From cf982549d74b620f8d7d416b7610088227ad95e0 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 24 Dec 2018 09:22:13 -0600
Subject: [PATCH] Added in test data for comparisions.
---
.gitlab-ci.yml | 18 ++++++++++++++++--
test_data/design_diff_PE.txt | 7 +++++++
test_data/design_diff_SE.txt | 9 +++++++++
test_data/fetch_test_data.sh | 10 ++++++++++
workflow/main.nf | 4 ++--
5 files changed, 44 insertions(+), 4 deletions(-)
create mode 100644 test_data/design_diff_PE.txt
create mode 100644 test_data/design_diff_SE.txt
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 15ec0bd..cc3b607 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -2,7 +2,7 @@ before_script:
- module add python/3.6.1-2-anaconda
- pip install --user pytest-pythonpath pytest-cov
- module load nextflow/0.31.0
- - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/chipseq/*fastq.gz test_data/
+ - ln -s /work/BICF/s163035/chipseq/*fastq.gz test_data/
stages:
- unit
@@ -25,6 +25,20 @@ single_end_mouse:
paired_end_human:
stage: integration
script:
- - nextflow run workflow/main.nf --designFile "/work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true -resume
+ - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true
+ artifacts:
+ expire_in: 2 days
+
+single_end_diff:
+ stage: integration
+ script:
+ - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38'
+ artifacts:
+ expire_in: 2 days
+
+paired_end_diff:
+ stage: integration
+ script:
+ - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true
artifacts:
expire_in: 2 days
diff --git a/test_data/design_diff_PE.txt b/test_data/design_diff_PE.txt
new file mode 100644
index 0000000..7b6f73c
--- /dev/null
+++ b/test_data/design_diff_PE.txt
@@ -0,0 +1,7 @@
+sample_id experiment_id biosample factor treatment replicate control_id fastq_read1 fastq_read2
+ENCLB637LZP ENCSR729LGA MCF-7 SP1 None 1 ENCLB678IDC ENCFF957SQS.fastq.gz ENCFF582IOZ.fastq.gz
+ENCLB568IYX ENCSR729LGA MCF-7 SP1 None 2 ENCLB336TVW ENCFF330MCZ.fastq.gz ENCFF293YFE.fastq.gz
+ENCLB678IDC ENCSR217LRF MCF-7 Control None 1 ENCLB678IDC ENCFF002DTU.fastq.gz ENCFF002EFI.fastq.gz
+ENCLB336TVW ENCSR217LRF MCF-7 Control None 2 ENCLB336TVW ENCFF002EFG.fastq.gz ENCFF002DTS.fastq.gz
+ENCLB552ACZ ENCSR757EMK MCF-7 SUZ12 None 1 ENCLB678IDC ENCFF833EZX.fastq.gz ENCFF161HBP.fastq.gz
+ENCLB568IYX ENCSR757EMK MCF-7 SUZ12 None 2 ENCLB336TVW ENCFF776KZU.fastq.gz ENCFF119KHM.fastq.gz
diff --git a/test_data/design_diff_SE.txt b/test_data/design_diff_SE.txt
new file mode 100644
index 0000000..b5aac58
--- /dev/null
+++ b/test_data/design_diff_SE.txt
@@ -0,0 +1,9 @@
+sample_id experiment_id biosample factor treatment replicate control_id fastq_read1
+ENCLB144FDT ENCSR238SGC limb H3K4me1 None 1 ENCLB304SBJ ENCFF833BLU.fastq.gz
+ENCLB831RUI ENCSR238SGC limb H3K4me1 None 2 ENCLB410VVO ENCFF646LXU.fastq.gz
+ENCLB304SBJ ENCSR687ALB limb Control None 1 ENCLB304SBJ ENCFF524CAC.fastq.gz
+ENCLB410VVO ENCSR687ALB limb Control None 2 ENCLB410VVO ENCFF163AJI.fastq.gz
