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Commit 1fd6d350 authored by Jeremy Mathews's avatar Jeremy Mathews
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Fix countDesign

parent 6dda9f06
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2 merge requests!45Develop,!44Resolve "Fix CountDesign"
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# v1.3.0 (in development) # v1.3.0 (in development)
**User Facing** **User Facing**
* Change Cellranger Version to 3.1.0 * Change Cellranger Version to 3.1.0
* Fix countDesign to take multiple samples
**Background** **Background**
* Add CI artifacts * Add CI artifacts
......
#!/bin/bash #!/bin/bash
#countDesign.sh #countDesign.sh
fastqs=$(ls *.fastq.gz) fastqs=($(ls *.fastq.gz))
design=$(ls *.csv) design=$(ls *.csv)
sample=$(cat ${design} | tail -n +2 | cut -d ',' -f2) sample=$(cat ${design} | tail -n +2 | cut -d ',' -f2)
for i in ${fastqs}; echo "Sample,fastq_R1,fastq_R2" > Cellranger_Count_Design.csv;
for i in ${sample};
do do
if [[ ${i} == *_S0_* ]]; then for j in $(seq 1 ${#fastqs[@]});
continue do
elif [[ ${i} == *_I* ]]; then if [[ ${fastqs[${j}-1]} == *_I* ]]; then
continue continue
else elif [[ ${fastqs[${j}-1]} == *${i}* && ${fastqs[${j}]} == *${i}* ]]; then
good=(${good[@]} ${i}) echo "${i},${fastqs[${j}-1]},${fastqs[${j}]}" >> Cellranger_Count_Design.csv
fi fi
done
done done
echo "Sample,fastq_R1,fastq_R2" > Cellranger_Count_Design.csv;
echo "${sample},${good[0]},${good[1]}" >> Cellranger_Count_Design.csv;
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