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renamed accession parameter
1 parent da5d9db commit b03f9ad

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  • Metagenomics/Illumina/Workflow_Documentation/NF_MGIllumina-A/workflow_code/modules

1 file changed

+9
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Metagenomics/Illumina/Workflow_Documentation/NF_MGIllumina-A/workflow_code/modules/create_runsheet.nf

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -1,15 +1,15 @@
11
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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4-
//params.GLDS_accession = "OSD-574"
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//params.accession = "OSD-574"
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//params.RawFilePattern = null // Pattern of files on OSDR for the OSD accession you want to process
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process GET_RUNSHEET {
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beforeScript "chmod +x ${baseDir}/bin/create_runsheet.sh"
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input:
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val(GLDS_accession)
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val(accession)
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output:
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path("a_*metagenomic*.txt"), emit: assay_TABLE
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path("*.zip"), emit: zip
@@ -18,19 +18,19 @@ process GET_RUNSHEET {
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script:
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"""
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# Download ISA zip file for the GLDS_accession then unzip it
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GL-download-GLDS-data -g ${GLDS_accession} -p ISA -f && unzip *-ISA.zip
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GL-download-GLDS-data -g ${accession} -p ISA -f && unzip *-ISA.zip
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if [ ${params.RawFilePattern} == null ];then
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# Attempt to download the sequences using the assay table, if that fails then
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# attempt retrieving all fastq.gz files
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GL-download-GLDS-data -f -g ${GLDS_accession} -a a_*metagenomic*.txt -o Raw_Sequence_Data || \\
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GL-download-GLDS-data -f -g ${GLDS_accession} -p ".fastq.gz" -o Raw_Sequence_Data
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GL-download-GLDS-data -f -g ${accession} -a a_*metagenomic*.txt -o Raw_Sequence_Data || \\
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GL-download-GLDS-data -f -g ${accession} -p ".fastq.gz" -o Raw_Sequence_Data
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else
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GL-download-GLDS-data -f -g ${GLDS_accession} -p ${params.RawFilePattern} -o Raw_Sequence_Data
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GL-download-GLDS-data -f -g ${accession} -p ${params.RawFilePattern} -o Raw_Sequence_Data
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fi
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@@ -39,8 +39,8 @@ process GET_RUNSHEET {
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grep '+' *wanted-file-download-commands.sh | \\
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sort -u | \\
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awk '{gsub(/\\+/,"%2B", \$NF);print}' \\
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> plus_containing_${GLDS_accession}-wanted-file-download-commands.sh
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cat plus_containing_${GLDS_accession}-wanted-file-download-commands.sh | parallel -j $task.cpus
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> plus_containing_${accession}-wanted-file-download-commands.sh
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cat plus_containing_${accession}-wanted-file-download-commands.sh | parallel -j $task.cpus
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fi
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# Create runsheet from the assay table
@@ -52,7 +52,7 @@ process GET_RUNSHEET {
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workflow {
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GET_RUNSHEET(params.GLDS_accession)
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GET_RUNSHEET(params.accession)
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file_ch = GET_RUNSHEET.out.input_file
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.splitCsv(header:true)
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