcl"
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# download tar gz
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target/docker/download/download_file/download_file \
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--input https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-1.2.0.tar.gz \
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--output "${OUT}/bcl/cellranger-tiny-bcl-1.2.0.tar.gz"
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# untar
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tar -xf "${OUT}/bcl/cellranger-tiny-bcl-1.2.0.tar.gz" \
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--strip-components=1 \
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-C "$OUT/bcl"
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# remove tar
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rm "${OUT}/bcl/cellranger-tiny-bcl-1.2.0.tar.gz"
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# download sample sheet
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target/docker/download/download_file/download_file \
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--input https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-simple-1.2.0.csv \
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--output "${OUT}/bcl/sample_sheet.csv"
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fi
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if [ ! -d "${OUT}/fastqs" ]; then
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mkdir -p "$OUT/fastqs"
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target/docker/demux/cellranger_mkfastq/cellranger_mkfastq \
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--input "${OUT}/bcl" \
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--sample_sheet "${OUT}/bcl/sample_sheet.csv" \
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--output "${OUT}/fastqs"
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fi
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# bcl-convert requires a v2 sample sheet
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# bcl-convert is a bit more strict concerning filter files being present or not.
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# We make a copy and make the necessary adaptations.
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# We are using the tiny bcl dataset provided by Illumina:
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# https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq
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# Unfortunately,
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# 1. the sample sheet delivered with it does not work with bcl-convert (v1 of the format)
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# 2. 2 filter files are missing from the run directory that bcl-convert requires to run
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#
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# We worked around this by
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# 1. Manually editing a sample sheet file suited for bcl-convert (format v2)
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# 2. Adding a filter file
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#
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# The filter file is a binary file, we just created an empty file use that.
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# bcl-convert might complain about it, but at least something is written out.
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# An alternative is to use a filter file from a different project. This also generates
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# a warning, but the fastq ouput files contain reads. The drawback is that those filter files
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# are generally above 100MB in size.
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#
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# TODO: Check if a (binary) filter file can be generated that is small but works.
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if [ ! -f "${OUT}/bcl2/sample_sheet.csv" ]; then
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mkdir "${OUT}/bcl2/"
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cp -r ${OUT}/bcl/* "${OUT}/bcl2/"
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cat > "${OUT}/bcl2/sample_sheet.csv" << HERE
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[Header],,,,,,,,,
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FileFormatVersion,2,,,,,,
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RunName,hiseq_test,,,,,,
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InstrumentPlatform,NextSeq,,,,,,
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IndexOrientation,Forward,,,,,,
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,,,,,,,,,
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[Reads],,,,,,,,,
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Read1Cycles,26,,,,,,,,,
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Read2Cycles,98,,,,,,
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,,,,,,,,,
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[Sequencing_Settings],,,,,,,
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,,,,,,,
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[BCLConvert_Settings],,,,,,,
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SoftwareVersion,3.8.4,,,,,,
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NoLaneSplitting,true,,,,,,
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FastqCompressionFormat,gzip,,,,,,
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,,,,,,,,,
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[BCLConvert_Data],,,,,,,
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Sample_ID,index,,,,,,
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s1,GGTTTACT,,,,,,
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,,,,,,,
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[Cloud_Settings],,,,,,,
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GeneratedVersion,1.3.0.202111171923,,,,,,
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,,,,,,,
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[Cloud_Data],,,,,,,
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Sample_ID,ProjectName,LibraryName,LibraryPrepKitName,IndexAdapterKitName,I7_Index_ID,Sample_Name,Description,Instrument,Type
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s1,p1,s1_SI-P03-C9,,,IDT01,SI-P03-C9,s1,NextSeq,HighOutput_75cycles
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HERE
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touch "${OUT}/bcl2/Data/Intensities/BaseCalls/L001/s_1_1101.filter"
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fi
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