+ENCLB140BPV ENCSR272GNQ midbrain H3K4me1 None 1 ENCLB841FLB ENCFF278VQW.fastq.gz
+ENCLB785CNN ENCSR272GNQ midbrain H3K4me1 None 2 ENCLB735ZEL ENCFF466CFM.fastq.gz
+ENCLB841FLB ENCSR842LMA midbrain Control None 1 ENCLB841FLB ENCFF914QXH.fastq.gz
+ENCLB735ZEL ENCSR842LMA midbrain Control None 2 ENCLB735ZEL ENCFF942UQV.fastq.gz
diff --git a/test_data/fetch_test_data.sh b/test_data/fetch_test_data.sh
index a6107cd..8b9a331 100644
--- a/test_data/fetch_test_data.sh
+++ b/test_data/fetch_test_data.sh
@@ -3,6 +3,11 @@ wget https://www.encodeproject.org/files/ENCFF833BLU/@@download/ENCFF833BLU.fast
wget https://www.encodeproject.org/files/ENCFF646LXU/@@download/ENCFF646LXU.fastq.gz
wget https://www.encodeproject.org/files/ENCFF524CAC/@@download/ENCFF524CAC.fastq.gz
wget https://www.encodeproject.org/files/ENCFF163AJI/@@download/ENCFF163AJI.fastq.gz
+echo "Downloading Single-end data set Mouse ENCSR272GNQ and ENCSR842LMA"
+wget https://www.encodeproject.org/files/ENCFF278VQW/@@download/ENCFF278VQW.fastq.gz
+wget https://www.encodeproject.org/files/ENCFF466CFM/@@download/ENCFF466CFM.fastq.gz
+wget https://www.encodeproject.org/files/ENCFF914QXH/@@download/ENCFF914QXH.fastq.gz
+wget https://www.encodeproject.org/files/ENCFF942UQV/@@download/ENCFF942UQV.fastq.gz
echo "Done with Single-end"
echo "Downloading Paired-end data set Human ENCSR729LGA and ENCSR217LRF"
@@ -14,4 +19,9 @@ wget https://www.encodeproject.org/files/ENCFF002DTU/@@download/ENCFF002DTU.fast
wget https://www.encodeproject.org/files/ENCFF002EFI/@@download/ENCFF002EFI.fastq.gz
wget https://www.encodeproject.org/files/ENCFF002EFG/@@download/ENCFF002EFG.fastq.gz
wget https://www.encodeproject.org/files/ENCFF002DTS/@@download/ENCFF002DTS.fastq.gz
+echo "Downloading Paired-end data set Human ENCSR757EMK"
+wget https://www.encodeproject.org/files/ENCFF833EZX/@@download/ENCFF833EZX.fastq.gz
+wget https://www.encodeproject.org/files/ENCFF161HBP/@@download/ENCFF161HBP.fastq.gz
+wget https://www.encodeproject.org/files/ENCFF776KZU/@@download/ENCFF776KZU.fastq.gz
+wget https://www.encodeproject.org/files/ENCFF119KHM/@@download/ENCFF119KHM.fastq.gz
echo "Done with Paired-end"
diff --git a/workflow/main.nf b/workflow/main.nf
index 2905ed0..2dbf708 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -384,7 +384,7 @@ process consensusPeaks {
}
// Define channel to find number of unique experiments
-uniqueExperiments.splitCsv(sep: '\t', header: true).toList().map{ it.size().toInteger() }.set { noUniqueExperiments }
+noUniqueExperiments = uniqueExperiments.splitCsv(sep: '\t', header: true).toList()
// Annotate Peaks
process peakAnnotation {
@@ -426,7 +426,7 @@ process diffPeaks {
file 'normcount_peaksets.txt' into normCountPeaks
script:
- if (noUniqueExperiments <= 1) {
+ if (noUniqueExperiments.size() == 1) {
"""
touch design_diffpeak_annotatePeaks.tsv
touch no_diffbind.bed
--
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