From 2b746c8c8f75b1455929d3c37ce02b1891f3c023 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 8 Mar 2021 20:30:30 -0600
Subject: [PATCH] Fix xsmall fastqs
---
.gitlab-ci.yml | 2 +-
test_data/createTestData.sh | 12 ++++++------
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 03b768f..32f9e67 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1028,7 +1028,7 @@ dnanexus:
- module load dxtoolkit/python27/0.294.0
- export NXF_XPACK_LICENSE=${nxf_license}
- dx upload ./test_data/auth/c* --path /ci-env/auth/ --parents --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace}
- - dx upload ./test_data/fastq/xsmall/Q-Y5F6_1M.R{1,2}.fastq.gz --path /ci-env/input/ --parents --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace}
+ - dx upload ./test_data/fastq/xsmall/Q-Y5F6_1K.R{1,2}.fastq.gz --path /ci-env/input/ --parents --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace}
- >
dx run nf-dxapp-bicf --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace} \
--delay-workspace-destruction \
diff --git a/test_data/createTestData.sh b/test_data/createTestData.sh
index a730c53..60ccf67 100644
--- a/test_data/createTestData.sh
+++ b/test_data/createTestData.sh
@@ -32,12 +32,12 @@ cp Q-Y5F6_1M.R1.fastq.gz ./NEW_test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz
cp Q-Y5F6_1M.R2.fastq.gz ./NEW_test_data/fastq/small/Q-Y5F6_1M.R2.fastq.gz
mkdir -p ./NEW_test_data/fastq/xsmall
-singularity exec 'docker://gudmaprbk/seqtk1.3:1.0.0' seqtk sample -s100 ./NEW_test_data/fastq/Q-Y5F6.R1.fastq.gz 1000 1> Q-Y5F6_1M.R1.fastq
-singularity exec 'docker://gudmaprbk/seqtk1.3:1.0.0' seqtk sample -s100 ./NEW_test_data/fastq/Q-Y5F6.R2.fastq.gz 1000 1> Q-Y5F6_1M.R2.fastq
-pigz Q-Y5F6_1M.R1.fastq
-pigz Q-Y5F6_1M.R2.fastq
-cp Q-Y5F6_1M.R1.fastq.gz ./NEW_test_data/fastq/xsmall/Q-Y5F6_1M.R1.fastq.gz
-cp Q-Y5F6_1M.R2.fastq.gz ./NEW_test_data/fastq/xsmall/Q-Y5F6_1M.R2.fastq.gz
+singularity exec 'docker://gudmaprbk/seqtk1.3:1.0.0' seqtk sample -s100 ./NEW_test_data/fastq/Q-Y5F6.R1.fastq.gz 1000 1> Q-Y5F6_1K.R1.fastq
+singularity exec 'docker://gudmaprbk/seqtk1.3:1.0.0' seqtk sample -s100 ./NEW_test_data/fastq/Q-Y5F6.R2.fastq.gz 1000 1> Q-Y5F6_1K.R2.fastq
+pigz Q-Y5F6_1K.R1.fastq
+pigz Q-Y5F6_1K.R2.fastq
+cp Q-Y5F6_1K.R1.fastq.gz ./NEW_test_data/fastq/xsmall/Q-Y5F6_1K.R1.fastq.gz
+cp Q-Y5F6_1K.R2.fastq.gz ./NEW_test_data/fastq/xsmall/Q-Y5F6_1K.R2.fastq.gz
mkdir -p ./NEW_test_data/meta
singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --gzip -q 25 --illumina --length 35 --basename Q-Y5F6_1M.se -j 20 ./NEW_test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz
--
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