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Sample info #17

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7a7cf77
Update README.md
capuccino26 Jan 17, 2024
236bc5f
Update sampleinfo.sh
capuccino26 Jan 17, 2024
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2 changes: 2 additions & 0 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,8 @@ Contact information:
* Nextflow version 23.10.0 build 5889
* ffq v0.3
* Trimmomatic v0.39
* jq v1.7.1
* [edirect](https://www.ncbi.nlm.nih.gov/books/NBK25501/)


### Pipeline execution
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9 changes: 5 additions & 4 deletions nextflow/bin/sampleinfo.sh
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Expand Up @@ -4,22 +4,23 @@

# Creating the file variable from outside the script (from nextflow pipeline or command line flag)
filejs=${1}
jqpth=`which jq`

# Creating variable with BioSample value
bspl=`jq '.[].sample' "$filejs"`; echo BioSample: "${bspl//\"/}"
bspl=`$jqpth '.[].sample' "$filejs"`; echo BioSample: "${bspl//\"/}"

# Creating variable with Accession number
filnm=`jq '.[].accession' "$filejs"`; echo Acession: "${filnm//\"/}"
filnm=`$jqpth '.[].accession' "$filejs"`; echo Acession: "${filnm//\"/}"

# Gathering .json metadata information from Entrez Utilities into variable
smr=`esearch -db biosample -query $bspl | esummary -mode json`

# Parsing attributes information from metadata into variables
## Sample Name
splnm=`echo "$smr" | jq '.. | select(.title?).title'`
splnm=`echo "$smr" | $jqpth '.. | select(.title?).title'`
splnm=${splnm^^}
## Sample Data including all attributes from file
attb=`jq '.. | select(.sampledata?).sampledata' <<< "$smr"`
attb=`$jqpth '.. | select(.sampledata?).sampledata' <<< "$smr"`
attb=${attb##*<Attributes>}
attb=${attb%</Attributes>*}
## Listing each attribute
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