From d6cee4a5efd65eff8a19e502720f1bc9e3f548d9 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 13 Jan 2020 19:03:19 -0600
Subject: [PATCH] Cleanup .nf
---
workflow/rna-seq.nf | 46 +-----------------------------------
workflow/scripts/splitBag.sh | 7 ------
2 files changed, 1 insertion(+), 52 deletions(-)
delete mode 100644 workflow/scripts/splitBag.sh
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 0a43a13..454f6e7 100755
--- a/workflow/rna-seq.nf
+++ b/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
*/
diff --git a/workflow/scripts/splitBag.sh b/workflow/scripts/splitBag.sh
deleted file mode 100644
index 3f6f6cd..0000000
--- a/workflow/scripts/splitBag.sh
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/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
--
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