Cleanup .nf

workflow/rna-seq.nf

@@ -5,7 +5,6 @@ params.deriva = "${baseDir}/../test_data/credential.json"
 params.bdbag = "${baseDir}/../test_data/cookies.txt"
 //params.repRID = "16-1ZX4"
 params.repRID = "Q-Y5JA"
-//params.bdbag = "${baseDir}/../test_data/Study_Q-Y4H0.zip"
 
 params.outDir = "${baseDir}/../output"
 
@@ -16,9 +15,6 @@ deriva = Channel
 bdbag = Channel
   .fromPath(params.bdbag)
   .ifEmpty { exit 1, "deriva cookie file for bdbag not found: ${params.bdbag}" }
-//bdbag = Channel
-//  .fromPath(params.bdbag)
-//  .ifEmpty { exit 1, "bdbag zip file not found: ${params.bdbag}" }
 
 Channel.from(params.repRID)
   .into {
@@ -30,49 +26,9 @@ Channel.from(params.repRID)
 outDir = params.outDir
 logsDir = "${outDir}/Logs"
 
+// Define fixed files
 derivaConfig = Channel.fromPath("${baseDir}/conf/replicate_export_config.json")
 
-/*
- * splitData: split bdbag files by replicate so fetch can occure in parallel, and rename files to replicate rid
- */
- /*
-process splitData {
-  tag "${bdbag.baseName}"
-  executor 'local'
-  publishDir "${logsDir}/splitData", mode: 'symlink', pattern: "${bdbag.baseName}.splitData.err"
-
-  input:
-    file bdbag
-    path cookies, stageAs: 'cookies.txt' from deriva
-
-  output:
-    file("Replicate_*.zip") into bdbagSplit mode flatten
-    file("${bdbag.baseName}/data/File.csv") into fileMeta
-    file("${bdbag.baseName}/data/Experiment Settings.csv") into experimentSettingsMeta
-    file("${bdbag.baseName}/data/Experiment.csv") into experimentMeta
-    file ("${bdbag.baseName}.splitData.err")
-
-  script:
-    """
-    hostname >> ${bdbag.baseName}.splitData.err
-    ulimit -a >> ${bdbag.baseName}.splitData.err
-    ln -sf `readlink -e cookies.txt` ~/.bdbag/deriva-cookies.txt 2>>${bdbag.baseName}.splitData.err
-    echo "LOG: deriva cookie linked" >> ${bdbag.baseName}.splitData.err 
-    study=`echo "${bdbag}" | cut -d '.' -f1` 2>>${bdbag.baseName}.splitData.err
-    echo "LOG: \${study}" >> ${bdbag.baseName}.splitData.err
-    unzip ${bdbag} 2>>${bdbag.baseName}.splitData.err
-    echo "LOG: bdgag unzipped" >> ${bdbag.baseName}.splitData.err
-    python3 ${baseDir}/scripts/modifyFetch.py --fetchFile \${study} 2>>${bdbag.baseName}.splitData.err
-    echo "LOG: fetch file filtered for only .fastq.gz" >> ${bdbag.baseName}.splitData.err
-    python3 ${baseDir}/scripts/splitFetch.py --fetchFile \${study} 2>>${bdbag.baseName}.splitData.err
-    echo "LOG: fetch file split by replicates" >> ${bdbag.baseName}.splitData.err
-    sh ${baseDir}/scripts/splitBag.sh \${study} 2>>${bdbag.baseName}.splitData.err
-    echo "LOG: bag recreated with replicate split fetch file" >> ${bdbag.baseName}.splitData.err
-    """
-}
-*/
-
-
 /*
  * getData: get bagit file from consortium
  */

workflow/scripts/splitBag.sh

-#!/bin
-
-for i in $(ls -d Replicate_*)
-do
-rsync -r $1/ ${i} --exclude=fetch.txt
-zip -r ${i}.zip ${i}
-done
\ No newline at end of file