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STOmics / SAW

GNU General Public License v3.0
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Script requires `bash` #89

Closed gringer closed 1 month ago

gringer commented 5 months ago

The script references sh in its usage, but it uses bash-specific features:

https://github.com/STOmics/SAW/blob/411bab897e0d4642715f1f7b60780b545fb21d12/Scripts/stereoPipeline_v7.0.sh#L4C1-L5C23

$ sh stereoPipeline_v7.0.sh 
stereoPipeline_v7.0.sh: 4: [[: not found
stereoPipeline_v7.0.sh: 25: [[: not found
Tue Jan 30 16:56:43 NZDT 2024  singularity check: pass, and singularity path is /usr/bin/singularity
stereoPipeline_v7.0.sh: 75: [[: not found
Tue Jan 30 16:56:43 NZDT 2024  singularity image file check: file does not exist, please double check your SIF file is in the current directory or the path given by the option -s is valid.
stereoPipeline_v7.0.sh: 83: [[: not found
basename: missing operand
Try 'basename --help' for more information.
$ bash stereoPipeline_v7.0.sh 
usage: sh stereoPipeline_v7.0.sh -splitCount -maskFile -fq1 -fq2 -refIndex -genomeFile -speciesName -tissueType -annotationFile -outDir -imageRecordFile -imageCompressedFile -doCellBin -rRNARemove -threads -sif
    -splitCount : count of splited stereochip mask file, usually 16 for SE+Q4 fq data and 1 for PE+Q40 fq data
    -maskFile : stereochip mask file
    -fq1 : fastq file path of read1, if there are more than one fastq file, please separate them with comma, e.g:lane1_read_1.fq.gz,lane2_read_1.fq.gz
    -fq2 : fastq file path of read2, if there are more than one fastq file, please separate them with comma, not requested for 'Q4' fastq data, e.g:lane1_read_2.fq.gz,lane2_read_2.fq.gz
    -refIndex : reference genome indexed folder, please build index before SAW analysis run
    -speciesName : specie of the sample
    -tissueType : tissue type of the sample
    -annotationFile :  annotations file in gff or gtf format, the file must contain gene and exon annotations
    -outDir : output directory path
    -imageRecordFile : image file(*.ipr) generated by ImageQC/ImageStudio software, not requested
    -imageCompressedFile : image file(*.tar.gz) generated by ImageQC/ImageStudio software, not requested  
    -doCellBin : [Y/N]
    -rRNAremove : [Y/N]
    -threads : the number of threads to be used in running the pipeline
    -sif : the file format of the visual software
TheSallyGardens commented 5 months ago

Thank you for your suggestion. We will update it in the future.